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Zhou S, Sosina OA, Bovijn J, Laurent L, Sharma V, Akbari P, Forgetta V, Jiang L, Kosmicki JA, Banerjee N, Morris JA, Oerton E, Jones M, LeBlanc MG, Idone V, Overton JD, Reid JG, Cantor M, Abecasis GR, Goltzman D, Greenwood CMT, Langenberg C, Baras A, Economides AN, Ferreira MAR, Hatsell S, Ohlsson C, Richards JB, Lotta LA. Converging evidence from exome sequencing and common variants implicates target genes for osteoporosis. Nat Genet 2023; 55:1277-1287. [PMID: 37558884 DOI: 10.1038/s41588-023-01444-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 06/09/2023] [Indexed: 08/11/2023]
Abstract
In this study, we leveraged the combined evidence of rare coding variants and common alleles to identify therapeutic targets for osteoporosis. We undertook a large-scale multiancestry exome-wide association study for estimated bone mineral density, which showed that the burden of rare coding alleles in 19 genes was associated with estimated bone mineral density (P < 3.6 × 10-7). These genes were highly enriched for a set of known causal genes for osteoporosis (65-fold; P = 2.5 × 10-5). Exome-wide significant genes had 96-fold increased odds of being the top ranked effector gene at a given GWAS locus (P = 1.8 × 10-10). By integrating proteomics Mendelian randomization evidence, we prioritized CD109 (cluster of differentiation 109) as a gene for which heterozygous loss of function is associated with higher bone density. CRISPR-Cas9 editing of CD109 in SaOS-2 osteoblast-like cell lines showed that partial CD109 knockdown led to increased mineralization. This study demonstrates that the convergence of common and rare variants, proteomics and CRISPR can highlight new bone biology to guide therapeutic development.
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Affiliation(s)
- Sirui Zhou
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - Olukayode A Sosina
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Jonas Bovijn
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Laetitia Laurent
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Vasundhara Sharma
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Parsa Akbari
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Five Prime Sciences Inc, Montréal, Québec, Canada
| | - Lai Jiang
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Jack A Kosmicki
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Nilanjana Banerjee
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | | | - Erin Oerton
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Marcus Jones
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Michelle G LeBlanc
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | | | - John D Overton
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Jeffrey G Reid
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Michael Cantor
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Goncalo R Abecasis
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - David Goltzman
- Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Celia M T Greenwood
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health, Charité University Medicine Berlin, Berlin, Germany
| | - Aris Baras
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Aris N Economides
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Manuel A R Ferreira
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | | | - Claes Ohlsson
- Centre of Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Drug Treatment, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada.
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada.
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.
- Five Prime Sciences Inc, Montréal, Québec, Canada.
- Department of Twin Research, King's College London, London, UK.
| | - Luca A Lotta
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
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Weinstock JS, Laurie CA, Broome JG, Taylor KD, Guo X, Shuldiner AR, O’Connell JR, Lewis JP, Boerwinkle E, Barnes KC, Chami N, Kenny EE, Loos RJ, Fornage M, Redline S, Cade BE, Gilliland FD, Chen Z, Gauderman WJ, Kumar R, Grammer L, Schleimer RP, Psaty BM, Bis JC, Brody JA, Silverman EK, Yun JH, Qiao D, Weiss ST, Lasky-Su J, DeMeo DL, Palmer ND, Freedman BI, Bowden DW, Cho MH, Vasan RS, Johnson AD, Yanek LR, Becker LC, Kardia S, He J, Kaplan R, Heckbert SR, Smith NL, Wiggins KL, Arnett DK, Irvin MR, Tiwari H, Correa A, Raffield LM, Gao Y, de Andrade M, Rotter JI, Rich SS, Manichaikul AW, Konkle BA, Johnsen JM, Wheeler MM, Custer BS, Duggirala R, Curran JE, Blangero J, Gui H, Xiao S, Williams LK, Meyers DA, Li X, Ortega V, McGarvey S, Gu CC, Chen YDI, Lee WJ, Shoemaker MB, Darbar D, Roden D, Albert C, Kooperberg C, Desai P, Blackwell TW, Abecasis GR, Smith AV, Kang HM, Mathias R, Natarajan P, Jaiswal S, Reiner AP, Bick AG. The genetic determinants of recurrent somatic mutations in 43,693 blood genomes. Sci Adv 2023; 9:eabm4945. [PMID: 37126548 PMCID: PMC10132750 DOI: 10.1126/sciadv.abm4945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Nononcogenic somatic mutations are thought to be uncommon and inconsequential. To test this, we analyzed 43,693 National Heart, Lung and Blood Institute Trans-Omics for Precision Medicine blood whole genomes from 37 cohorts and identified 7131 non-missense somatic mutations that are recurrently mutated in at least 50 individuals. These recurrent non-missense somatic mutations (RNMSMs) are not clearly explained by other clonal phenomena such as clonal hematopoiesis. RNMSM prevalence increased with age, with an average 50-year-old having 27 RNMSMs. Inherited germline variation associated with RNMSM acquisition. These variants were found in genes involved in adaptive immune function, proinflammatory cytokine production, and lymphoid lineage commitment. In addition, the presence of eight specific RNMSMs associated with blood cell traits at effect sizes comparable to Mendelian genetic mutations. Overall, we found that somatic mutations in blood are an unexpectedly common phenomenon with ancestry-specific determinants and human health consequences.
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Affiliation(s)
- Joshua S. Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Cecelia A. Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Jai G. Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Alan R. Shuldiner
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD 21201, USA
| | - Jeffrey R. O’Connell
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD 21201, USA
| | - Joshua P. Lewis
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD 21201, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kathleen C. Barnes
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nathalie Chami
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ruth J. F. Loos
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Brian E. Cade
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Frank D. Gilliland
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Zhanghua Chen
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - W. James Gauderman
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Rajesh Kumar
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Leslie Grammer
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | | | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jeong H. Yun
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Scott T. Weiss
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jessica Lasky-Su
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Dawn L. DeMeo
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Donald W. Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Michael H. Cho
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ramachandran S. Vasan
- National Heart, Lung, and Blood Institute’s, Boston University’s Framingham Heart Study, Framingham, MA 01701, USA
| | - Andrew D. Johnson
- National Heart, Lung, and Blood Institute’s, Boston University’s Framingham Heart Study, Framingham, MA 01701, USA
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA 01701, USA
| | - Lisa R. Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lewis C. Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sharon Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Susan R. Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98101, USA
| | - Nicholas L. Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98101, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA 98108, USA
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Donna K. Arnett
- Dean’s Office, College of Public Health, University of Kentucky, Lexington, KY 40506, USA
| | | | - Hemant Tiwari
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Adolfo Correa
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yan Gao
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Stephen S. Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Ani W. Manichaikul
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Barbara A. Konkle
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jill M. Johnsen
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Research Institute, Bloodworks Northwest, Seattle, WA 98102, USA
| | | | | | - Ravindranath Duggirala
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Joanne E. Curran
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Hongsheng Gui
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Health System, Detroit, MI 48202, USA
- Department of Medicine, Henry Ford Health System, Detroit, MI 48202, USA
| | - Shujie Xiao
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Health System, Detroit, MI 48202, USA
- Department of Medicine, Henry Ford Health System, Detroit, MI 48202, USA
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Health System, Detroit, MI 48202, USA
- Department of Medicine, Henry Ford Health System, Detroit, MI 48202, USA
| | - Deborah A. Meyers
- Division of Genetics, Genomics, and Precision Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Xingnan Li
- Department of Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Victor Ortega
- Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
| | - Stephen McGarvey
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI 02903, USA
| | - C. Charles Gu
- Division of Biostatistics, Washington University School of Medicine, Campus Box 8067, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, 1650, Sec. 4, Taiwan Boulevard, Taichung City, Taiwan
| | - M. Benjamin Shoemaker
- Division of Cardiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Dawood Darbar
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Dan Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Christine Albert
- Department of Cardiology, Cedars-Sinai, Los Angeles, CA 90048, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Pinkal Desai
- Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY 10065, USA
- Englander Institute of Precision Medicine, Weill Cornell Medicine, New York 10065, NY, USA
| | - Thomas W. Blackwell
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Goncalo R. Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Albert V. Smith
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Hyun M. Kang
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Rasika Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Alexander G. Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD 21201, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- National Heart, Lung, and Blood Institute’s, Boston University’s Framingham Heart Study, Framingham, MA 01701, USA
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA 01701, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98101, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA 98108, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
- Dean’s Office, College of Public Health, University of Kentucky, Lexington, KY 40506, USA
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Research Institute, Bloodworks Northwest, Seattle, WA 98102, USA
- Genome Science, University of Washington, Seattle, WA 98195, USA
- Vitalant Research Institute, San Francisco, CA 94105, USA
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Health System, Detroit, MI 48202, USA
- Department of Medicine, Henry Ford Health System, Detroit, MI 48202, USA
- Division of Genetics, Genomics, and Precision Medicine, University of Arizona, Tucson, AZ 85721, USA
- Department of Medicine, University of Arizona, Tucson, AZ 85721, USA
- Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI 02903, USA
- Division of Biostatistics, Washington University School of Medicine, Campus Box 8067, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Department of Medical Research, Taichung Veterans General Hospital, 1650, Sec. 4, Taiwan Boulevard, Taichung City, Taiwan
- Division of Cardiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL 60607, USA
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Cardiology, Cedars-Sinai, Los Angeles, CA 90048, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY 10065, USA
- Englander Institute of Precision Medicine, Weill Cornell Medicine, New York 10065, NY, USA
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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3
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Weinstock JS, Gopakumar J, Burugula BB, Uddin MM, Jahn N, Belk JA, Bouzid H, Daniel B, Miao Z, Ly N, Mack TM, Luna SE, Prothro KP, Mitchell SR, Laurie CA, Broome JG, Taylor KD, Guo X, Sinner MF, von Falkenhausen AS, Kääb S, Shuldiner AR, O'Connell JR, Lewis JP, Boerwinkle E, Barnes KC, Chami N, Kenny EE, Loos RJF, Fornage M, Hou L, Lloyd-Jones DM, Redline S, Cade BE, Psaty BM, Bis JC, Brody JA, Silverman EK, Yun JH, Qiao D, Palmer ND, Freedman BI, Bowden DW, Cho MH, DeMeo DL, Vasan RS, Yanek LR, Becker LC, Kardia SLR, Peyser PA, He J, Rienstra M, Van der Harst P, Kaplan R, Heckbert SR, Smith NL, Wiggins KL, Arnett DK, Irvin MR, Tiwari H, Cutler MJ, Knight S, Muhlestein JB, Correa A, Raffield LM, Gao Y, de Andrade M, Rotter JI, Rich SS, Tracy RP, Konkle BA, Johnsen JM, Wheeler MM, Smith JG, Melander O, Nilsson PM, Custer BS, Duggirala R, Curran JE, Blangero J, McGarvey S, Williams LK, Xiao S, Yang M, Gu CC, Chen YDI, Lee WJ, Marcus GM, Kane JP, Pullinger CR, Shoemaker MB, Darbar D, Roden DM, Albert C, Kooperberg C, Zhou Y, Manson JE, Desai P, Johnson AD, Mathias RA, Blackwell TW, Abecasis GR, Smith AV, Kang HM, Satpathy AT, Natarajan P, Kitzman JO, Whitsel EA, Reiner AP, Bick AG, Jaiswal S. Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis. Nature 2023; 616:755-763. [PMID: 37046083 PMCID: PMC10360040 DOI: 10.1038/s41586-023-05806-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/08/2023] [Indexed: 04/14/2023]
Abstract
Mutations in a diverse set of driver genes increase the fitness of haematopoietic stem cells (HSCs), leading to clonal haematopoiesis1. These lesions are precursors for blood cancers2-6, but the basis of their fitness advantage remains largely unknown, partly owing to a paucity of large cohorts in which the clonal expansion rate has been assessed by longitudinal sampling. Here, to circumvent this limitation, we developed a method to infer the expansion rate from data from a single time point. We applied this method to 5,071 people with clonal haematopoiesis. A genome-wide association study revealed that a common inherited polymorphism in the TCL1A promoter was associated with a slower expansion rate in clonal haematopoiesis overall, but the effect varied by driver gene. Those carrying this protective allele exhibited markedly reduced growth rates or prevalence of clones with driver mutations in TET2, ASXL1, SF3B1 and SRSF2, but this effect was not seen in clones with driver mutations in DNMT3A. TCL1A was not expressed in normal or DNMT3A-mutated HSCs, but the introduction of mutations in TET2 or ASXL1 led to the expression of TCL1A protein and the expansion of HSCs in vitro. The protective allele restricted TCL1A expression and expansion of mutant HSCs, as did experimental knockdown of TCL1A expression. Forced expression of TCL1A promoted the expansion of human HSCs in vitro and mouse HSCs in vivo. Our results indicate that the fitness advantage of several commonly mutated driver genes in clonal haematopoiesis may be mediated by TCL1A activation.
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Affiliation(s)
- Joshua S Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | | | | | - Md Mesbah Uddin
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nikolaus Jahn
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia A Belk
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hind Bouzid
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bence Daniel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Zhuang Miao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nghi Ly
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Taralynn M Mack
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Sofia E Luna
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Katherine P Prothro
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Shaneice R Mitchell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | - Jai G Broome
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kent D Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Institute for Translational Genomics and Populations Sciences, Lundquist Institute, Torrance, CA, USA
| | - Xiuqing Guo
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Lundquist Institute, Torrance, CA, USA
| | - Moritz F Sinner
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Aenne S von Falkenhausen
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Stefan Kääb
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Alan R Shuldiner
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Jeffrey R O'Connell
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Joshua P Lewis
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
- University of Maryland, Baltimore, MD, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- University of Texas Health at Houston, Houston, TX, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Nathalie Chami
- The Charles Bronfman Institute of Personalized Medicine, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E Kenny
- Institute for Genomic Health, New York, NY, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute of Personalized Medicine, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Myriam Fornage
- University of Texas Health at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northeastern University, Chicago, IL, USA
| | | | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Brian E Cade
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce M Psaty
- University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A Brody
- University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Edwin K Silverman
- Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jeong H Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dandi Qiao
- Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest Baptist Health, Winston-Salem, NC, USA
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest Baptist Health, Winston-Salem, NC, USA
| | - Michael H Cho
- Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ramachandran S Vasan
- National Heart Lung and Blood Institute's, Boston University's Framingham Heart Study, Framingham, MA, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | - Lewis C Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- University of Michigan, Ann Arbor, MI, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- University of Michigan, Ann Arbor, MI, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane University, New Orleans, LA, USA
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Pim Van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Albert Einstein College of Medicine, New York, NY, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
- Broad Institute, Cambridge, MA, USA
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
- University of Kentucky, Lexington, KY, USA
| | | | - Hemant Tiwari
- Department of Biostatistics, University of Alabama, Birmingham, AL, USA
| | - Michael J Cutler
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA
| | - Stacey Knight
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA
| | - J Brent Muhlestein
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA
| | - Adolfo Correa
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Population Health Science, University of Mississippi, Jackson, MS, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yan Gao
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
- University of Mississippi, Jackson, MS, USA
| | - Mariza de Andrade
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Jerome I Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, Lundquist Institute, Torrance, CA, USA
| | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- University of Virginia, Charlottesville, VA, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine and Biochemistry, Larner College of Medicine at the University of Vermont, Colchester, VT, USA
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, USA
| | - Barbara A Konkle
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
- Blood Works Northwest, Seattle, WA, USA
| | - Jill M Johnsen
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
- Research Institute, Bloodworks Northwest, Seattle, WA, USA
| | | | - J Gustav Smith
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University, Gothenburg, Sweden
- Wallenberg Center for Molecular Medicine and Lund University Diabetes Center, Lund University, Lund, Sweden
- Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Olle Melander
- Department of Internal Medicine, Clinical Sciences, Lund University and Skane University Hospital, Malmo, Sweden
| | - Peter M Nilsson
- Department of Internal Medicine, Clinical Sciences, Lund University and Skane University Hospital, Malmo, Sweden
| | | | - Ravindranath Duggirala
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Joanne E Curran
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Stephen McGarvey
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI, USA
- Department of Epidemiology, Brown University, Providence, RI, USA
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
- Henry Ford Health System, Detroit, MI, USA
| | - Shujie Xiao
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Mao Yang
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - C Charles Gu
- Division of Biostatistics, Washington University School of Medicine, St Louis, MO, USA
- Washington University in St Louis, St Louis, MO, USA
| | - Yii-Der Ida Chen
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Lundquist Institute, Torrance, CA, USA
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Taichung Veterans General Hospital Taiwan, Taichung City, Taiwan
| | - Gregory M Marcus
- Division of Cardiology, University of California, San Francisco, San Francisco, CA, USA
| | - John P Kane
- Department of Medicine, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Clive R Pullinger
- Cardiovascular Research Institute, University of California, San Francisco, USA
| | - M Benjamin Shoemaker
- Division of Cardiology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine and Cardiology, Vanderbilt University, Nashville, TN, USA
| | - Dawood Darbar
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL, USA
- University of Illinois at Chicago, Chicago, IL, USA
| | - Dan M Roden
- Departments of Medicine, Pharmacology and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christine Albert
- Department of Cardiology, Cedars-Sinai, Los Angeles, CA, USA
- Cedars-Sinai, Boston, MA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ying Zhou
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - JoAnn E Manson
- Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Pinkal Desai
- Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY, USA
- Englander Institute of Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrew D Johnson
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | - Thomas W Blackwell
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Goncalo R Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Albert V Smith
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Hyun M Kang
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Alexander P Reiner
- Broad Institute, Cambridge, MA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA.
| | - Siddhartha Jaiswal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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4
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Wheeler MM, Stilp AM, Rao S, Halldórsson BV, Beyter D, Wen J, Mihkaylova AV, McHugh CP, Lane J, Jiang MZ, Raffield LM, Jun G, Sedlazeck FJ, Metcalf G, Yao Y, Bis JB, Chami N, de Vries PS, Desai P, Floyd JS, Gao Y, Kammers K, Kim W, Moon JY, Ratan A, Yanek LR, Almasy L, Becker LC, Blangero J, Cho MH, Curran JE, Fornage M, Kaplan RC, Lewis JP, Loos RJF, Mitchell BD, Morrison AC, Preuss M, Psaty BM, Rich SS, Rotter JI, Tang H, Tracy RP, Boerwinkle E, Abecasis GR, Blackwell TW, Smith AV, Johnson AD, Mathias RA, Nickerson DA, Conomos MP, Li Y, Þorsteinsdóttir U, Magnússon MK, Stefansson K, Pankratz ND, Bauer DE, Auer PL, Reiner AP. Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program. Nat Commun 2022; 13:7592. [PMID: 36481753 PMCID: PMC9732337 DOI: 10.1038/s41467-022-35354-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies have identified thousands of single nucleotide variants and small indels that contribute to variation in hematologic traits. While structural variants are known to cause rare blood or hematopoietic disorders, the genome-wide contribution of structural variants to quantitative blood cell trait variation is unknown. Here we utilized whole genome sequencing data in ancestrally diverse participants of the NHLBI Trans Omics for Precision Medicine program (N = 50,675) to detect structural variants associated with hematologic traits. Using single variant tests, we assessed the association of common and rare structural variants with red cell-, white cell-, and platelet-related quantitative traits and observed 21 independent signals (12 common and 9 rare) reaching genome-wide significance. The majority of these associations (N = 18) replicated in independent datasets. In genome-editing experiments, we provide evidence that a deletion associated with lower monocyte counts leads to disruption of an S1PR3 monocyte enhancer and decreased S1PR3 expression.
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Affiliation(s)
- Marsha M. Wheeler
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA 98105 USA
| | - Adrienne M. Stilp
- grid.34477.330000000122986657Department of Biostatistics, University of Washington, Seattle, WA 98105 USA
| | - Shuquan Rao
- grid.2515.30000 0004 0378 8438Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115 USA ,grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115 USA ,grid.511171.2Harvard Stem Cell Institute, Boston, MA 02138 USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA 02115 USA ,grid.506261.60000 0001 0706 7839State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020 China
| | - Bjarni V. Halldórsson
- grid.421812.c0000 0004 0618 6889deCODE genetics/Amgen Inc., Reykjavik, Iceland ,grid.9580.40000 0004 0643 5232School of Technology, Reykjavik University, Reykjavík, Iceland
| | - Doruk Beyter
- grid.421812.c0000 0004 0618 6889deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | - Jia Wen
- grid.10698.360000000122483208Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Anna V. Mihkaylova
- grid.34477.330000000122986657Department of Biostatistics, University of Washington, Seattle, WA 98105 USA
| | - Caitlin P. McHugh
- grid.34477.330000000122986657Department of Biostatistics, University of Washington, Seattle, WA 98105 USA
| | - John Lane
- grid.17635.360000000419368657Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455 USA
| | - Min-Zhi Jiang
- grid.10698.360000000122483208Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Laura M. Raffield
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Goo Jun
- grid.267308.80000 0000 9206 2401Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Fritz J. Sedlazeck
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Ginger Metcalf
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Yao Yao
- grid.2515.30000 0004 0378 8438Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115 USA ,grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115 USA ,grid.511171.2Harvard Stem Cell Institute, Boston, MA 02138 USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA 02115 USA
| | - Joshua B. Bis
- grid.34477.330000000122986657Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101 USA
| | - Nathalie Chami
- grid.59734.3c0000 0001 0670 2351The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Paul S. de Vries
- grid.267308.80000 0000 9206 2401Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Pinkal Desai
- grid.5386.8000000041936877XDivision of Hematology and Oncology, Weill Cornell Medical College, New York, NY 10065 USA
| | - James S. Floyd
- grid.34477.330000000122986657Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101 USA
| | - Yan Gao
- grid.251313.70000 0001 2169 2489Jackson Heart Study, Department of Medicine, University of Mississippi, Jackson, MS 39216 USA
| | - Kai Kammers
- grid.21107.350000 0001 2171 9311GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Wonji Kim
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 2115 USA
| | - Jee-Young Moon
- grid.251993.50000000121791997Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Aakrosh Ratan
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA 22908 USA
| | - Lisa R. Yanek
- grid.21107.350000 0001 2171 9311GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Laura Almasy
- grid.25879.310000 0004 1936 8972Children’s Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, PA 19104 USA
| | - Lewis C. Becker
- grid.21107.350000 0001 2171 9311GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - John Blangero
- grid.449717.80000 0004 5374 269XDepartment of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520 USA
| | - Michael H. Cho
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 2115 USA
| | - Joanne E. Curran
- grid.449717.80000 0004 5374 269XDepartment of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520 USA
| | - Myriam Fornage
- grid.267308.80000 0000 9206 2401Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Robert C. Kaplan
- grid.251993.50000000121791997Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Joshua P. Lewis
- grid.411024.20000 0001 2175 4264Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD USA
| | - Ruth J. F. Loos
- grid.59734.3c0000 0001 0670 2351The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA ,grid.59734.3c0000 0001 0670 2351Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.5254.60000 0001 0674 042XNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Braxton D. Mitchell
- grid.411024.20000 0001 2175 4264Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD USA
| | - Alanna C. Morrison
- grid.267308.80000 0000 9206 2401Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Michael Preuss
- grid.59734.3c0000 0001 0670 2351The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Bruce M. Psaty
- grid.34477.330000000122986657Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101 USA
| | - Stephen S. Rich
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA 22908 USA
| | - Jerome I. Rotter
- grid.513199.6The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Hua Tang
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Russell P. Tracy
- grid.59062.380000 0004 1936 7689Departments of Pathology & Laboratory Medicine and Biochemistry, Larner College of Medicine at the University of Vermont, Colchester, VT 5446 USA
| | - Eric Boerwinkle
- grid.267308.80000 0000 9206 2401Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Goncalo R. Abecasis
- grid.214458.e0000000086837370TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109 USA
| | - Thomas W. Blackwell
- grid.214458.e0000000086837370TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109 USA
| | - Albert V. Smith
- grid.214458.e0000000086837370TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109 USA
| | - Andrew D. Johnson
- grid.279885.90000 0001 2293 4638Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA 1702 USA
| | - Rasika A. Mathias
- grid.21107.350000 0001 2171 9311GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Deborah A. Nickerson
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA 98105 USA
| | - Matthew P. Conomos
- grid.34477.330000000122986657Department of Biostatistics, University of Washington, Seattle, WA 98105 USA
| | - Yun Li
- grid.10698.360000000122483208Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Unnur Þorsteinsdóttir
- grid.421812.c0000 0004 0618 6889deCODE genetics/Amgen Inc., Reykjavik, Iceland ,grid.14013.370000 0004 0640 0021Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Magnús K. Magnússon
- grid.421812.c0000 0004 0618 6889deCODE genetics/Amgen Inc., Reykjavik, Iceland ,grid.14013.370000 0004 0640 0021Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Kari Stefansson
- grid.421812.c0000 0004 0618 6889deCODE genetics/Amgen Inc., Reykjavik, Iceland ,grid.14013.370000 0004 0640 0021Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Nathan D. Pankratz
- grid.17635.360000000419368657Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455 USA
| | - Daniel E. Bauer
- grid.2515.30000 0004 0378 8438Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115 USA ,grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115 USA ,grid.511171.2Harvard Stem Cell Institute, Boston, MA 02138 USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA 02115 USA
| | - Paul L. Auer
- grid.30760.320000 0001 2111 8460Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Alex P. Reiner
- grid.34477.330000000122986657Department of Epidemiology, University of Washington, Seattle, WA 98105 USA
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Yengo L, Vedantam S, Marouli E, Sidorenko J, Bartell E, Sakaue S, Graff M, Eliasen AU, Jiang Y, Raghavan S, Miao J, Arias JD, Graham SE, Mukamel RE, Spracklen CN, Yin X, Chen SH, Ferreira T, Highland HH, Ji Y, Karaderi T, Lin K, Lüll K, Malden DE, Medina-Gomez C, Machado M, Moore A, Rüeger S, Sim X, Vrieze S, Ahluwalia TS, Akiyama M, Allison MA, Alvarez M, Andersen MK, Ani A, Appadurai V, Arbeeva L, Bhaskar S, Bielak LF, Bollepalli S, Bonnycastle LL, Bork-Jensen J, Bradfield JP, Bradford Y, Braund PS, Brody JA, Burgdorf KS, Cade BE, Cai H, Cai Q, Campbell A, Cañadas-Garre M, Catamo E, Chai JF, Chai X, Chang LC, Chang YC, Chen CH, Chesi A, Choi SH, Chung RH, Cocca M, Concas MP, Couture C, Cuellar-Partida G, Danning R, Daw EW, Degenhard F, Delgado GE, Delitala A, Demirkan A, Deng X, Devineni P, Dietl A, Dimitriou M, Dimitrov L, Dorajoo R, Ekici AB, Engmann JE, Fairhurst-Hunter Z, Farmaki AE, Faul JD, Fernandez-Lopez JC, Forer L, Francescatto M, Freitag-Wolf S, Fuchsberger C, Galesloot TE, Gao Y, Gao Z, Geller F, Giannakopoulou O, Giulianini F, Gjesing AP, Goel A, Gordon SD, Gorski M, Grove J, Guo X, Gustafsson S, Haessler J, Hansen TF, Havulinna AS, Haworth SJ, He J, Heard-Costa N, Hebbar P, Hindy G, Ho YLA, Hofer E, Holliday E, Horn K, Hornsby WE, Hottenga JJ, Huang H, Huang J, Huerta-Chagoya A, Huffman JE, Hung YJ, Huo S, Hwang MY, Iha H, Ikeda DD, Isono M, Jackson AU, Jäger S, Jansen IE, Johansson I, Jonas JB, Jonsson A, Jørgensen T, Kalafati IP, Kanai M, Kanoni S, Kårhus LL, Kasturiratne A, Katsuya T, Kawaguchi T, Kember RL, Kentistou KA, Kim HN, Kim YJ, Kleber ME, Knol MJ, Kurbasic A, Lauzon M, Le P, Lea R, Lee JY, Leonard HL, Li SA, Li X, Li X, Liang J, Lin H, Lin SY, Liu J, Liu X, Lo KS, Long J, Lores-Motta L, Luan J, Lyssenko V, Lyytikäinen LP, Mahajan A, Mamakou V, Mangino M, Manichaikul A, Marten J, Mattheisen M, Mavarani L, McDaid AF, Meidtner K, Melendez TL, Mercader JM, Milaneschi Y, Miller JE, Millwood IY, Mishra PP, Mitchell RE, Møllehave LT, Morgan A, Mucha S, Munz M, Nakatochi M, Nelson CP, Nethander M, Nho CW, Nielsen AA, Nolte IM, Nongmaithem SS, Noordam R, Ntalla I, Nutile T, Pandit A, Christofidou P, Pärna K, Pauper M, Petersen ERB, Petersen LV, Pitkänen N, Polašek O, Poveda A, Preuss MH, Pyarajan S, Raffield LM, Rakugi H, Ramirez J, Rasheed A, Raven D, Rayner NW, Riveros C, Rohde R, Ruggiero D, Ruotsalainen SE, Ryan KA, Sabater-Lleal M, Saxena R, Scholz M, Sendamarai A, Shen B, Shi J, Shin JH, Sidore C, Sitlani CM, Slieker RC, Smit RAJ, Smith AV, Smith JA, Smyth LJ, Southam L, Steinthorsdottir V, Sun L, Takeuchi F, Tallapragada DSP, Taylor KD, Tayo BO, Tcheandjieu C, Terzikhan N, Tesolin P, Teumer A, Theusch E, Thompson DJ, Thorleifsson G, Timmers PRHJ, Trompet S, Turman C, Vaccargiu S, van der Laan SW, van der Most PJ, van Klinken JB, van Setten J, Verma SS, Verweij N, Veturi Y, Wang CA, Wang C, Wang L, Wang Z, Warren HR, Bin Wei W, Wickremasinghe AR, Wielscher M, Wiggins KL, Winsvold BS, Wong A, Wu Y, Wuttke M, Xia R, Xie T, Yamamoto K, Yang J, Yao J, Young H, Yousri NA, Yu L, Zeng L, Zhang W, Zhang X, Zhao JH, Zhao W, Zhou W, Zimmermann ME, Zoledziewska M, Adair LS, Adams HHH, Aguilar-Salinas CA, Al-Mulla F, Arnett DK, Asselbergs FW, Åsvold BO, Attia J, Banas B, Bandinelli S, Bennett DA, Bergler T, Bharadwaj D, Biino G, Bisgaard H, Boerwinkle E, Böger CA, Bønnelykke K, Boomsma DI, Børglum AD, Borja JB, Bouchard C, Bowden DW, Brandslund I, Brumpton B, Buring JE, Caulfield MJ, Chambers JC, Chandak GR, Chanock SJ, Chaturvedi N, Chen YDI, Chen Z, Cheng CY, Christophersen IE, Ciullo M, Cole JW, Collins FS, Cooper RS, Cruz M, Cucca F, Cupples LA, Cutler MJ, Damrauer SM, Dantoft TM, de Borst GJ, de Groot LCPGM, De Jager PL, de Kleijn DPV, Janaka de Silva H, Dedoussis GV, den Hollander AI, Du S, Easton DF, Elders PJM, Eliassen AH, Ellinor PT, Elmståhl S, Erdmann J, Evans MK, Fatkin D, Feenstra B, Feitosa MF, Ferrucci L, Ford I, Fornage M, Franke A, Franks PW, Freedman BI, Gasparini P, Gieger C, Girotto G, Goddard ME, Golightly YM, Gonzalez-Villalpando C, Gordon-Larsen P, Grallert H, Grant SFA, Grarup N, Griffiths L, Gudnason V, Haiman C, Hakonarson H, Hansen T, Hartman CA, Hattersley AT, Hayward C, Heckbert SR, Heng CK, Hengstenberg C, Hewitt AW, Hishigaki H, Hoyng CB, Huang PL, Huang W, Hunt SC, Hveem K, Hyppönen E, Iacono WG, Ichihara S, Ikram MA, Isasi CR, Jackson RD, Jarvelin MR, Jin ZB, Jöckel KH, Joshi PK, Jousilahti P, Jukema JW, Kähönen M, Kamatani Y, Kang KD, Kaprio J, Kardia SLR, Karpe F, Kato N, Kee F, Kessler T, Khera AV, Khor CC, Kiemeney LALM, Kim BJ, Kim EK, Kim HL, Kirchhof P, Kivimaki M, Koh WP, Koistinen HA, Kolovou GD, Kooner JS, Kooperberg C, Köttgen A, Kovacs P, Kraaijeveld A, Kraft P, Krauss RM, Kumari M, Kutalik Z, Laakso M, Lange LA, Langenberg C, Launer LJ, Le Marchand L, Lee H, Lee NR, Lehtimäki T, Li H, Li L, Lieb W, Lin X, Lind L, Linneberg A, Liu CT, Liu J, Loeffler M, London B, Lubitz SA, Lye SJ, Mackey DA, Mägi R, Magnusson PKE, Marcus GM, Vidal PM, Martin NG, März W, Matsuda F, McGarrah RW, McGue M, McKnight AJ, Medland SE, Mellström D, Metspalu A, Mitchell BD, Mitchell P, Mook-Kanamori DO, Morris AD, Mucci LA, Munroe PB, Nalls MA, Nazarian S, Nelson AE, Neville MJ, Newton-Cheh C, Nielsen CS, Nöthen MM, Ohlsson C, Oldehinkel AJ, Orozco L, Pahkala K, Pajukanta P, Palmer CNA, Parra EJ, Pattaro C, Pedersen O, Pennell CE, Penninx BWJH, Perusse L, Peters A, Peyser PA, Porteous DJ, Posthuma D, Power C, Pramstaller PP, Province MA, Qi Q, Qu J, Rader DJ, Raitakari OT, Ralhan S, Rallidis LS, Rao DC, Redline S, Reilly DF, Reiner AP, Rhee SY, Ridker PM, Rienstra M, Ripatti S, Ritchie MD, Roden DM, Rosendaal FR, Rotter JI, Rudan I, Rutters F, Sabanayagam C, Saleheen D, Salomaa V, Samani NJ, Sanghera DK, Sattar N, Schmidt B, Schmidt H, Schmidt R, Schulze MB, Schunkert H, Scott LJ, Scott RJ, Sever P, Shiroma EJ, Shoemaker MB, Shu XO, Simonsick EM, Sims M, Singh JR, Singleton AB, Sinner MF, Smith JG, Snieder H, Spector TD, Stampfer MJ, Stark KJ, Strachan DP, 't Hart LM, Tabara Y, Tang H, Tardif JC, Thanaraj TA, Timpson NJ, Tönjes A, Tremblay A, Tuomi T, Tuomilehto J, Tusié-Luna MT, Uitterlinden AG, van Dam RM, van der Harst P, Van der Velde N, van Duijn CM, van Schoor NM, Vitart V, Völker U, Vollenweider P, Völzke H, Wacher-Rodarte NH, Walker M, Wang YX, Wareham NJ, Watanabe RM, Watkins H, Weir DR, Werge TM, Widen E, Wilkens LR, Willemsen G, Willett WC, Wilson JF, Wong TY, Woo JT, Wright AF, Wu JY, Xu H, Yajnik CS, Yokota M, Yuan JM, Zeggini E, Zemel BS, Zheng W, Zhu X, Zmuda JM, Zonderman AB, Zwart JA, Chasman DI, Cho YS, Heid IM, McCarthy MI, Ng MCY, O'Donnell CJ, Rivadeneira F, Thorsteinsdottir U, Sun YV, Tai ES, Boehnke M, Deloukas P, Justice AE, Lindgren CM, Loos RJF, Mohlke KL, North KE, Stefansson K, Walters RG, Winkler TW, Young KL, Loh PR, Yang J, Esko T, Assimes TL, Auton A, Abecasis GR, Willer CJ, Locke AE, Berndt SI, Lettre G, Frayling TM, Okada Y, Wood AR, Visscher PM, Hirschhorn JN. A saturated map of common genetic variants associated with human height. Nature 2022; 610:704-712. [PMID: 36224396 PMCID: PMC9605867 DOI: 10.1038/s41586-022-05275-y] [Citation(s) in RCA: 135] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 08/24/2022] [Indexed: 02/08/2023]
Abstract
Common single-nucleotide polymorphisms (SNPs) are predicted to collectively explain 40-50% of phenotypic variation in human height, but identifying the specific variants and associated regions requires huge sample sizes1. Here, using data from a genome-wide association study of 5.4 million individuals of diverse ancestries, we show that 12,111 independent SNPs that are significantly associated with height account for nearly all of the common SNP-based heritability. These SNPs are clustered within 7,209 non-overlapping genomic segments with a mean size of around 90 kb, covering about 21% of the genome. The density of independent associations varies across the genome and the regions of increased density are enriched for biologically relevant genes. In out-of-sample estimation and prediction, the 12,111 SNPs (or all SNPs in the HapMap 3 panel2) account for 40% (45%) of phenotypic variance in populations of European ancestry but only around 10-20% (14-24%) in populations of other ancestries. Effect sizes, associated regions and gene prioritization are similar across ancestries, indicating that reduced prediction accuracy is likely to be explained by linkage disequilibrium and differences in allele frequency within associated regions. Finally, we show that the relevant biological pathways are detectable with smaller sample sizes than are needed to implicate causal genes and variants. Overall, this study provides a comprehensive map of specific genomic regions that contain the vast majority of common height-associated variants. Although this map is saturated for populations of European ancestry, further research is needed to achieve equivalent saturation in other ancestries.
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Affiliation(s)
- Loïc Yengo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
| | - Sailaja Vedantam
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eirini Marouli
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Julia Sidorenko
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Eric Bartell
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Saori Sakaue
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Divisions of Genetics and Rheumatology, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Marielisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anders U Eliasen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | | | - Sridharan Raghavan
- Department of Veterans Affairs, Eastern Colorado Healthcare System, Aurora, CO, USA
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jenkai Miao
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joshua D Arias
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Sarah E Graham
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Ronen E Mukamel
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Cassandra N Spracklen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA, USA
| | - Xianyong Yin
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Shyh-Huei Chen
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Teresa Ferreira
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Heather H Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yingjie Ji
- Genetics of Complex Traits, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Tugce Karaderi
- Center for Health Data Science, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Kreete Lüll
- Institute of Genomics, Estonian Genome Centre, University of Tartu, Tartu, Estonia
| | - Deborah E Malden
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Moara Machado
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Amy Moore
- Division of Biostatistics and Epidemiology, RTI International, Durham, NC, USA
| | - Sina Rüeger
- Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Tarunveer S Ahluwalia
- Steno Diabetes Center Copenhagen, Herlev, Denmark
- Department of Biology, The Bioinformatics Center, University of Copenhagen, Copenhagen, Denmark
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Matthew A Allison
- Department of Family Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Marcus Alvarez
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Mette K Andersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alireza Ani
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Bioinformatics, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Vivek Appadurai
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark
| | - Liubov Arbeeva
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Seema Bhaskar
- Genomic Research on Complex diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Lawrence F Bielak
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Lori L Bonnycastle
- Molecular Genetics Section, Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan P Bradfield
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Quantinuum Research, Wayne, PA, USA
| | - Yuki Bradford
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter S Braund
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kristoffer S Burgdorf
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- NovoNordic Center for Protein Research, Copenhagen University, Copenhagen, Denmark
| | - Brian E Cade
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Hui Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Eulalia Catamo
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, Trieste, Italy
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Xiaoran Chai
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore, Singapore
| | - Li-Ching Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Cheng Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, Medical College, National Taiwan University, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Alessandra Chesi
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Seung Hoan Choi
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ren-Hua Chung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Massimiliano Cocca
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, Trieste, Italy
| | - Maria Pina Concas
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, Trieste, Italy
| | - Christian Couture
- Department of Kinesiology, Faculty of Medicine, Université Laval, Québec City, Quebec, Canada
| | - Gabriel Cuellar-Partida
- 23andMe, Sunnyvale, CA, USA
- Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Rebecca Danning
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - E Warwick Daw
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Frauke Degenhard
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Alessandro Delitala
- Dipartimento di Scienze Mediche Chirurgiche e Sperimentali, Università degli Studi di Sassari, Sassari, Italy
| | - Ayse Demirkan
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Section of Statistical Multi-omics, Department of Clinical and Experimental Medicine, University of Surrey, Guildford, UK
| | - Xuan Deng
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Poornima Devineni
- Center for Data and Computational Sciences, VA Boston Healthcare System, Boston, MA, USA
| | - Alexander Dietl
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
- Department of Internal Medicine II, University Hospital Regensburg, Regensburg, Germany
| | - Maria Dimitriou
- Department of Nutrition and Dietetics, School of Health and Education, Harokopio University of Athens, Athens, Greece
| | - Latchezar Dimitrov
- Center for Precision Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Arif B Ekici
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jorgen E Engmann
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
| | | | - Aliki-Eleni Farmaki
- Department of Nutrition and Dietetics, School of Health and Education, Harokopio University of Athens, Athens, Greece
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | | | - Lukas Forer
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Sandra Freitag-Wolf
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - Christian Fuchsberger
- Eurac Research, Institute for Biomedicine, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Tessel E Galesloot
- Radboud University Medical Center, Radboud Institute for Health Sciences, Department for Health Evidence, Nijmegen, The Netherlands
| | - Yan Gao
- Jackson Heart Study, Department of Medicine, University of Mississippi, Jackson, MS, USA
| | - Zishan Gao
- Nanjing University of Chinese Medicine, Nanjing, China
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Olga Giannakopoulou
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Anette P Gjesing
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anuj Goel
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Scott D Gordon
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mathias Gorski
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Jakob Grove
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- BiRC-Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Thomas F Hansen
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark
- NovoNordic Center for Protein Research, Copenhagen University, Copenhagen, Denmark
- Danish Headache Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet, Rigshospitalet, Copenhagen, Denmark
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Simon J Haworth
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
| | - Jing He
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nancy Heard-Costa
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Prashantha Hebbar
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - George Hindy
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Clinical Sciences in Malmö, Lund University, Malmö, Sweden
| | - Yuk-Lam A Ho
- Veterans Affairs Boston Healthcare System, Boston, MA, USA
| | - Edith Hofer
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Elizabeth Holliday
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
| | - Katrin Horn
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Medical Faculty, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Medical Faculty, Leipzig, Germany
| | - Whitney E Hornsby
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Behaviour and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Hongyan Huang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jie Huang
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, China
- Institute for Global Health and Development, Peking University, Beijing, China
| | - Alicia Huerta-Chagoya
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México Ciudad Universitaria, Mexico City, Mexico
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición, Mexico City, Mexico
| | | | - Yi-Jen Hung
- Division of Endocrine and Metabolism, Tri-Service General Hospital Songshan Branch, Taipei, Taiwan
| | - Shaofeng Huo
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Mi Yeong Hwang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, Republic of Korea
| | - Hiroyuki Iha
- Biomedical Technology Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Tokushima, Japan
| | - Daisuke D Ikeda
- Biomedical Technology Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Tokushima, Japan
| | - Masato Isono
- Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Susanne Jäger
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Iris E Jansen
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry and Pediatric Psychology, Section Complex Trait Genetics, Amsterdam Neuroscience, Vrije Universiteit Medical Center, Amsterdam, The Netherlands
| | - Ingegerd Johansson
- Department of Biobank Research, Umeå University, Umeå, Sweden
- Department of Odontology, Umeå University, Umeå, Sweden
| | - Jost B Jonas
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Privatpraxis Prof Jonas und Dr Panda-Jonas, Heidelberg, Germany
- Department of Ophthalmology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing, China
| | - Anna Jonsson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Jørgensen
- Center for Clinical Research and Prevention, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark
- Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ioanna-Panagiota Kalafati
- Department of Nutrition and Dietetics, School of Health and Education, Harokopio University of Athens, Athens, Greece
| | - Masahiro Kanai
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Line L Kårhus
- Center for Clinical Research and Prevention, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | | | - Tomohiro Katsuya
- Department of Geriatric and General Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Rachel L Kember
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Katherine A Kentistou
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
- Centre for Cardiovascular Sciences, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Han-Na Kim
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Clinical Research Design and Evaluation (SAIHST), Sungkyunkwan University, Seoul, Republic of Korea
| | - Young Jin Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, Republic of Korea
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Maria J Knol
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Azra Kurbasic
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Malmö, Sweden
| | - Marie Lauzon
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Phuong Le
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Rodney Lea
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland, Australia
| | - Jong-Young Lee
- Oneomics, Soonchunhyang Mirai Medical Center, Bucheon-si, Republic of Korea
| | - Hampton L Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Glen Echo, MD, USA
| | - Shengchao A Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Rockville, MD, USA
| | - Xiaohui Li
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiaoyin Li
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Department of Mathematics and Statistics, St Cloud State University, St Cloud, MN, USA
| | - Jingjing Liang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Honghuang Lin
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Shih-Yi Lin
- Center for Geriatrics and Gerontology, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jun Liu
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Xueping Liu
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Ken Sin Lo
- Montreal Heart Institute, Montreal, Quebec, Canada
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Laura Lores-Motta
- Departments of Ophthalmology and Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Valeriya Lyssenko
- Department of Clinical Science, Center for Diabetes Research, University of Bergen, Bergen, Norway
- Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, Finland
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Vasiliki Mamakou
- National and Kapodistrian University of Athens, Dromokaiteio Psychiatric Hospital, Athens, Greece
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, UK
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jonathan Marten
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Manuel Mattheisen
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, Aarhus, Denmark
- Department of Psychiatry and Department of Community Health and Epidemiology, Dalhousie University, Halifax, Nova Scotia, Canada
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
| | - Laven Mavarani
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Aaron F McDaid
- Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Karina Meidtner
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Tori L Melendez
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Josep M Mercader
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Public Health and Amsterdam Neuroscience, Amsterdam UMC and Vrije Universiteit, Amsterdam, The Netherlands
| | - Jason E Miller
- Biomedical and Translational Informatics Institute, Geisinger, Danville, PA, USA
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iona Y Millwood
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ruth E Mitchell
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Line T Møllehave
- Center for Clinical Research and Prevention, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Anna Morgan
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, Trieste, Italy
| | - Soeren Mucha
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research) partner site Hamburg/Lübeck/Kiel and University Heart Center Lübeck, Lübeck, Germany
| | - Matthias Munz
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research) partner site Hamburg/Lübeck/Kiel and University Heart Center Lübeck, Lübeck, Germany
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Maria Nethander
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Chu Won Nho
- Korea Institute of Science and Technology, Gangneung Institute of Natural Products, Gangneung, Republic of Korea
| | - Aneta A Nielsen
- Department of Clinical Biochemistry, Lillebaelt Hospital, Kolding, Denmark
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Suraj S Nongmaithem
- Genomic Research on Complex diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Teresa Nutile
- Institute of Genetics and Biophysics A. Buzzati-Traverso, CNR, Naples, Italy
| | - Anita Pandit
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | | | - Katri Pärna
- Institute of Genomics, Estonian Genome Centre, University of Tartu, Tartu, Estonia
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marc Pauper
- Departments of Ophthalmology and Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Eva R B Petersen
- Department of Clinical Biochemistry and Immunology, Hospital of Southern Jutland, Aabenraa, Denmark
| | - Liselotte V Petersen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- The National Centre for Register-based Research, University of Aarhus, Aarhus, Denmark
| | - Niina Pitkänen
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Ozren Polašek
- Medical School, University of Split, Split, Croatia
- Algebra University College, Zagreb, Croatia
| | - Alaitz Poveda
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Malmö, Sweden
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Saiju Pyarajan
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Center for Data and Computational Sciences, VA Boston Healthcare System, Boston, MA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hiromi Rakugi
- Department of Geriatric and General Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Julia Ramirez
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Aragon Institute of Engineering Research, University of Zaragoza, Zaragoza, Spain
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Asif Rasheed
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Dennis Raven
- Department of Psychiatry, Interdisciplinary Center Psychopathology and Emotion Regulation, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nigel W Rayner
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Churchill Hospital, Oxford, UK
| | - Carlos Riveros
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle, New Lambton Heights, New South Wales, Australia
| | - Rebecca Rohde
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniela Ruggiero
- Institute of Genetics and Biophysics A. Buzzati-Traverso, CNR, Naples, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Sanni E Ruotsalainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Kathleen A Ryan
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Maria Sabater-Lleal
- Unit of Genomics of Complex Diseases, Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona, Spain
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden
| | - Richa Saxena
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Medical Faculty, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Medical Faculty, Leipzig, Germany
| | - Anoop Sendamarai
- Center for Data and Computational Sciences, VA Boston Healthcare System, Boston, MA, USA
| | - Botong Shen
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | | | - Jae Hun Shin
- Department of Biomedical Science, Hallym University, Chuncheon, Republic of Korea
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Roderick C Slieker
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Epidemiology and Data Science, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - Roelof A J Smit
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Albert V Smith
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Icelandic Heart Association, Kópavogur, Iceland
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Laura J Smyth
- Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | - Lorraine Southam
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Wellcome Sanger Institute, Hinxton, UK
| | | | - Liang Sun
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fumihiko Takeuchi
- Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Divya Sri Priyanka Tallapragada
- Genomic Research on Complex diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Mohn Nutrition Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Bamidele O Tayo
- Department of Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA
| | - Catherine Tcheandjieu
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Natalie Terzikhan
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Paola Tesolin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Elizabeth Theusch
- Cardiology Division, Department of Pediatrics, University of California, San Francisco, Oakland, CA, USA
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Paul R H J Timmers
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Stella Trompet
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simona Vaccargiu
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jan B van Klinken
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jessica van Setten
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Shefali S Verma
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Yogasudha Veturi
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Carol A Wang
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle, New Lambton Heights, New South Wales, Australia
| | - Chaolong Wang
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lihua Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Helen R Warren
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Wen Bin Wei
- Department of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | | | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Bendik S Winsvold
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing at UCL, Institute of Cardiovascular Science, University College London, London, UK
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
- Department of Medicine IV - Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Rui Xia
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Tian Xie
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Japan
| | - Jingyun Yang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Hannah Young
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Noha A Yousri
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
- Department of Computer and Systems Engineering, Alexandria University, Alexandria, Egypt
| | - Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Lingyao Zeng
- Department of Cardiology, German Heart Centre Munich, Technical University Munich, Munich, Germany
| | - Weihua Zhang
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, UK
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Xinyuan Zhang
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jing-Hua Zhao
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Wei Zhao
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martina E Zimmermann
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Magdalena Zoledziewska
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Linda S Adair
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hieab H H Adams
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Latin American Brain Health (BrainLat), Universidad Adolfo Ibáñez, Santiago, Chile
| | - Carlos A Aguilar-Salinas
- Unidad de Investigacion de Enfermedades Metabolicas and Direction of Nutrition, Instituto Nacional de Ciencias Medicas y Nutricion, Mexico City, Mexico
- Escuela de Medicina y Ciencias de la Salud, Tecnologico de Monterrey, Monterrey, Mexico
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Donna K Arnett
- Department of Epidemiology and Dean's Office, College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | - Bjørn Olav Åsvold
- KG Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Levanger, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - John Attia
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
| | - Bernhard Banas
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | | | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Tobias Bergler
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Dwaipayan Bharadwaj
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University (JNU), New Delhi, India
| | - Ginevra Biino
- Institute of Molecular Genetics, National Research Council of Italy, Pavia, Italy
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Eric Boerwinkle
- Human Genetics Center and Department of Epidemiology, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Carsten A Böger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
- Department of Nephrology and Rheumatology, Kliniken Südostbayern, Regensburg, Germany
- KfH Kidney Center Traunstein, Traunstein, Germany
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Dorret I Boomsma
- Department of Biological Psychology, Behaviour and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Anders D Børglum
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine (CGPM), Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Judith B Borja
- USC-Office of Population Studies Foundation, University of San Carlos, Cebu City, Philippines
- Department of Nutrition and Dietetics, University of San Carlos, Cebu City, Philippines
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Donald W Bowden
- Center for Precision Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Ivan Brandslund
- Department of Clinical Biochemistry, Lillebaelt Hospital, Vejle, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Ben Brumpton
- KG Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
- Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Julie E Buring
- Harvard Medical School, Boston, MA, USA
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Mark J Caulfield
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - John C Chambers
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, UK
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
| | - Giriraj R Chandak
- Genomic Research on Complex diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Adjunct Faculty, JSS University Academy of Higher Education and Research (JSSAHER), JSS (Deemed to be) University, Mysuru, India
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nish Chaturvedi
- MRC Unit for Lifelong Health and Ageing at UCL, Institute of Cardiovascular Science, University College London, London, UK
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Ching-Yu Cheng
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Ingrid E Christophersen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Department of Medical Research, Bærum Hospital, Vestre Viken Hospital Trust, Gjettum, Norway
| | - Marina Ciullo
- Institute of Genetics and Biophysics A. Buzzati-Traverso, CNR, Naples, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - John W Cole
- Department of Neurology, Division of Vascular Neurology, University of Maryland School of Medicine, Baltimore, MD, USA
- Baltimore Veterans Affairs Medical Center, Department of Neurology, Baltimore, MD, USA
| | - Francis S Collins
- Molecular Genetics Section, Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Richard S Cooper
- Department of Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA
| | - Miguel Cruz
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Michael J Cutler
- Intermountain Heart Institute, Intermountain Medical Center, Murray, UT, USA
| | - Scott M Damrauer
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Thomas M Dantoft
- Center for Clinical Research and Prevention, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Gert J de Borst
- Department of Vascular Surgery, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | | | - Philip L De Jager
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Dominique P V de Kleijn
- Department of Vascular Surgery, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | | | - George V Dedoussis
- Department of Nutrition and Dietetics, School of Health and Education, Harokopio University of Athens, Athens, Greece
| | - Anneke I den Hollander
- Departments of Ophthalmology and Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Shufa Du
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Petra J M Elders
- Department of General Practice, Amsterdam Public Health Institute, Amsterdam UMC, location VUmc, Amsterdam, The Netherlands
| | - A Heather Eliassen
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiac Arrhythmia Service, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Sölve Elmståhl
- Department of Clinical Sciences in Malmö, Division of Geriatric Medicine, Lund University, Malmö, Sweden
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research) partner site Hamburg/Lübeck/Kiel and University Heart Center Lübeck, Lübeck, Germany
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Diane Fatkin
- Molecular Cardiology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- Cardiology Department, St Vincent's Hospital, Darlinghurst, New South Wales, Australia
- Faculty of Medicine, UNSW Sydney, Kensington, New South Wales, Australia
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Ian Ford
- Robertson Center for Biostatistics, University of Glasgow, Glasgow, UK
| | - Myriam Fornage
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Paul W Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Malmö, Sweden
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Barry I Freedman
- Department of Internal Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Paolo Gasparini
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Giorgia Girotto
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Michael E Goddard
- Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville, Victoria, Australia
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Bundoora, Victoria, Australia
| | - Yvonne M Golightly
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Injury Prevention Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Physical Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Clicerio Gonzalez-Villalpando
- Centro de Investigacion en Salud Poblacional Instituto Nacional de Salud Publica and Centro de Estudios en Diabetes, Cuernavaca, Mexico
| | - Penny Gordon-Larsen
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Struan F A Grant
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Departments of Pediatrics and Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lyn Griffiths
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland, Australia
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kópavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Catharina A Hartman
- Department of Psychiatry, Interdisciplinary Center Psychopathology and Emotion Regulation, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Susan R Heckbert
- Cardiovascular Health Research Unit, Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Christian Hengstenberg
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, Vienna, Austria
| | - Alex W Hewitt
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Tasmania, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, Melbourne, Victoria, Australia
- Lions Eye Institute, Centre for Ophthalmology and Vision Science, University of Western Australia, Perth, Western Australia, Australia
| | - Haretsugu Hishigaki
- Biomedical Technology Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Tokushima, Japan
| | - Carel B Hoyng
- Departments of Ophthalmology and Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Paul L Huang
- Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiology Division, Massachusetts General Hospital, Boston, MA, USA
| | - Wei Huang
- Department of Genetics, Shanghai-MOST Key Laboratory of Heath and Disease Genomics, Chinese National Human Genome Center and Shanghai Industrial Technology Institute, Shanghai, China
| | - Steven C Hunt
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Kristian Hveem
- KG Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Levanger, Norway
| | - Elina Hyppönen
- Australian Centre for Precision Health, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - William G Iacono
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Sahoko Ichihara
- Department of Environmental and Preventive Medicine, Jichi Medical University School of Medicine, Shimotsuke, Japan
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Carmen R Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, School of Medicine, Ohio State University, Columbus, OH, USA
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing, China
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Peter K Joshi
- Centre for Cardiovascular Sciences, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Pekka Jousilahti
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, LUMC, Leiden, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Kui Dong Kang
- Department of Ophthalmology, The Catholic University of Korea Incheon St. Mary's Hospital, Incheon, Republic of Korea
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Churchill Hospital, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Norihiro Kato
- Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Frank Kee
- Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | - Thorsten Kessler
- Department of Cardiology, German Heart Centre Munich, Technical University Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Amit V Khera
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Lambertus A L M Kiemeney
- Radboud University Medical Center, Radboud Institute for Health Sciences, Department for Health Evidence, Nijmegen, The Netherlands
- Radboud University Medical Center, Radboud Institute for Health Sciences, Department of Urology, Nijmegen, The Netherlands
| | - Bong-Jo Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, Republic of Korea
| | - Eung Kweon Kim
- Corneal Dystrophy Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
- Saevit Eye Hospital, Goyang, Republic of Korea
| | - Hyung-Lae Kim
- Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Paulus Kirchhof
- Department of Cardiology, University Heart and Vascular Center UKE Hamburg, Hamburg, Germany
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- German Center for Cardiovascular Research, partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
- Atrial Fibrillation NETwork, Münster, Germany
| | - Mika Kivimaki
- Department of Epidemiology and Public Health, UCL Institute of Epidemiology and Health Care, University College London, London, UK
| | - Woon-Puay Koh
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Heikki A Koistinen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- University of Helsinki and Department of Medicine, Helsinki University Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Genovefa D Kolovou
- Department of Preventive Cardiology, Lipoprotein Apheresis Unit and Lipid Disorders Clinic, Metropolitan Hospital, Athens, Greece
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Adriaan Kraaijeveld
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ronald M Krauss
- Cardiology Division, Department of Pediatrics, University of California, San Francisco, Oakland, CA, USA
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | - Zoltan Kutalik
- Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Leslie A Lange
- Department of Medicine, University of Colorado at Denver, Aurora, CO, USA
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Hyejin Lee
- Department of Internal Medicine, Ewha Womans University School of Medicine, Seoul, Republic of Korea
| | - Nanette R Lee
- USC-Office of Population Studies Foundation, University of San Carlos, Cebu City, Philippines
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Huaixing Li
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Liming Li
- Department of Epidemiology and Biostatistics, Peking University Health Science Center, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Kiel University, Kiel, Germany
| | - Xu Lin
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Medical Faculty, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Medical Faculty, Leipzig, Germany
| | - Barry London
- Division of Cardiovascular Medicine and Abboud Cardiovascular Research Center, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Steven A Lubitz
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiac Arrhythmia Service, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Stephen J Lye
- Alliance for Human Development, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - David A Mackey
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Tasmania, Australia
- Lions Eye Institute, Centre for Ophthalmology and Vision Science, University of Western Australia, Perth, Western Australia, Australia
| | - Reedik Mägi
- Institute of Genomics, Estonian Genome Centre, University of Tartu, Tartu, Estonia
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Gregory M Marcus
- Division of Cardiology, University of California, San Francisco, San Francisco, CA, USA
| | - Pedro Marques Vidal
- Department of Medicine, Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
- University of Lausanne, Lausanne, Switzerland
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- SYNLAB Academy, SYNLAB Holding Deutschland, Mannheim, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Robert W McGarrah
- Department of Medicine, Division of Cardiology, Duke University School of Medicine, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | | | - Sarah E Medland
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Dan Mellström
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Geriatric Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Andres Metspalu
- Institute of Genomics, Estonian Genome Centre, University of Tartu, Tartu, Estonia
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Paul Mitchell
- Centre for Vision Research and Department of Ophthalmology, Westmead Millennium Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Andrew D Morris
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Patricia B Munroe
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Glen Echo, MD, USA
| | - Saman Nazarian
- Electrophysiology Section, Division of Cardiovascular Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda E Nelson
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Matt J Neville
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Churchill Hospital, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Christopher Newton-Cheh
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher S Nielsen
- Department of Chronic Diseases, Norwegian Institute of Public Health, Oslo, Norway
- Department of Pain Management and Research, Oslo University Hospital, Oslo, Norway
| | - Markus M Nöthen
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Claes Ohlsson
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Sahlgrenska University Hospital, Department of Drug Treatment, Gothenburg, Sweden
| | - Albertine J Oldehinkel
- Department of Psychiatry, Interdisciplinary Center Psychopathology and Emotion Regulation, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lorena Orozco
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica, CDMX, Mexico City, Mexico
| | - Katja Pahkala
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Paavo Nurmi Centre, Sports and Exercise Medicine Unit, Department of Physical Activity and Health, University of Turku, Turku, Finland
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Institute for Precision Health, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Colin N A Palmer
- Pat MacPherson Centre for Pharmacogenetics and Pharmacogenomics, Division of Population Health and Genomics, School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Cristian Pattaro
- Eurac Research, Institute for Biomedicine, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Craig E Pennell
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle, New Lambton Heights, New South Wales, Australia
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Public Health and Amsterdam Neuroscience, Amsterdam UMC and Vrije Universiteit, Amsterdam, The Netherlands
| | - Louis Perusse
- Department of Kinesiology, Faculty of Medicine, Université Laval, Québec City, Quebec, Canada
- Centre Nutrition, Santé et Société (NUTRISS), Institute of Nutrition and Functional Foods, Université Laval, Québec City, Quebec, Canada
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- IBE-Chair of Epidemiology, LMU Munich, Neuherberg, Germany
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Chris Power
- Population, Policy and Practice, UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Peter P Pramstaller
- Eurac Research, Institute for Biomedicine, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jia Qu
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
| | - Daniel J Rader
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Sarju Ralhan
- Hero DMC Heart Institute, Dyanand Medical College, Ludhiana, India
| | - Loukianos S Rallidis
- Second Department of Cardiology, Medical School, National and Kapodistrian University of Athens, University General Hospital Attikon, Athens, Greece
| | - Dabeeru C Rao
- Division of Biostatistics, Washington University School of Medicine, St Louis, MO, USA
| | - Susan Redline
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Sang Youl Rhee
- Department of Endocrinology and Metabolism, Kyung Hee University School of Medicine, Seoul, Korea
| | - Paul M Ridker
- Harvard Medical School, Boston, MA, USA
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Samuli Ripatti
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Igor Rudan
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Femke Rutters
- Department of Epidemiology and Data Science, Amsterdam Public Health Institute, Amsterdam Cardiovascular Sciences Institute, Amsterdam UMC, location VUmc, Amsterdam, The Netherlands
| | - Charumathi Sabanayagam
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Danish Saleheen
- Center for Non-Communicable Diseases, Karachi, Pakistan
- Department of Cardiology and Department of Medicine, Columbia University, New York, NY, USA
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Dharambir K Sanghera
- Department of Pediatrics, Section of Genetics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Börge Schmidt
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Helena Schmidt
- Gottfried Schatz Research Center (for Cell Signaling, Metabolism and Aging), Medical University of Graz, Graz, Austria
| | - Reinhold Schmidt
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Cardiology, Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK) - Munich Heart Alliance, and Technische Universität München, München, Germany
| | - Laura J Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Rodney J Scott
- School of Biomedical Science and Pharmacy, University of Newcastle, New Lambton Heights, New South Wales, Australia
| | - Peter Sever
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Eric J Shiroma
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - M Benjamin Shoemaker
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eleanor M Simonsick
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Mario Sims
- Jackson Heart Study, Department of Medicine, University of Mississippi, Jackson, MS, USA
| | | | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Moritz F Sinner
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
| | - J Gustav Smith
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University and the Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Wallenberg Center for Molecular Medicine and Lund University Diabetes Center, Lund University, Lund, Sweden
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Meir J Stampfer
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Klaus J Stark
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Leen M 't Hart
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Epidemiology and Data Science, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
- Molecular Epidemiology Section, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jean-Claude Tardif
- Montreal Heart Institute, Montreal, Quebec, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Thangavel A Thanaraj
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Anke Tönjes
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Angelo Tremblay
- Department of Kinesiology, Faculty of Medicine, Université Laval, Québec City, Quebec, Canada
- Centre Nutrition, Santé et Société (NUTRISS), Institute of Nutrition and Functional Foods, Université Laval, Québec City, Quebec, Canada
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
- Helsinki University Central Hospital, Research Program for Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Jaakko Tuomilehto
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maria-Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Pim van der Harst
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nathalie Van der Velde
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department Geriatric Medicine, Amsterdam Public Health, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Cornelia M van Duijn
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Natasja M van Schoor
- Department of Epidemiology and Data Science, Amsterdam UMC, Amsterdam, The Netherlands
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Uwe Völker
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Peter Vollenweider
- Department of Medicine, Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
- University of Lausanne, Lausanne, Switzerland
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Niels H Wacher-Rodarte
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Mark Walker
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing, China
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Richard M Watanabe
- Department of Population and Public Health Sciences, Keck School of Medicine of USC, Los Angeles, CA, USA
- Department of Physiology and Neuroscience, Keck School of Medicine of USC, Los Angeles, CA, USA
- USC Diabetes and Obesity Research Institute, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Hugh Watkins
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Thomas M Werge
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Lundbeck Foundation Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Lynne R Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Gonneke Willemsen
- Department of Biological Psychology, Behaviour and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Walter C Willett
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - James F Wilson
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Tien-Yin Wong
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Jeong-Taek Woo
- Department of Endocrinology and Metabolism, Kyung Hee University School of Medicine, Seoul, Korea
| | - Alan F Wright
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Huichun Xu
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Wellcome Sanger Institute, Hinxton, UK
- TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, Munich, Germany
| | - Babette S Zemel
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Joseph M Zmuda
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - John-Anker Zwart
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Daniel I Chasman
- Harvard Medical School, Boston, MA, USA
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chuncheon, Republic of Korea
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Churchill Hospital, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Maggie C Y Ng
- Center for Precision Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher J O'Donnell
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Veterans Affairs Boston Healthcare System, Boston, MA, USA
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Yan V Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
- Atlanta VA Health Care System, Decatur, GA, USA
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Panos Deloukas
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anne E Justice
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Population Health Sciences, Geisinger, Danville, PA, USA
| | - Cecilia M Lindgren
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ruth J F Loos
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kari Stefansson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Tõnu Esko
- Institute of Genomics, Estonian Genome Centre, University of Tartu, Tartu, Estonia
| | - Themistocles L Assimes
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Adam E Locke
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montreal, Quebec, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Timothy M Frayling
- Genetics of Complex Traits, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Yukinori Okada
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan.
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan.
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Andrew R Wood
- Genetics of Complex Traits, College of Medicine and Health, University of Exeter, Exeter, UK.
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
| | - Joel N Hirschhorn
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA.
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Departments of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA.
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6
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Akbari P, Sosina OA, Bovijn J, Landheer K, Nielsen JB, Kim M, Aykul S, De T, Haas ME, Hindy G, Lin N, Dinsmore IR, Luo JZ, Hectors S, Geraghty B, Germino M, Panagis L, Parasoglou P, Walls JR, Halasz G, Atwal GS, Jones M, LeBlanc MG, Still CD, Carey DJ, Giontella A, Orho-Melander M, Berumen J, Kuri-Morales P, Alegre-Díaz J, Torres JM, Emberson JR, Collins R, Rader DJ, Zambrowicz B, Murphy AJ, Balasubramanian S, Overton JD, Reid JG, Shuldiner AR, Cantor M, Abecasis GR, Ferreira MAR, Sleeman MW, Gusarova V, Altarejos J, Harris C, Economides AN, Idone V, Karalis K, Della Gatta G, Mirshahi T, Yancopoulos GD, Melander O, Marchini J, Tapia-Conyer R, Locke AE, Baras A, Verweij N, Lotta LA. Multiancestry exome sequencing reveals INHBE mutations associated with favorable fat distribution and protection from diabetes. Nat Commun 2022; 13:4844. [PMID: 35999217 PMCID: PMC9399235 DOI: 10.1038/s41467-022-32398-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/28/2022] [Indexed: 12/13/2022] Open
Abstract
Body fat distribution is a major, heritable risk factor for cardiometabolic disease, independent of overall adiposity. Using exome-sequencing in 618,375 individuals (including 160,058 non-Europeans) from the UK, Sweden and Mexico, we identify 16 genes associated with fat distribution at exome-wide significance. We show 6-fold larger effect for fat-distribution associated rare coding variants compared with fine-mapped common alleles, enrichment for genes expressed in adipose tissue and causal genes for partial lipodystrophies, and evidence of sex-dimorphism. We describe an association with favorable fat distribution (p = 1.8 × 10-09), favorable metabolic profile and protection from type 2 diabetes (~28% lower odds; p = 0.004) for heterozygous protein-truncating mutations in INHBE, which encodes a circulating growth factor of the activin family, highly and specifically expressed in hepatocytes. Our results suggest that inhibin βE is a liver-expressed negative regulator of adipose storage whose blockade may be beneficial in fat distribution-associated metabolic disease.
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Affiliation(s)
- Parsa Akbari
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Olukayode A. Sosina
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Jonas Bovijn
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Karl Landheer
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Jonas B. Nielsen
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Minhee Kim
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Senem Aykul
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Tanima De
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Mary E. Haas
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - George Hindy
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Nan Lin
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Ian R. Dinsmore
- grid.280776.c0000 0004 0394 1447Department of Molecular and Functional Genomics, Geisinger Health System, Danville, PA USA
| | - Jonathan Z. Luo
- grid.280776.c0000 0004 0394 1447Department of Molecular and Functional Genomics, Geisinger Health System, Danville, PA USA
| | - Stefanie Hectors
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Benjamin Geraghty
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Mary Germino
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Lampros Panagis
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Prodromos Parasoglou
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Johnathon R. Walls
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Gabor Halasz
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Gurinder S. Atwal
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | | | | | - Marcus Jones
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Michelle G. LeBlanc
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Christopher D. Still
- grid.280776.c0000 0004 0394 1447Geisinger Obesity Institute, Geisinger Health System, Danville, PA USA
| | - David J. Carey
- grid.280776.c0000 0004 0394 1447Geisinger Obesity Institute, Geisinger Health System, Danville, PA USA
| | - Alice Giontella
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden ,grid.5611.30000 0004 1763 1124Department of Medicine, University of Verona, Verona, Italy
| | - Marju Orho-Melander
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Jaime Berumen
- grid.9486.30000 0001 2159 0001Unidad de Medicina Experimental de la Facultad de Medicina de la Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Pablo Kuri-Morales
- grid.9486.30000 0001 2159 0001Unidad de Medicina Experimental de la Facultad de Medicina de la Universidad Nacional Autónoma de México, Mexico City, Mexico ,grid.419886.a0000 0001 2203 4701Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, Mexico
| | - Jesus Alegre-Díaz
- grid.9486.30000 0001 2159 0001Unidad de Medicina Experimental de la Facultad de Medicina de la Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jason M. Torres
- grid.4991.50000 0004 1936 8948MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK ,grid.4991.50000 0004 1936 8948Clinical Trial Service Unit & Epidemiological Studies Unit Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jonathan R. Emberson
- grid.4991.50000 0004 1936 8948MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK ,grid.4991.50000 0004 1936 8948Clinical Trial Service Unit & Epidemiological Studies Unit Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Rory Collins
- grid.4991.50000 0004 1936 8948Clinical Trial Service Unit & Epidemiological Studies Unit Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Daniel J. Rader
- grid.25879.310000 0004 1936 8972Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Brian Zambrowicz
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Andrew J. Murphy
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Suganthi Balasubramanian
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - John D. Overton
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Jeffrey G. Reid
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Alan R. Shuldiner
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Michael Cantor
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Goncalo R. Abecasis
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Manuel A. R. Ferreira
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Mark W. Sleeman
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Viktoria Gusarova
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Judith Altarejos
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Charles Harris
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Aris N. Economides
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA ,grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Vincent Idone
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Katia Karalis
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Giusy Della Gatta
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Tooraj Mirshahi
- grid.280776.c0000 0004 0394 1447Geisinger Obesity Institute, Geisinger Health System, Danville, PA USA
| | | | - Olle Melander
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden ,grid.411843.b0000 0004 0623 9987Department of Emergency and Internal Medicine, Skåne University Hospital, Malmö, Sweden
| | - Jonathan Marchini
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Roberto Tapia-Conyer
- grid.419886.a0000 0001 2203 4701Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, Mexico
| | - Adam E. Locke
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Aris Baras
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA.
| | - Niek Verweij
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Luca A. Lotta
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
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7
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Pathak GA, Karjalainen J, Stevens C, Neale BM, Daly M, Ganna A, Andrews SJ, Kanai M, Cordioli M, Polimanti R, Harerimana N, Pirinen M, Liao RG, Chwialkowska K, Trankiem A, Balaconis MK, Nguyen H, Solomonson M, Veerapen K, Wolford B, Roberts G, Park D, Ball CA, Coignet M, McCurdy S, Knight S, Partha R, Rhead B, Zhang M, Berkowitz N, Gaddis M, Noto K, Ruiz L, Pavlovic M, Hong EL, Rand K, Girshick A, Guturu H, Baltzell AH, Niemi MEK, Rahmouni S, Guntz J, Beguin Y, Cordioli M, Pigazzini S, Nkambule L, Georges M, Moutschen M, Misset B, Darcis G, Guiot J, Azarzar S, Gofflot S, Claassen S, Malaise O, Huynen P, Meuris C, Thys M, Jacques J, Léonard P, Frippiat F, Giot JB, Sauvage AS, Frenckell CV, Belhaj Y, Lambermont B, Nakanishi T, Morrison DR, Mooser V, Richards JB, Butler-Laporte G, Forgetta V, Li R, Ghosh B, Laurent L, Belisle A, Henry D, Abdullah T, Adeleye O, Mamlouk N, Kimchi N, Afrasiabi Z, Rezk N, Vulesevic B, Bouab M, Guzman C, Petitjean L, Tselios C, Xue X, Afilalo J, Afilalo M, Oliveira M, Brenner B, Brassard N, Durand M, Schurr E, Lepage P, Ragoussis J, Auld D, Chassé M, Kaufmann DE, Lathrop GM, Adra D, Hayward C, Glessner JT, Shaw DM, Campbell A, Morris M, Hakonarson H, Porteous DJ, Below J, Richmond A, Chang X, Polikowski H, Lauren PE, Chen HH, Wanying Z, Fawns-Ritchie C, North K, McCormick JB, Chang X, Glessner JR, Hakonarson H, Gignoux CR, Wicks SJ, Crooks K, Barnes KC, Daya M, Shortt J, Rafaels N, Chavan S, Timmers PRHJ, Wilson JF, Tenesa A, Kerr SM, D’Mellow K, Shahin D, El-Sherbiny YM, von Hohenstaufen KA, Sobh A, Eltoukhy MM, Nkambul L, Elhadidy TA, Abd Elghafar MS, El-Jawhari JJ, Mohamed AAS, Elnagdy MH, Samir A, Abdel-Aziz M, Khafaga WT, El-Lawaty WM, Torky MS, El-shanshory MR, Yassen AM, Hegazy MAF, Okasha K, Eid MA, Moahmed HS, Medina-Gomez C, Ikram MA, Uitterlinden AG, Mägi R, Milani L, Metspalu A, Laisk T, Läll K, Lepamets M, Esko T, Reimann E, Naaber P, Laane E, Pesukova J, Peterson P, Kisand K, Tabri J, Allos R, Hensen K, Starkopf J, Ringmets I, Tamm A, Kallaste A, Alavere H, Metsalu K, Puusepp M, Batini C, Tobin MD, Venn LD, Lee PH, Shrine N, Williams AT, Guyatt AL, John C, Packer RJ, Ali A, Free RC, Wang X, Wain LV, Hollox EJ, Bee CE, Adams EL, Palotie A, Ripatti S, Ruotsalainen S, Kristiansson K, Koskelainen S, Perola M, Donner K, Kivinen K, Palotie A, Kaunisto M, Rivolta C, Bochud PY, Bibert S, Boillat N, Nussle SG, Albrich W, Quinodoz M, Kamdar D, Suh N, Neofytos D, Erard V, Voide C, Bochud PY, Rivolta C, Bibert S, Quinodoz M, Kamdar D, Neofytos D, Erard V, Voide C, Friolet R, Vollenweider P, Pagani JL, Oddo M, zu Bentrup FM, Conen A, Clerc O, Marchetti O, Guillet A, Guyat-Jacques C, Foucras S, Rime M, Chassot J, Jaquet M, Viollet RM, Lannepoudenx Y, Portopena L, Bochud PY, Vollenweider P, Pagani JL, Desgranges F, Filippidis P, Guéry B, Haefliger D, Kampouri EE, Manuel O, Munting A, Papadimitriou-Olivgeris M, Regina J, Rochat-Stettler L, Suttels V, Tadini E, Tschopp J, Van Singer M, Viala B, Boillat-Blanco N, Brahier T, Hügli O, Meuwly JY, Pantet O, Gonseth Nussle S, Bochud M, D’Acremont V, Estoppey Younes S, Albrich WC, Suh N, Cerny A, O’Mahony L, von Mering C, Bochud PY, Frischknecht M, Kleger GR, Filipovic M, Kahlert CR, Wozniak H, Negro TR, Pugin J, Bouras K, Knapp C, Egger T, Perret A, Montillier P, di Bartolomeo C, Barda B, de Cid R, Carreras A, Moreno V, Kogevinas M, Galván-Femenía I, Blay N, Farré X, Sumoy L, Cortés B, Mercader JM, Guindo-Martinez M, Torrents D, Garcia-Aymerich J, Castaño-Vinyals G, Dobaño C, Gori M, Renieri A, Mari F, Mondelli MU, Castelli F, Vaghi M, Rusconi S, Montagnani F, Bargagli E, Franchi F, Mazzei MA, Cantarini L, Tacconi D, Feri M, Scala R, Spargi G, Nencioni C, Bandini M, Caldarelli GP, Canaccini A, Ognibene A, D’Arminio Monforte A, Girardis M, Antinori A, Francisci D, Schiaroli E, Scotton PG, Panese S, Scaggiante R, Monica MD, Capasso M, Fiorentino G, Castori M, Aucella F, Biagio AD, Masucci L, Valente S, Mandalà M, Zucchi P, Giannattasio F, Coviello DA, Mussini C, Tavecchia L, Crotti L, Rizzi M, Rovere MTL, Sarzi-Braga S, Bussotti M, Ravaglia S, Artuso R, Perrella A, Romani D, Bergomi P, Catena E, Vincenti A, Ferri C, Grassi D, Pessina G, Tumbarello M, Pietro MD, Sabrina R, Luchi S, Furini S, Dei S, Benetti E, Picchiotti N, Sanarico M, Ceri S, Pinoli P, Raimondi F, Biscarini F, Stella A, Zguro K, Capitani K, Nkambule L, Tanfoni M, Fallerini C, Daga S, Baldassarri M, Fava F, Frullanti E, Valentino F, Doddato G, Giliberti A, Tita R, Amitrano S, Bruttini M, Croci S, Meloni I, Mencarelli MA, Rizzo CL, Pinto AM, Beligni G, Tommasi A, Sarno LD, Palmieri M, Carriero ML, Alaverdian D, Busani S, Bruno R, Vecchia M, Belli MA, Mantovani S, Ludovisi S, Quiros-Roldan E, Antoni MD, Zanella I, Siano M, Emiliozzi A, Fabbiani M, Rossetti B, Bergantini L, D’Alessandro M, Cameli P, Bennett D, Anedda F, Marcantonio S, Scolletta S, Guerrini S, Conticini E, Frediani B, Spertilli C, Donati A, Guidelli L, Corridi M, Croci L, Piacentini P, Desanctis E, Cappelli S, Verzuri A, Anemoli V, Pancrazzi A, Lorubbio M, Miraglia FG, Venturelli S, Cossarizza A, Vergori A, Gabrieli A, Riva A, Paciosi F, Andretta F, Gatti F, Parisi SG, Baratti S, Piscopo C, Russo R, Andolfo I, Iolascon A, Carella M, Merla G, Squeo GM, Raggi P, Marciano C, Perna R, Bassetti M, Sanguinetti M, Giorli A, Salerni L, Parravicini P, Menatti E, Trotta T, Coiro G, Lena F, Martinelli E, Mancarella S, Gabbi C, Maggiolo F, Ripamonti D, Bachetti T, Suardi C, Parati G, Bottà G, Domenico PD, Rancan I, Bianchi F, Colombo R, Barbieri C, Acquilini D, Andreucci E, Segala FV, Tiseo G, Falcone M, Lista M, Poscente M, Vivo OD, Petrocelli P, Guarnaccia A, Baroni S, Hayward C, Porteous DJ, Fawns-Ritchie C, Richmond A, Campbell A, van Heel DA, Hunt KA, Trembath RC, Huang QQ, Martin HC, Mason D, Trivedi B, Wright J, Finer S, Akhtar S, Anwar M, Arciero E, Ashraf S, Breen G, Chung R, Curtis CJ, Chowdhury M, Colligan G, Deloukas P, Durham C, Finer S, Griffiths C, Huang QQ, Hurles M, Hunt KA, Hussain S, Islam K, Khan A, Khan A, Lavery C, Lee SH, Lerner R, MacArthur D, MacLaughlin B, Martin H, Mason D, Miah S, Newman B, Safa N, Tahmasebi F, Trembath RC, Trivedi B, van Heel DA, Wright J, Griffiths CJ, Smith AV, Boughton AP, Li KW, LeFaive J, Annis A, Niavarani A, Aliannejad R, Sharififard B, Amirsavadkouhi A, Naderpour Z, Tadi HA, Aleagha AE, Ahmadi S, Moghaddam SBM, Adamsara A, Saeedi M, Abdollahi H, Hosseini A, Chariyavilaskul P, Jantarabenjakul W, Hirankarn N, Chamnanphon M, Suttichet TB, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Putchareon O, Torvorapanit P, Puthanakit T, Suchartlikitwong P, Nilaratanakul V, Sodsai P, Brumpton BM, Hveem K, Willer C, Wolford B, Zhou W, Rogne T, Solligard E, Åsvold BO, Franke L, Boezen M, Deelen P, Claringbould A, Lopera E, Warmerdam R, Vonk JM, van Blokland I, Lanting P, Ori APS, Feng YCA, Mercader J, Weiss ST, Karlson EW, Smoller JW, Murphy SN, Meigs JB, Woolley AE, Green RC, Perez EF, Wolford B, Zöllner S, Wang J, Beck A, Sloofman LG, Ascolillo S, Sebra RP, Collins BL, Levy T, Buxbaum JD, Sealfon SC, Jordan DM, Thompson RC, Gettler K, Chaudhary K, Belbin GM, Preuss M, Hoggart C, Choi S, Underwood SJ, Salib I, Britvan B, Keller K, Tang L, Peruggia M, Hiester LL, Niblo K, Aksentijevich A, Labkowsky A, Karp A, Zlatopolsky M, Zyndorf M, Charney AW, Beckmann ND, Schadt EE, Abul-Husn NS, Cho JH, Itan Y, Kenny EE, Loos RJF, Nadkarni GN, Do R, O’Reilly P, Huckins LM, Ferreira MAR, Abecasis GR, Leader JB, Cantor MN, Justice AE, Carey DJ, Chittoor G, Josyula NS, Kosmicki JA, Horowitz JE, Baras A, Gass MC, Yadav A, Mirshahi T, Hottenga JJ, Bartels M, de geus EEJC, Nivard MMG, Verma A, Ritchie MD, Rader D, Li B, Verma SS, Lucas A, Bradford Y, Abedalthagafi M, Alaamery M, Alshareef A, Sawaji M, Massadeh S, AlMalik A, Alqahtani S, Baraka D, Harthi FA, Alsolm E, Safieh LA, Alowayn AM, Alqubaishi F, Mutairi AA, Mangul S, Almutairi M, Aljawini N, Albesher N, Arabi YM, Mahmoud ES, Khattab AK, Halawani RT, Alahmadey ZZ, Albakri JK, Felemban WA, Suliman BA, Hasanato R, Al-Awdah L, Alghamdi J, AlZahrani D, AlJohani S, Al-Afghani H, AlDhawi N, AlBardis H, Alkwai S, Alswailm M, Almalki F, Albeladi M, Almohammed I, Barhoush E, Albader A, Alotaibi S, Alghamdi B, Jung J, fawzy MS, Alrashed M, Zeberg H, Nkambul L, Frithiof R, Hultström M, Lipcsey M, Tardif N, Rooyackers O, Grip J, Maricic T, Helgeland Ø, Magnus P, Trogstad LIS, Lee Y, Harris JR, Mangino M, Spector TD, Emma D, Moutsianas L, Caulfield MJ, Scott RH, Kousathanas A, Pasko D, Walker S, Stuckey A, Odhams CA, Rhodes D, Fowler T, Rendon A, Chan G, Arumugam P, Karczewski KJ, Martin AR, Wilson DJ, Spencer CCA, Crook DW, Wyllie DH, O’Connell AM, Atkinson EG, Kanai M, Tsuo K, Baya N, Turley P, Gupta R, Walters RK, Palmer DS, Sarma G, Solomonson M, Cheng N, Lu W, Churchhouse C, Goldstein JI, King D, Zhou W, Seed C, Daly MJ, Neale BM, Finucane H, Bryant S, Satterstrom FK, Band G, Earle SG, Lin SK, Arning N, Koelling N, Armstrong J, Rudkin JK, Callier S, Bryant S, 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VE, Baillie JK. A first update on mapping the human genetic architecture of COVID-19. Nature 2022; 608:E1-E10. [PMID: 35922517 PMCID: PMC9352569 DOI: 10.1038/s41586-022-04826-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/29/2022] [Indexed: 01/04/2023]
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Verweij N, Haas ME, Nielsen JB, Sosina OA, Kim M, Akbari P, De T, Hindy G, Bovijn J, Persaud T, Miloscio L, Germino M, Panagis L, Watanabe K, Mbatchou J, Jones M, LeBlanc M, Balasubramanian S, Lammert C, Enhörning S, Melander O, Carey DJ, Still CD, Mirshahi T, Rader DJ, Parasoglou P, Walls JR, Overton JD, Reid JG, Economides A, Cantor MN, Zambrowicz B, Murphy AJ, Abecasis GR, Ferreira MAR, Smagris E, Gusarova V, Sleeman M, Yancopoulos GD, Marchini J, Kang HM, Karalis K, Shuldiner AR, Della Gatta G, Locke AE, Baras A, Lotta LA. Germline Mutations in CIDEB and Protection against Liver Disease. N Engl J Med 2022; 387:332-344. [PMID: 35939579 DOI: 10.1056/nejmoa2117872] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Exome sequencing in hundreds of thousands of persons may enable the identification of rare protein-coding genetic variants associated with protection from human diseases like liver cirrhosis, providing a strategy for the discovery of new therapeutic targets. METHODS We performed a multistage exome sequencing and genetic association analysis to identify genes in which rare protein-coding variants were associated with liver phenotypes. We conducted in vitro experiments to further characterize associations. RESULTS The multistage analysis involved 542,904 persons with available data on liver aminotransferase levels, 24,944 patients with various types of liver disease, and 490,636 controls without liver disease. We found that rare coding variants in APOB, ABCB4, SLC30A10, and TM6SF2 were associated with increased aminotransferase levels and an increased risk of liver disease. We also found that variants in CIDEB, which encodes a structural protein found in hepatic lipid droplets, had a protective effect. The burden of rare predicted loss-of-function variants plus missense variants in CIDEB (combined carrier frequency, 0.7%) was associated with decreased alanine aminotransferase levels (beta per allele, -1.24 U per liter; 95% confidence interval [CI], -1.66 to -0.83; P = 4.8×10-9) and with 33% lower odds of liver disease of any cause (odds ratio per allele, 0.67; 95% CI, 0.57 to 0.79; P = 9.9×10-7). Rare coding variants in CIDEB were associated with a decreased risk of liver disease across different underlying causes and different degrees of severity, including cirrhosis of any cause (odds ratio per allele, 0.50; 95% CI, 0.36 to 0.70). Among 3599 patients who had undergone bariatric surgery, rare coding variants in CIDEB were associated with a decreased nonalcoholic fatty liver disease activity score (beta per allele in score units, -0.98; 95% CI, -1.54 to -0.41 [scores range from 0 to 8, with higher scores indicating more severe disease]). In human hepatoma cell lines challenged with oleate, CIDEB small interfering RNA knockdown prevented the buildup of large lipid droplets. CONCLUSIONS Rare germline mutations in CIDEB conferred substantial protection from liver disease. (Funded by Regeneron Pharmaceuticals.).
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Affiliation(s)
- Niek Verweij
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Mary E Haas
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Jonas B Nielsen
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Olukayode A Sosina
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Minhee Kim
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Parsa Akbari
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Tanima De
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - George Hindy
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Jonas Bovijn
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Trikaldarshi Persaud
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Lawrence Miloscio
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Mary Germino
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Lampros Panagis
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Kyoko Watanabe
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Joelle Mbatchou
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Marcus Jones
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Michelle LeBlanc
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Suganthi Balasubramanian
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Craig Lammert
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Sofia Enhörning
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Olle Melander
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - David J Carey
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Christopher D Still
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Tooraj Mirshahi
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Daniel J Rader
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Prodromos Parasoglou
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Johnathon R Walls
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - John D Overton
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Jeffrey G Reid
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Aris Economides
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Michael N Cantor
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Brian Zambrowicz
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Andrew J Murphy
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Goncalo R Abecasis
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Manuel A R Ferreira
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Eriks Smagris
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Viktoria Gusarova
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Mark Sleeman
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - George D Yancopoulos
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Jonathan Marchini
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Hyun M Kang
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Katia Karalis
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Alan R Shuldiner
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Giusy Della Gatta
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Adam E Locke
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Aris Baras
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
| | - Luca A Lotta
- From the Regeneron Genetics Center (N.V., M.E.H., J.B.N., O.A.S., M.K., P.A., T.D., G.H., J.B., T.P., L.M., K.W., J. Mbatchou, M.J., M.L., S.B., J.D.O., J.G.R., A.E., M.N.C., G.R.A., M.A.R.F., J. Marchini, H.M.K., K.K., A.R.S., G.D.G., A.E.L., A.B., L.A.L.), Regeneron Pharmaceuticals (M.G., L.P., P.P., J.R.W., B.Z., A.J.M., E.S., V.G., M.S., G.D.Y.), Tarrytown, NY; Indiana University School of Medicine, Indianapolis (C.L.); the Department of Clinical Sciences Malmö, Lund University, and the Department of Emergency and Internal Medicine, Skåne University Hospital - both in Malmö, Sweden (S.E., O.M.); and the Department of Molecular and Functional Genomics, Geisinger Health System, Danville (D.J.C., C.D.S., T.M.), and the Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.J.R.) - both in Pennsylvania
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9
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Kousathanas A, Pairo-Castineira E, Rawlik K, Stuckey A, Odhams CA, Walker S, Russell CD, Malinauskas T, Wu Y, Millar J, Shen X, Elliott KS, Griffiths F, Oosthuyzen W, Morrice K, Keating S, Wang B, Rhodes D, Klaric L, Zechner M, Parkinson N, Siddiq A, Goddard P, Donovan S, Maslove D, Nichol A, Semple MG, Zainy T, Maleady-Crowe F, Todd L, Salehi S, Knight J, Elgar G, Chan G, Arumugam P, Patch C, Rendon A, Bentley D, Kingsley C, Kosmicki JA, Horowitz JE, Baras A, Abecasis GR, Ferreira MAR, Justice A, Mirshahi T, Oetjens M, Rader DJ, Ritchie MD, Verma A, Fowler TA, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Elliott P, Walsh T, Tenesa A, Fawkes A, Murphy L, Rowan K, Ponting CP, Vitart V, Wilson JF, Yang J, Bretherick AD, Scott RH, Hendry SC, Moutsianas L, Law A, Caulfield MJ, Baillie JK. Whole-genome sequencing reveals host factors underlying critical COVID-19. Nature 2022; 607:97-103. [PMID: 35255492 PMCID: PMC9259496 DOI: 10.1038/s41586-022-04576-6] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/23/2022] [Indexed: 12/15/2022]
Abstract
Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2-4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.
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Affiliation(s)
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Clark D Russell
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Xia Shen
- Biostatistics Group, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | | | | | | | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Marie Zechner
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine and Institute in the Park, Alder Hey Children's Hospital and University of Liverpool, Liverpool, UK
| | | | | | | | | | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tom A Fowler
- Genomics England, London, UK
- Test and Trace, the Health Security Agency, Department of Health and Social Care, London, UK
| | - Manu Shankar-Hari
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - Charles Hinds
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust: London, London, UK
| | | | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit and Research Centre, London, UK
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Richard H Scott
- Genomics England, London, UK
- Great Ormond Street Hospital, London, UK
| | | | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Mark J Caulfield
- Genomics England, London, UK.
- William Harvey Research Institute, Queen Mary University of London, London, UK.
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
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10
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Little A, Hu Y, Sun Q, Jain D, Broome J, Chen MH, Thibord F, McHugh C, Surendran P, Blackwell TW, Brody JA, Bhan A, Chami N, de Vries PS, Ekunwe L, Heard-Costa N, Hobbs BD, Manichaikul A, Moon JY, Preuss MH, Ryan K, Wang Z, Wheeler M, Yanek LR, Abecasis GR, Almasy L, Beaty TH, Becker LC, Blangero J, Boerwinkle E, Butterworth AS, Choquet H, Correa A, Curran JE, Faraday N, Fornage M, Glahn DC, Hou L, Jorgenson E, Kooperberg C, Lewis JP, Lloyd-Jones DM, Loos RJF, Min YI, Mitchell BD, Morrison AC, Nickerson DA, North KE, O'Connell JR, Pankratz N, Psaty BM, Vasan RS, Rich SS, Rotter JI, Smith AV, Smith NL, Tang H, Tracy RP, Conomos MP, Laurie CA, Mathias RA, Li Y, Auer PL, Thornton T, Reiner AP, Johnson AD, Raffield LM. Whole genome sequence analysis of platelet traits in the NHLBI Trans-Omics for Precision Medicine (TOPMed) initiative. Hum Mol Genet 2022; 31:347-361. [PMID: 34553764 PMCID: PMC8825339 DOI: 10.1093/hmg/ddab252] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 12/15/2022] Open
Abstract
Platelets play a key role in thrombosis and hemostasis. Platelet count (PLT) and mean platelet volume (MPV) are highly heritable quantitative traits, with hundreds of genetic signals previously identified, mostly in European ancestry populations. We here utilize whole genome sequencing (WGS) from NHLBI's Trans-Omics for Precision Medicine initiative (TOPMed) in a large multi-ethnic sample to further explore common and rare variation contributing to PLT (n = 61 200) and MPV (n = 23 485). We identified and replicated secondary signals at MPL (rs532784633) and PECAM1 (rs73345162), both more common in African ancestry populations. We also observed rare variation in Mendelian platelet-related disorder genes influencing variation in platelet traits in TOPMed cohorts (not enriched for blood disorders). For example, association of GP9 with lower PLT and higher MPV was partly driven by a pathogenic Bernard-Soulier syndrome variant (rs5030764, p.Asn61Ser), and the signals at TUBB1 and CD36 were partly driven by loss of function variants not annotated as pathogenic in ClinVar (rs199948010 and rs571975065). However, residual signal remained for these gene-based signals after adjusting for lead variants, suggesting that additional variants in Mendelian genes with impacts in general population cohorts remain to be identified. Gene-based signals were also identified at several genome-wide association study identified loci for genes not annotated for Mendelian platelet disorders (PTPRH, TET2, CHEK2), with somatic variation driving the result at TET2. These results highlight the value of WGS in populations of diverse genetic ancestry to identify novel regulatory and coding signals, even for well-studied traits like platelet traits.
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Affiliation(s)
- Amarise Little
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Yao Hu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Jai Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Ming-Huei Chen
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Florian Thibord
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Caitlin McHugh
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK
- Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Thomas W Blackwell
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | | | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Paul S de Vries
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lynette Ekunwe
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Nancy Heard-Costa
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Brian D Hobbs
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ani Manichaikul
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Marsha Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Goncalo R Abecasis
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Lewis C Becker
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge CB1 8RN, UK
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Myriam Fornage
- University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Donald M Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Yuan-I Min
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jeffrey R O'Connell
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle WA 98101, USA
| | - Ramachandran S Vasan
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
- Departments of Cardiology and Preventive Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
| | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Jerome I Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Albert V Smith
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle WA 98101, USA
- Department of Veterans Affairs Office of Research and Development, Seattle Epidemiologic Research and Information Center, Seattle, WA 98108, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine and Biochemistry, University of Vermont Larner College of Medicine, Colchester, VT 05446, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yun Li
- Departments of Biostatistics, Genetics, Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
| | | | - Timothy Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
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11
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Stuart PE, Tsoi LC, Nair RP, Ghosh M, Kabra M, Shaiq PA, Raja GK, Qamar R, Thelma B, Patrick MT, Parihar A, Singh S, Khandpur S, Kumar U, Wittig M, Degenhardt F, Tejasvi T, Voorhees JJ, Weidinger S, Franke A, Abecasis GR, Sharma VK, Elder JT. Transethnic analysis of psoriasis susceptibility in South Asians and Europeans enhances fine-mapping in the MHC and genomewide. HGG Adv 2022; 3:100069. [PMID: 34927100 PMCID: PMC8682265 DOI: 10.1016/j.xhgg.2021.100069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 10/24/2021] [Indexed: 02/06/2023] Open
Abstract
Because transethnic analysis may facilitate prioritization of causal genetic variants, we performed a genomewide association study (GWAS) of psoriasis in South Asians (SAS), consisting of 2,590 cases and 1,720 controls. Comparison with our existing European-origin (EUR) GWAS showed that effect sizes of known psoriasis signals were highly correlated in SAS and EUR (Spearman ρ = 0.78; p < 2 × 10-14). Transethnic meta-analysis identified two non-MHC psoriasis loci (1p36.22 and 1q24.2) not previously identified in EUR, which may have regulatory roles. For these two loci, the transethnic GWAS provided higher genetic resolution and reduced the number of potential causal variants compared to using the EUR sample alone. We then explored multiple strategies to develop reference panels for accurately imputing MHC genotypes in both SAS and EUR populations and conducted a fine-mapping of MHC psoriasis associations in SAS and the largest such effort for EUR. HLA-C*06 was the top-ranking MHC locus in both populations but was even more prominent in SAS based on odds ratio, disease liability, model fit and predictive power. Transethnic modeling also substantially boosted the probability that the HLA-C*06 protein variant is causal. Secondary MHC signals included coding variants of HLA-C and HLA-B, but also potential regulatory variants of these two genes as well as HLA-A and several HLA class II genes, with effects on both chromatin accessibility and gene expression. This study highlights the shared genetic basis of psoriasis in SAS and EUR populations and the value of transethnic meta-analysis for discovery and fine-mapping of susceptibility loci.
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Affiliation(s)
- Philip E. Stuart
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lam C. Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor MI, USA
| | - Rajan P. Nair
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Manju Ghosh
- Department of Pediatrics Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Department of Pediatrics Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Pakeeza A. Shaiq
- Department of Biochemistry, PMASAA University, Rawalpindi, Pakistan
| | - Ghazala K. Raja
- Department of Biochemistry, PMASAA University, Rawalpindi, Pakistan
| | - Raheel Qamar
- COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - B.K. Thelma
- Department of Genetics, University of Delhi South Campus, 110021 New Delhi, India
| | - Matthew T. Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Anita Parihar
- Department of Dermatology, All India Institute of Medical Sciences, New Delhi, India
| | - Sonam Singh
- Department of Dermatology, All India Institute of Medical Sciences, New Delhi, India
| | - Sujay Khandpur
- Department of Dermatology, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kumar
- Department of Rheumatology, All India Institute of Medical Sciences, New Delhi, India
| | - Michael Wittig
- Institute of Clinical Molecular Biology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA
| | - John J. Voorhees
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Stephan Weidinger
- Department of Dermatology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Goncalo R. Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Vinod K. Sharma
- Department of Dermatology, All India Institute of Medical Sciences, New Delhi, India
| | - James T. Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA
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12
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Mikhaylova AV, McHugh CP, Polfus LM, Raffield LM, Boorgula MP, Blackwell TW, Brody JA, Broome J, Chami N, Chen MH, Conomos MP, Cox C, Curran JE, Daya M, Ekunwe L, Glahn DC, Heard-Costa N, Highland HM, Hobbs BD, Ilboudo Y, Jain D, Lange LA, Miller-Fleming TW, Min N, Moon JY, Preuss MH, Rosen J, Ryan K, Smith AV, Sun Q, Surendran P, de Vries PS, Walter K, Wang Z, Wheeler M, Yanek LR, Zhong X, Abecasis GR, Almasy L, Barnes KC, Beaty TH, Becker LC, Blangero J, Boerwinkle E, Butterworth AS, Chavan S, Cho MH, Choquet H, Correa A, Cox N, DeMeo DL, Faraday N, Fornage M, Gerszten RE, Hou L, Johnson AD, Jorgenson E, Kaplan R, Kooperberg C, Kundu K, Laurie CA, Lettre G, Lewis JP, Li B, Li Y, Lloyd-Jones DM, Loos RJF, Manichaikul A, Meyers DA, Mitchell BD, Morrison AC, Ngo D, Nickerson DA, Nongmaithem S, North KE, O'Connell JR, Ortega VE, Pankratz N, Perry JA, Psaty BM, Rich SS, Soranzo N, Rotter JI, Silverman EK, Smith NL, Tang H, Tracy RP, Thornton TA, Vasan RS, Zein J, Mathias RA, Reiner AP, Auer PL. Whole-genome sequencing in diverse subjects identifies genetic correlates of leukocyte traits: The NHLBI TOPMed program. Am J Hum Genet 2021; 108:1836-1851. [PMID: 34582791 PMCID: PMC8546043 DOI: 10.1016/j.ajhg.2021.08.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
Many common and rare variants associated with hematologic traits have been discovered through imputation on large-scale reference panels. However, the majority of genome-wide association studies (GWASs) have been conducted in Europeans, and determining causal variants has proved challenging. We performed a GWAS of total leukocyte, neutrophil, lymphocyte, monocyte, eosinophil, and basophil counts generated from 109,563,748 variants in the autosomes and the X chromosome in the Trans-Omics for Precision Medicine (TOPMed) program, which included data from 61,802 individuals of diverse ancestry. We discovered and replicated 7 leukocyte trait associations, including (1) the association between a chromosome X, pseudo-autosomal region (PAR), noncoding variant located between cytokine receptor genes (CSF2RA and CLRF2) and lower eosinophil count; and (2) associations between single variants found predominantly among African Americans at the S1PR3 (9q22.1) and HBB (11p15.4) loci and monocyte and lymphocyte counts, respectively. We further provide evidence indicating that the newly discovered eosinophil-lowering chromosome X PAR variant might be associated with reduced susceptibility to common allergic diseases such as atopic dermatitis and asthma. Additionally, we found a burden of very rare FLT3 (13q12.2) variants associated with monocyte counts. Together, these results emphasize the utility of whole-genome sequencing in diverse samples in identifying associations missed by European-ancestry-driven GWASs.
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MESH Headings
- Asthma/epidemiology
- Asthma/genetics
- Asthma/metabolism
- Asthma/pathology
- Biomarkers/metabolism
- Dermatitis, Atopic/epidemiology
- Dermatitis, Atopic/genetics
- Dermatitis, Atopic/metabolism
- Dermatitis, Atopic/pathology
- Genetic Predisposition to Disease
- Genome, Human
- Genome-Wide Association Study
- Humans
- Leukocytes/pathology
- National Heart, Lung, and Blood Institute (U.S.)
- Phenotype
- Polymorphism, Single Nucleotide
- Prognosis
- Proteome/analysis
- Proteome/metabolism
- Pulmonary Disease, Chronic Obstructive/epidemiology
- Pulmonary Disease, Chronic Obstructive/genetics
- Pulmonary Disease, Chronic Obstructive/metabolism
- Pulmonary Disease, Chronic Obstructive/pathology
- Quantitative Trait Loci
- United Kingdom/epidemiology
- United States/epidemiology
- Whole Genome Sequencing
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Affiliation(s)
- Anna V Mikhaylova
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Caitlin P McHugh
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Linda M Polfus
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Meher Preethi Boorgula
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Thomas W Blackwell
- TOPMed Informatics Research Center, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Jai Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Ming-Huei Chen
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA; National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Corey Cox
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Michelle Daya
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lynette Ekunwe
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA 02155, USA
| | - Nancy Heard-Costa
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA; Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yann Ilboudo
- Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada; Faculté de Médecine, Université de Montréal, Montréal, Québec H1T 1C8, Canada
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tyne W Miller-Fleming
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Nancy Min
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Jonathon Rosen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Albert V Smith
- TOPMed Informatics Research Center, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK; Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Klaudia Walter
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Marsha Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xue Zhong
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Goncalo R Abecasis
- TOPMed Informatics Research Center, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Terri H Beaty
- School of Public Health, John Hopkins University, Baltimore, MD 21205, USA
| | - Lewis C Becker
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge CB1 8RN, UK
| | - Sameer Chavan
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94601, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Nancy Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Myriam Fornage
- University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Lifang Hou
- Institute for Public Health and Medicine, Northwestern University, Chicago, IL 60661, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA; National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA
| | | | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kousik Kundu
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Guillaume Lettre
- Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada; Faculté de Médecine, Université de Montréal, Montréal, Québec H1T 1C8, Canada
| | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Yun Li
- Departments of Biostatistics, Genetics, and Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Donald M Lloyd-Jones
- Division of Cardiology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60661, USA; Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60661, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Debby Ngo
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Suraj Nongmaithem
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffrey R O'Connell
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Victor E Ortega
- Department of Internal Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - James A Perry
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Bruce M Psaty
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Department of Health Service, University of Washington, Seattle, WA 98105, USA; Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Nicole Soranzo
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; Department of Haematology, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge CB1 8RN, UK
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Department of Health Service, University of Washington, Seattle, WA 98105, USA; Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA 98105, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine and Department of Biochemistry, University of Vermont Larner College of Medicine, Colchester, VT 05446, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA; Regeneron Genetics Center, Tarrytown, NY 10591, USA
| | - Ramachandran S Vasan
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA; Departments of Cardiology and Preventive Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
| | - Joe Zein
- Respiratory Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alexander P Reiner
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin, Milwaukee, Milwaukee, WI 53205, USA.
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13
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Ratnapriya R, Acar İE, Geerlings MJ, Branham K, Kwong A, Saksens NTM, Pauper M, Corominas J, Kwicklis M, Zipprer D, Starostik MR, Othman M, Yashar B, Abecasis GR, Chew EY, Ferrington DA, Hoyng CB, Swaroop A, den Hollander AI. Family-based exome sequencing identifies rare coding variants in age-related macular degeneration. Hum Mol Genet 2021; 29:2022-2034. [PMID: 32246154 PMCID: PMC7390936 DOI: 10.1093/hmg/ddaa057] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/18/2020] [Accepted: 03/26/2020] [Indexed: 12/24/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified 52 independent variants at 34 genetic loci that are associated with age-related macular degeneration (AMD), the most common cause of incurable vision loss in the elderly worldwide. However, causal genes at the majority of these loci remain unknown. In this study, we performed whole exome sequencing of 264 individuals from 63 multiplex families with AMD and analyzed the data for rare protein-altering variants in candidate target genes at AMD-associated loci. Rare coding variants were identified in the CFH, PUS7, RXFP2, PHF12 and TACC2 genes in three or more families. In addition, we detected rare coding variants in the C9, SPEF2 and BCAR1 genes, which were previously suggested as likely causative genes at respective AMD susceptibility loci. Identification of rare variants in the CFH and C9 genes in our study validated previous reports of rare variants in complement pathway genes in AMD. We then extended our exome-wide analysis and identified rare protein-altering variants in 13 genes outside the AMD-GWAS loci in three or more families. Two of these genes, SCN10A and KIR2DL4, are of interest because variants in these genes also showed association with AMD in case-control cohorts, albeit not at the level of genome-wide significance. Our study presents the first large-scale, exome-wide analysis of rare variants in AMD. Further independent replications and molecular investigation of candidate target genes, reported here, would assist in gaining novel insights into mechanisms underlying AMD pathogenesis.
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Affiliation(s)
- Rinki Ratnapriya
- Neurobiology, Neurodegeneration and Repair Laboratory (NNRL), National Eye Institute, Bethesda, MD 20892, USA.,Department of Ophthalmology, Baylor College of Medicine, Houston, TX 77030, USA
| | - İlhan E Acar
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500, The Netherlands
| | - Maartje J Geerlings
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500, The Netherlands
| | - Kari Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | - Alan Kwong
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nicole T M Saksens
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500, The Netherlands
| | - Marc Pauper
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500, The Netherlands
| | - Jordi Corominas
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500, The Netherlands
| | - Madeline Kwicklis
- Neurobiology, Neurodegeneration and Repair Laboratory (NNRL), National Eye Institute, Bethesda, MD 20892, USA
| | - David Zipprer
- Neurobiology, Neurodegeneration and Repair Laboratory (NNRL), National Eye Institute, Bethesda, MD 20892, USA
| | - Margaret R Starostik
- Neurobiology, Neurodegeneration and Repair Laboratory (NNRL), National Eye Institute, Bethesda, MD 20892, USA
| | - Mohammad Othman
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | - Beverly Yashar
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | - Goncalo R Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emily Y Chew
- Neurobiology, Neurodegeneration and Repair Laboratory (NNRL), National Eye Institute, Bethesda, MD 20892, USA
| | - Deborah A Ferrington
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500, The Netherlands
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory (NNRL), National Eye Institute, Bethesda, MD 20892, USA
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500, The Netherlands
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14
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Akbari P, Gilani A, Sosina O, Kosmicki JA, Khrimian L, Fang YY, Persaud T, Garcia V, Sun D, Li A, Mbatchou J, Locke AE, Benner C, Verweij N, Lin N, Hossain S, Agostinucci K, Pascale JV, Dirice E, Dunn M, Kraus WE, Shah SH, Chen YDI, Rotter JI, Rader DJ, Melander O, Still CD, Mirshahi T, Carey DJ, Berumen-Campos J, Kuri-Morales P, Alegre-Díaz J, Torres JM, Emberson JR, Collins R, Balasubramanian S, Hawes A, Jones M, Zambrowicz B, Murphy AJ, Paulding C, Coppola G, Overton JD, Reid JG, Shuldiner AR, Cantor M, Kang HM, Abecasis GR, Karalis K, Economides AN, Marchini J, Yancopoulos GD, Sleeman MW, Altarejos J, Della Gatta G, Tapia-Conyer R, Schwartzman ML, Baras A, Ferreira MAR, Lotta LA. Sequencing of 640,000 exomes identifies GPR75 variants associated with protection from obesity. Science 2021; 373:373/6550/eabf8683. [PMID: 34210852 DOI: 10.1126/science.abf8683] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/17/2021] [Indexed: 12/11/2022]
Abstract
Large-scale human exome sequencing can identify rare protein-coding variants with a large impact on complex traits such as body adiposity. We sequenced the exomes of 645,626 individuals from the United Kingdom, the United States, and Mexico and estimated associations of rare coding variants with body mass index (BMI). We identified 16 genes with an exome-wide significant association with BMI, including those encoding five brain-expressed G protein-coupled receptors (CALCR, MC4R, GIPR, GPR151, and GPR75). Protein-truncating variants in GPR75 were observed in ~4/10,000 sequenced individuals and were associated with 1.8 kilograms per square meter lower BMI and 54% lower odds of obesity in the heterozygous state. Knock out of Gpr75 in mice resulted in resistance to weight gain and improved glycemic control in a high-fat diet model. Inhibition of GPR75 may provide a therapeutic strategy for obesity.
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Affiliation(s)
- Parsa Akbari
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Ankit Gilani
- Department of Pharmacology and Medicine, New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Olukayode Sosina
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Jack A Kosmicki
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Lori Khrimian
- Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Yi-Ya Fang
- Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Trikaldarshi Persaud
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Victor Garcia
- Department of Pharmacology and Medicine, New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Dylan Sun
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Alexander Li
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Joelle Mbatchou
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Adam E Locke
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Christian Benner
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Niek Verweij
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Nan Lin
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Sakib Hossain
- Department of Pharmacology and Medicine, New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Kevin Agostinucci
- Department of Pharmacology and Medicine, New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Jonathan V Pascale
- Department of Pharmacology and Medicine, New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Ercument Dirice
- Department of Pharmacology and Medicine, New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Michael Dunn
- Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | | | | | - William E Kraus
- Division of Cardiology, Duke University Medical Center, Durham, NC 27710, USA.,Duke Center for Living, Duke University Medical Center, Durham, NC 27705, USA
| | - Svati H Shah
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
| | - Yii-Der I Chen
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation, and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation, and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Olle Melander
- Department of Clinical Sciences Malmö, Lund University, 221 00 Malmö, Sweden.,Department of Emergency and Internal Medicine, Skåne University Hospital, 214 28, Malmö, Sweden
| | - Christopher D Still
- Geisinger Obesity Institute, Geisinger Health System, Danville, PA 17882, USA
| | - Tooraj Mirshahi
- Geisinger Obesity Institute, Geisinger Health System, Danville, PA 17882, USA
| | - David J Carey
- Geisinger Obesity Institute, Geisinger Health System, Danville, PA 17882, USA
| | - Jaime Berumen-Campos
- Faculty of Medicine, National Autonomous University of Mexico, Copilco Universidad, Coyoacán, 4360 Ciudad de México, Mexico
| | - Pablo Kuri-Morales
- Faculty of Medicine, National Autonomous University of Mexico, Copilco Universidad, Coyoacán, 4360 Ciudad de México, Mexico
| | - Jesus Alegre-Díaz
- Faculty of Medicine, National Autonomous University of Mexico, Copilco Universidad, Coyoacán, 4360 Ciudad de México, Mexico
| | - Jason M Torres
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, England, UK
| | - Jonathan R Emberson
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, England, UK
| | - Rory Collins
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, England, UK
| | | | - Alicia Hawes
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Marcus Jones
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | | | | | - Charles Paulding
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Giovanni Coppola
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - John D Overton
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Jeffrey G Reid
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Alan R Shuldiner
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Michael Cantor
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Hyun M Kang
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Goncalo R Abecasis
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Katia Karalis
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Aris N Economides
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA.,Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Jonathan Marchini
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | | | - Mark W Sleeman
- Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | | | - Giusy Della Gatta
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Roberto Tapia-Conyer
- Faculty of Medicine, National Autonomous University of Mexico, Copilco Universidad, Coyoacán, 4360 Ciudad de México, Mexico
| | - Michal L Schwartzman
- Department of Pharmacology and Medicine, New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Aris Baras
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA.
| | - Manuel A R Ferreira
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Luca A Lotta
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA.
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15
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Kosmicki JA, Horowitz JE, Banerjee N, Lanche R, Marcketta A, Maxwell E, Bai X, Sun D, Backman JD, Sharma D, Kury FSP, Kang HM, O'Dushlaine C, Yadav A, Mansfield AJ, Li AH, Watanabe K, Gurski L, McCarthy SE, Locke AE, Khalid S, O'Keeffe S, Mbatchou J, Chazara O, Huang Y, Kvikstad E, O'Neill A, Nioi P, Parker MM, Petrovski S, Runz H, Szustakowski JD, Wang Q, Wong E, Cordova-Palomera A, Smith EN, Szalma S, Zheng X, Esmaeeli S, Davis JW, Lai YP, Chen X, Justice AE, Leader JB, Mirshahi T, Carey DJ, Verma A, Sirugo G, Ritchie MD, Rader DJ, Povysil G, Goldstein DB, Kiryluk K, Pairo-Castineira E, Rawlik K, Pasko D, Walker S, Meynert A, Kousathanas A, Moutsianas L, Tenesa A, Caulfield M, Scott R, Wilson JF, Baillie JK, Butler-Laporte G, Nakanishi T, Lathrop M, Richards JB, Jones M, Balasubramanian S, Salerno W, Shuldiner AR, Marchini J, Overton JD, Habegger L, Cantor MN, Reid JG, Baras A, Abecasis GR, Ferreira MAR. Pan-ancestry exome-wide association analyses of COVID-19 outcomes in 586,157 individuals. Am J Hum Genet 2021; 108:1350-1355. [PMID: 34115965 PMCID: PMC8173480 DOI: 10.1016/j.ajhg.2021.05.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/24/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a respiratory illness that can result in hospitalization or death. We used exome sequence data to investigate associations between rare genetic variants and seven COVID-19 outcomes in 586,157 individuals, including 20,952 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome wide or when specifically focusing on (1) 13 interferon pathway genes in which rare deleterious variants have been reported in individuals with severe COVID-19, (2) 281 genes located in susceptibility loci identified by the COVID-19 Host Genetics Initiative, or (3) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, and results are publicly available through the Regeneron Genetics Center COVID-19 Results Browser.
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Affiliation(s)
- Jack A Kosmicki
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Julie E Horowitz
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Nilanjana Banerjee
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Rouel Lanche
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Anthony Marcketta
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Evan Maxwell
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Xiaodong Bai
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Dylan Sun
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Joshua D Backman
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Deepika Sharma
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Fabricio S P Kury
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Hyun M Kang
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Colm O'Dushlaine
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Ashish Yadav
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Adam J Mansfield
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Alexander H Li
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Kyoko Watanabe
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Lauren Gurski
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Shane E McCarthy
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Adam E Locke
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Shareef Khalid
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Sean O'Keeffe
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Joelle Mbatchou
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Olympe Chazara
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | | | - Erika Kvikstad
- Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, NJ 08543, USA
| | - Amanda O'Neill
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Paul Nioi
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Meg M Parker
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Heiko Runz
- Biogen, 300 Binney Street, Cambridge, MA 02142, USA
| | | | - Quanli Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Emily Wong
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, CA 92121, USA
| | | | - Erin N Smith
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, CA 92121, USA
| | - Sandor Szalma
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, CA 92121, USA
| | - Xiuwen Zheng
- AbbVie, Inc., 1 N. Waukegan Road, North Chicago, IL 60064, USA
| | - Sahar Esmaeeli
- AbbVie, Inc., 1 N. Waukegan Road, North Chicago, IL 60064, USA
| | - Justin W Davis
- AbbVie, Inc., 1 N. Waukegan Road, North Chicago, IL 60064, USA
| | - Yi-Pin Lai
- Pfizer, Inc., 1 Portland Street, Cambridge, MA 02139, USA
| | - Xing Chen
- Pfizer, Inc., 1 Portland Street, Cambridge, MA 02139, USA
| | | | | | | | | | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Giorgio Sirugo
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Krzysztof Kiryluk
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | | | | | - Alison Meynert
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | | | | | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK
| | - Mark Caulfield
- Genomics England, London EC1M 6BQ, UK; William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Richard Scott
- Genomics England, London EC1M 6BQ, UK; Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh EH16 5SA, UK
| | - Guillaume Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC H3A 0G4, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Human Genetics, McGill University, Montréal, QC H3A 0G4, Canada; Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Mark Lathrop
- Department of Human Genetics, McGill University, Montréal, QC H3A 0G4, Canada; Canadian Centre for Computational Genomics, McGill University, Montréal, QC H3A 0G4, Canada
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC H3A 0G4, Canada; Department of Human Genetics, McGill University, Montréal, QC H3A 0G4, Canada; Department of Twins Research, King's College London, London WC2R 2LS, UK
| | - Marcus Jones
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | | | - William Salerno
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Alan R Shuldiner
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Jonathan Marchini
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - John D Overton
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Lukas Habegger
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Michael N Cantor
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Jeffrey G Reid
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Aris Baras
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Goncalo R Abecasis
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
| | - Manuel A R Ferreira
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
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Huyghe JR, Harrison TA, Bien SA, Hampel H, Figueiredo JC, Schmit SL, Conti DV, Chen S, Qu C, Lin Y, Barfield R, Baron JA, Cross AJ, Diergaarde B, Duggan D, Harlid S, Imaz L, Kang HM, Levine DM, Perduca V, Perez-Cornago A, Sakoda LC, Schumacher FR, Slattery ML, Toland AE, van Duijnhoven FJB, Van Guelpen B, Agudo A, Albanes D, Alonso MH, Anderson K, Arnau-Collell C, Arndt V, Banbury BL, Bassik MC, Berndt SI, Bézieau S, Bishop DT, Boehm J, Boeing H, Boutron-Ruault MC, Brenner H, Brezina S, Buch S, Buchanan DD, Burnett-Hartman A, Caan BJ, Campbell PT, Carr PR, Castells A, Castellví-Bel S, Chan AT, Chang-Claude J, Chanock SJ, Curtis KR, de la Chapelle A, Easton DF, English DR, Feskens EJM, Gala M, Gallinger SJ, Gauderman WJ, Giles GG, Goodman PJ, Grady WM, Grove JS, Gsur A, Gunter MJ, Haile RW, Hampe J, Hoffmeister M, Hopper JL, Hsu WL, Huang WY, Hudson TJ, Jenab M, Jenkins MA, Joshi AD, Keku TO, Kooperberg C, Kühn T, Küry S, Le Marchand L, Lejbkowicz F, Li CI, Li L, Lieb W, Lindblom A, Lindor NM, Männistö S, Markowitz SD, Milne RL, Moreno L, Murphy N, Nassir R, Offit K, Ogino S, Panico S, Parfrey PS, Pearlman R, Pharoah PDP, Phipps AI, Platz EA, Potter JD, Prentice RL, Qi L, Raskin L, Rennert G, Rennert HS, Riboli E, Schafmayer C, Schoen RE, Seminara D, Song M, Su YR, Tangen CM, Thibodeau SN, Thomas DC, Trichopoulou A, Ulrich CM, Visvanathan K, Vodicka P, Vodickova L, Vymetalkova V, Weigl K, Weinstein SJ, White E, Wolk A, Woods MO, Wu AH, Abecasis GR, Nickerson DA, Scacheri PC, Kundaje A, Casey G, Gruber SB, Hsu L, Moreno V, Hayes RB, Newcomb PA, Peters U. Genetic architectures of proximal and distal colorectal cancer are partly distinct. Gut 2021; 70:1325-1334. [PMID: 33632709 PMCID: PMC8223655 DOI: 10.1136/gutjnl-2020-321534] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 11/26/2020] [Accepted: 12/18/2020] [Indexed: 01/14/2023]
Abstract
OBJECTIVE An understanding of the etiologic heterogeneity of colorectal cancer (CRC) is critical for improving precision prevention, including individualized screening recommendations and the discovery of novel drug targets and repurposable drug candidates for chemoprevention. Known differences in molecular characteristics and environmental risk factors among tumors arising in different locations of the colorectum suggest partly distinct mechanisms of carcinogenesis. The extent to which the contribution of inherited genetic risk factors for CRC differs by anatomical subsite of the primary tumor has not been examined. DESIGN To identify new anatomical subsite-specific risk loci, we performed genome-wide association study (GWAS) meta-analyses including data of 48 214 CRC cases and 64 159 controls of European ancestry. We characterised effect heterogeneity at CRC risk loci using multinomial modelling. RESULTS We identified 13 loci that reached genome-wide significance (p<5×10-8) and that were not reported by previous GWASs for overall CRC risk. Multiple lines of evidence support candidate genes at several of these loci. We detected substantial heterogeneity between anatomical subsites. Just over half (61) of 109 known and new risk variants showed no evidence for heterogeneity. In contrast, 22 variants showed association with distal CRC (including rectal cancer), but no evidence for association or an attenuated association with proximal CRC. For two loci, there was strong evidence for effects confined to proximal colon cancer. CONCLUSION Genetic architectures of proximal and distal CRC are partly distinct. Studies of risk factors and mechanisms of carcinogenesis, and precision prevention strategies should take into consideration the anatomical subsite of the tumour.
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Affiliation(s)
- Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Jane C Figueiredo
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | | | - David V Conti
- Department of Preventive Medicine and USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Sai Chen
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Richard Barfield
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - John A Baron
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Amanda J Cross
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Brenda Diergaarde
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - David Duggan
- Translational Genomics Research Institute - An Affiliate of City of Hope, Phoenix, Arizona, USA
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Liher Imaz
- Public Health Division of Gipuzkoa, Health Department of Basque Country, San Sebastian, Spain
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - David M Levine
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Vittorio Perduca
- Laboratoire de Mathématiques Appliquées MAP5 (UMR CNRS 8145), Université Paris Descartes, Paris, France
- Centre for Research in Epidemiology and Population Health (CESP), Institut pour la Santé et la Recherche Médicale (INSERM) U1018, Université Paris-Saclay, Villejuif, France
| | - Aurora Perez-Cornago
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah, USA
| | - Amanda E Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | | | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Antonio Agudo
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - M Henar Alonso
- Cancer Prevention and Control Program, Catalan Institute of Oncology - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Kristin Anderson
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Coral Arnau-Collell
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Barbara L Banbury
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) de Nantes, Nantes, France
| | - D Timothy Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Juergen Boehm
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah Health, Salt Lake City, Utah, USA
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition (DIfE), Potsdam-Rehbrücke, Germany
| | - Marie-Christine Boutron-Ruault
- Centre for Research in Epidemiology and Population Health (CESP), Institut pour la Santé et la Recherche Médicale (INSERM) U1018, Université Paris-Saclay, Villejuif, France
- Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Centre (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | | | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program, Oakland, California, USA
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia, USA
| | - Prudence R Carr
- Division of Clinical Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Keith R Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dallas R English
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Edith J M Feskens
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, The Netherlands
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Steven J Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - W James Gauderman
- Department of Preventive Medicine and USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - John S Grove
- University of Hawai'i Cancer Center, Honolulu, Hawaii, USA
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Robert W Haile
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Epidemiology, School of Public Health and Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Wan-Ling Hsu
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Mazda Jenab
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Tilman Kühn
- Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Sébastien Küry
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) de Nantes, Nantes, France
| | | | - Flavio Lejbkowicz
- The Clalit Health Services, Personalized Genomic Service, Carmel Medical Center, Haifa, Israel
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Wolfgang Lieb
- Institute of Epidemiology, PopGen Biobank, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, Arizona, USA
| | - Satu Männistö
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Sanford D Markowitz
- Departments of Medicine and Genetics, Case Comprehensive Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Lorena Moreno
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Neil Murphy
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rami Nassir
- Department of Pathology, School of Medicine, Umm Al-Qura'a University, Mecca, Saudi Arabia
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Shuji Ogino
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, University of Naples Federico II, Naples, Italy
| | - Patrick S Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Ross L Prentice
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lihong Qi
- Department of Public Health Sciences, School of Medicine, University of California Davis, Davis, California, USA
| | - Leon Raskin
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hedy S Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock, Germany
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland, USA
| | - Mingyang Song
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Yu-Ru Su
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, MayoClinic, Rochester, Minnesota, USA
| | - Duncan C Thomas
- Department of Preventive Medicine and USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Antonia Trichopoulou
- Hellenic Health Foundation, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah Health, Salt Lake City, Utah, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Korbinian Weigl
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Michael O Woods
- Discipline of Genetics, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Anna H Wu
- Department of Preventive Medicine and USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, Ohio, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Computer Science, Stanford University, Stanford, California, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, USA
- City of Hope National Medical Center, Duarte, California, USA
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, New York, USA
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
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17
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Horowitz JE, Kosmicki JA, Damask A, Sharma D, Roberts GHL, Justice AE, Banerjee N, Coignet MV, Yadav A, Leader JB, Marcketta A, Park DS, Lanche R, Maxwell E, Knight SC, Bai X, Guturu H, Sun D, Baltzell A, Kury FSP, Backman JD, Girshick AR, O'Dushlaine C, McCurdy SR, Partha R, Mansfield AJ, Turissini DA, Li AH, Zhang M, Mbatchou J, Watanabe K, Gurski L, McCarthy SE, Kang HM, Dobbyn L, Stahl E, Verma A, Sirugo G, Ritchie MD, Jones M, Balasubramanian S, Siminovitch K, Salerno WJ, Shuldiner AR, Rader DJ, Mirshahi T, Locke AE, Marchini J, Overton JD, Carey DJ, Habegger L, Cantor MN, Rand KA, Hong EL, Reid JG, Ball CA, Baras A, Abecasis GR, Ferreira MA. Genome-wide analysis in 756,646 individuals provides first genetic evidence that ACE2 expression influences COVID-19 risk and yields genetic risk scores predictive of severe disease. medRxiv 2021. [PMID: 33619501 PMCID: PMC7899471 DOI: 10.1101/2020.12.14.20248176] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2 enters host cells by binding angiotensin-converting enzyme 2 (ACE2). Through a genome-wide association study, we show that a rare variant (MAF = 0.3%, odds ratio 0.60, P=4.5×10-13) that down-regulates ACE2 expression reduces risk of COVID-19 disease, providing human genetics support for the hypothesis that ACE2 levels influence COVID-19 risk. Further, we show that common genetic variants define a risk score that predicts severe disease among COVID-19 cases.
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Affiliation(s)
- J E Horowitz
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J A Kosmicki
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Damask
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - D Sharma
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - G H L Roberts
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | | | - N Banerjee
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - M V Coignet
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - A Yadav
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | | | - A Marcketta
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - D S Park
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - R Lanche
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - E Maxwell
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S C Knight
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - X Bai
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - H Guturu
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - D Sun
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Baltzell
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - F S P Kury
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J D Backman
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A R Girshick
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - C O'Dushlaine
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S R McCurdy
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - R Partha
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - A J Mansfield
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - D A Turissini
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - A H Li
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - M Zhang
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - J Mbatchou
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - K Watanabe
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - L Gurski
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S E McCarthy
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - H M Kang
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - L Dobbyn
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - E Stahl
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - G Sirugo
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - M D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - M Jones
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S Balasubramanian
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - K Siminovitch
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - W J Salerno
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A R Shuldiner
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - D J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - A E Locke
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J Marchini
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J D Overton
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | | | - L Habegger
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - M N Cantor
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - K A Rand
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - E L Hong
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - J G Reid
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - C A Ball
- AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043, USA
| | - A Baras
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - G R Abecasis
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - M A Ferreira
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
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Hu Y, Stilp AM, McHugh CP, Rao S, Jain D, Zheng X, Lane J, Méric de Bellefon S, Raffield LM, Chen MH, Yanek LR, Wheeler M, Yao Y, Ren C, Broome J, Moon JY, de Vries PS, Hobbs BD, Sun Q, Surendran P, Brody JA, Blackwell TW, Choquet H, Ryan K, Duggirala R, Heard-Costa N, Wang Z, Chami N, Preuss MH, Min N, Ekunwe L, Lange LA, Cushman M, Faraday N, Curran JE, Almasy L, Kundu K, Smith AV, Gabriel S, Rotter JI, Fornage M, Lloyd-Jones DM, Vasan RS, Smith NL, North KE, Boerwinkle E, Becker LC, Lewis JP, Abecasis GR, Hou L, O’Connell JR, Morrison AC, Beaty TH, Kaplan R, Correa A, Blangero J, Jorgenson E, Psaty BM, Kooperberg C, Walton RT, Kleinstiver BP, Tang H, Loos RJ, Soranzo N, Butterworth AS, Nickerson D, Rich SS, Mitchell BD, Johnson AD, Auer PL, Li Y, Mathias RA, Lettre G, Pankratz N, Laurie CC, Laurie CA, Bauer DE, Conomos MP, Reiner AP. Whole-genome sequencing association analysis of quantitative red blood cell phenotypes: The NHLBI TOPMed program. Am J Hum Genet 2021; 108:1165. [PMID: 34087167 PMCID: PMC8206380 DOI: 10.1016/j.ajhg.2021.04.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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19
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Hu Y, Stilp AM, McHugh CP, Rao S, Jain D, Zheng X, Lane J, Méric de Bellefon S, Raffield LM, Chen MH, Yanek LR, Wheeler M, Yao Y, Ren C, Broome J, Moon JY, de Vries PS, Hobbs BD, Sun Q, Surendran P, Brody JA, Blackwell TW, Choquet H, Ryan K, Duggirala R, Heard-Costa N, Wang Z, Chami N, Preuss MH, Min N, Ekunwe L, Lange LA, Cushman M, Faraday N, Curran JE, Almasy L, Kundu K, Smith AV, Gabriel S, Rotter JI, Fornage M, Lloyd-Jones DM, Vasan RS, Smith NL, North KE, Boerwinkle E, Becker LC, Lewis JP, Abecasis GR, Hou L, O'Connell JR, Morrison AC, Beaty TH, Kaplan R, Correa A, Blangero J, Jorgenson E, Psaty BM, Kooperberg C, Walton RT, Kleinstiver BP, Tang H, Loos RJF, Soranzo N, Butterworth AS, Nickerson D, Rich SS, Mitchell BD, Johnson AD, Auer PL, Li Y, Mathias RA, Lettre G, Pankratz N, Laurie CC, Laurie CA, Bauer DE, Conomos MP, Reiner AP. Whole-genome sequencing association analysis of quantitative red blood cell phenotypes: The NHLBI TOPMed program. Am J Hum Genet 2021; 108:874-893. [PMID: 33887194 DOI: 10.1016/j.ajhg.2021.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Whole-genome sequencing (WGS), a powerful tool for detecting novel coding and non-coding disease-causing variants, has largely been applied to clinical diagnosis of inherited disorders. Here we leveraged WGS data in up to 62,653 ethnically diverse participants from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program and assessed statistical association of variants with seven red blood cell (RBC) quantitative traits. We discovered 14 single variant-RBC trait associations at 12 genomic loci, which have not been reported previously. Several of the RBC trait-variant associations (RPN1, ELL2, MIDN, HBB, HBA1, PIEZO1, and G6PD) were replicated in independent GWAS datasets imputed to the TOPMed reference panel. Most of these discovered variants are rare/low frequency, and several are observed disproportionately among non-European Ancestry (African, Hispanic/Latino, or East Asian) populations. We identified a 3 bp indel p.Lys2169del (g.88717175_88717177TCT[4]) (common only in the Ashkenazi Jewish population) of PIEZO1, a gene responsible for the Mendelian red cell disorder hereditary xerocytosis (MIM: 194380), associated with higher mean corpuscular hemoglobin concentration (MCHC). In stepwise conditional analysis and in gene-based rare variant aggregated association analysis, we identified several of the variants in HBB, HBA1, TMPRSS6, and G6PD that represent the carrier state for known coding, promoter, or splice site loss-of-function variants that cause inherited RBC disorders. Finally, we applied base and nuclease editing to demonstrate that the sentinel variant rs112097551 (nearest gene RPN1) acts through a cis-regulatory element that exerts long-range control of the gene RUVBL1 which is essential for hematopoiesis. Together, these results demonstrate the utility of WGS in ethnically diverse population-based samples and gene editing for expanding knowledge of the genetic architecture of quantitative hematologic traits and suggest a continuum between complex trait and Mendelian red cell disorders.
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Affiliation(s)
- Yao Hu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98105, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Caitlin P McHugh
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Shuquan Rao
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Xiuwen Zheng
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - John Lane
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | | | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ming-Huei Chen
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA; National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Marsha Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Yao Yao
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
| | - Chunyan Ren
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
| | - Jai Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Brian D Hobbs
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK; Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Thomas W Blackwell
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94601, USA
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes & Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Nancy Heard-Costa
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA; Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nancy Min
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Lynette Ekunwe
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mary Cushman
- Department of Medicine, Larner College of Medicine at the University of Vermont, Burlington, VT 05405, USA
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia and Department of Genetics University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kousik Kundu
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK
| | - Albert V Smith
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | | | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Myriam Fornage
- University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | | | - Ramachandran S Vasan
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA; Departments of Cardiology and Preventive Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98105, USA; Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA 98105, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lewis C Becker
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes & Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Goncalo R Abecasis
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Lifang Hou
- Northwestern University, Chicago, IL 60208, USA
| | - Jeffrey R O'Connell
- Department of Medicine, Division of Endocrinology, Diabetes & Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Terri H Beaty
- School of Public Health, John Hopkins University, Baltimore, MD 21205, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94601, USA
| | - Bruce M Psaty
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98105, USA; Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98105, USA
| | - Russell T Walton
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicole Soranzo
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Department of Human Genetics, Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge CB1 8RN, UK
| | - Debbie Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes & Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA; National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI 53205, USA
| | - Yun Li
- Departments of Biostatistics, Genetics, Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MA 21205, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; Faculté de Médecine, Université de Montréal, Montréal, QC H1T 1C8, Canada
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA.
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20
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Guo X, Lin W, Wen W, Huyghe J, Bien S, Cai Q, Harrison T, Chen Z, Qu C, Bao J, Long J, Yuan Y, Wang F, Bai M, Abecasis GR, Albanes D, Berndt SI, Bézieau S, Bishop DT, Brenner H, Buch S, Burnett-Hartman A, Campbell PT, Castellví-Bel S, Chan AT, Chang-Claude J, Chanock SJ, Cho SH, Conti DV, Chapelle ADL, Feskens EJM, Gallinger SJ, Giles GG, Goodman PJ, Gsur A, Guinter M, Gunter MJ, Hampe J, Hampel H, Hayes RB, Hoffmeister M, Kampman E, Kang HM, Keku TO, Kim HR, Le Marchand L, Lee SC, Li CI, Li L, Lindblom A, Lindor N, Milne RL, Moreno V, Murphy N, Newcomb PA, Nickerson DA, Offit K, Pearlman R, Pharoah PDP, Platz EA, Potter JD, Rennert G, Sakoda LC, Schafmayer C, Schmit SL, Schoen RE, Schumacher FR, Slattery ML, Su YR, Tangen CM, Ulrich CM, van Duijnhoven FJB, Van Guelpen B, Visvanathan K, Vodicka P, Vodickova L, Vymetalkova V, Wang X, White E, Wolk A, Woods MO, Casey G, Hsu L, Jenkins MA, Gruber SB, Peters U, Zheng W. Identifying Novel Susceptibility Genes for Colorectal Cancer Risk From a Transcriptome-Wide Association Study of 125,478 Subjects. Gastroenterology 2021; 160:1164-1178.e6. [PMID: 33058866 PMCID: PMC7956223 DOI: 10.1053/j.gastro.2020.08.062] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 08/20/2020] [Accepted: 08/28/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND AND AIMS Susceptibility genes and the underlying mechanisms for the majority of risk loci identified by genome-wide association studies (GWAS) for colorectal cancer (CRC) risk remain largely unknown. We conducted a transcriptome-wide association study (TWAS) to identify putative susceptibility genes. METHODS Gene-expression prediction models were built using transcriptome and genetic data from the 284 normal transverse colon tissues of European descendants from the Genotype-Tissue Expression (GTEx), and model performance was evaluated using data from The Cancer Genome Atlas (n = 355). We applied the gene-expression prediction models and GWAS data to evaluate associations of genetically predicted gene-expression with CRC risk in 58,131 CRC cases and 67,347 controls of European ancestry. Dual-luciferase reporter assays and knockdown experiments in CRC cells and tumor xenografts were conducted. RESULTS We identified 25 genes associated with CRC risk at a Bonferroni-corrected threshold of P < 9.1 × 10-6, including genes in 4 novel loci, PYGL (14q22.1), RPL28 (19q13.42), CAPN12 (19q13.2), MYH7B (20q11.22), and MAP1L3CA (20q11.22). In 9 known GWAS-identified loci, we uncovered 9 genes that have not been reported previously, whereas 4 genes remained statistically significant after adjusting for the lead risk variant of the locus. Through colocalization analysis in GWAS loci, we additionally identified 12 putative susceptibility genes that were supported by TWAS analysis at P < .01. We showed that risk allele of the lead risk variant rs1741640 affected the promoter activity of CABLES2. Knockdown experiments confirmed that CABLES2 plays a vital role in colorectal carcinogenesis. CONCLUSIONS Our study reveals new putative susceptibility genes and provides new insight into the biological mechanisms underlying CRC development.
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Affiliation(s)
- Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee.
| | - Weiqiang Lin
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jeroen Huyghe
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephanie Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Tabitha Harrison
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Conghui Qu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jiandong Bao
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Yuan Yuan
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Fangqin Wang
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengqiu Bai
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire, Nantes, France
| | - D Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden, Dresden, Germany
| | | | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany; University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg, Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sang Hee Cho
- Department of Hematology-Oncology, Chonnam National University Hospital, Hwasun, South Korea
| | - David V Conti
- Department of Preventive Medicine and University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Edith J M Feskens
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, the Netherlands
| | - Steven J Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Mark Guinter
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden, Dresden, Germany
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, New York
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Ellen Kampman
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, the Netherlands
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina
| | - Hyeong Rok Kim
- Department of Surgery, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | | | - Soo Chin Lee
- National University Cancer Institute, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Christopher I Li
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, Virginia
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Neil Murphy
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Polly A Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; School of Public Health, University of Washington, Seattle, Washington
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - John D Potter
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel; Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Lori C Sakoda
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock, Germany
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Yu-Ru Su
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, Utah
| | | | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Xiaoliang Wang
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St John's, Newfoundland and Labrador, Canada
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Li Hsu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen B Gruber
- Department of Preventive Medicine and University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
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21
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Kosmicki JA, Horowitz JE, Banerjee N, Lanche R, Marcketta A, Maxwell E, Bai X, Sun D, Backman JD, Sharma D, Kang HM, O'Dushlaine C, Yadav A, Mansfield AJ, Li AH, Watanabe K, Gurski L, McCarthy SE, Locke AE, Khalid S, O'Keeffe S, Mbatchou J, Chazara O, Huang Y, Kvikstad E, O'Neill A, Nioi P, Parker MM, Petrovski S, Runz H, Szustakowski JD, Wang Q, Wong E, Cordova-Palomera A, Smith EN, Szalma S, Zheng X, Esmaeeli S, Davis JW, Lai YP, Chen X, Justice AE, Leader JB, Mirshahi T, Carey DJ, Verma A, Sirugo G, Ritchie MD, Rader DJ, Povysil G, Goldstein DB, Kiryluk K, Pairo-Castineira E, Rawlik K, Pasko D, Walker S, Meynert A, Kousathanas A, Moutsianas L, Tenesa A, Caulfield M, Scott R, Wilson JF, Baillie JK, Butler-Laporte G, Nakanishi T, Lathrop M, Richards JB, Jones M, Balasubramanian S, Salerno W, Shuldiner AR, Marchini J, Overton JD, Habegger L, Cantor MN, Reid JG, Baras A, Abecasis GR, Ferreira MA. A catalog of associations between rare coding variants and COVID-19 outcomes. medRxiv 2021:2020.10.28.20221804. [PMID: 33655273 PMCID: PMC7924298 DOI: 10.1101/2020.10.28.20221804] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease-19 (COVID-19), a respiratory illness that can result in hospitalization or death. We investigated associations between rare genetic variants and seven COVID-19 outcomes in 543,213 individuals, including 8,248 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome-wide or when specifically focusing on (i) 14 interferon pathway genes in which rare deleterious variants have been reported in severe COVID-19 patients; (ii) 167 genes located in COVID-19 GWAS risk loci; or (iii) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, with results publicly browsable at https://rgc-covid19.regeneron.com.
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Affiliation(s)
- J A Kosmicki
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J E Horowitz
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - N Banerjee
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - R Lanche
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Marcketta
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - E Maxwell
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - X Bai
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - D Sun
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J D Backman
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - D Sharma
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - H M Kang
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - C O'Dushlaine
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Yadav
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A J Mansfield
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A H Li
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - K Watanabe
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - L Gurski
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S E McCarthy
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A E Locke
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S Khalid
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S O'Keeffe
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J Mbatchou
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - O Chazara
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Y Huang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - E Kvikstad
- Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, NJ 08543, USA
| | - A O'Neill
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - P Nioi
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - M M Parker
- Alnylam Pharmaceuticals, 675 West Kendall St, Cambridge, MA 02142, USA
| | - S Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - H Runz
- Biogen, 300 Binney St, Cambridge, MA 02142, USA
| | - J D Szustakowski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Q Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - E Wong
- Biogen, 300 Binney St, Cambridge, MA 02142, USA
| | | | - E N Smith
- Takeda California Inc., 9625 Towne Centre Dr, San Diego, CA 92121, USA
| | - S Szalma
- Takeda California Inc., 9625 Towne Centre Dr, San Diego, CA 92121, USA
| | - X Zheng
- AbbVie, Inc., 1 N. Waukegan Rd, North Chicago, IL 60064, USA
| | - S Esmaeeli
- AbbVie, Inc., 1 N. Waukegan Rd, North Chicago, IL 60064, USA
| | - J W Davis
- AbbVie, Inc., 1 N. Waukegan Rd, North Chicago, IL 60064, USA
| | - Y-P Lai
- Pfizer, Inc., 1 Portland Street, Cambridge MA 02139, USA
| | - X Chen
- Pfizer, Inc., 1 Portland Street, Cambridge MA 02139, USA
| | | | | | | | | | - A Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - G Sirugo
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - M D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - D J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - G Povysil
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - D B Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics & Development, Columbia University, New York, NY 10032, USA
| | - K Kiryluk
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - E Pairo-Castineira
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - K Rawlik
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - D Pasko
- Genomics England, London EC1M 6BQ, UK
| | - S Walker
- Genomics England, London EC1M 6BQ, UK
| | - A Meynert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | | | | | - A Tenesa
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK
| | - M Caulfield
- Genomics England, London EC1M 6BQ, UK
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - R Scott
- Genomics England, London EC1M 6BQ, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - J F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK
| | - J K Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK
| | - G Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec H3A 0G4, Canada
| | - T Nakanishi
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Research Fellow, Japan Society for the Promotion of Science
| | - M Lathrop
- Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec H3A 0G4, Canada
| | - J B Richards
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec H3A 0G4, Canada
- Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada
- Department of Twins Research, King's College London, London WC2R 2LS, UK
| | - M Jones
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S Balasubramanian
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - W Salerno
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A R Shuldiner
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J Marchini
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J D Overton
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - L Habegger
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - M N Cantor
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J G Reid
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Baras
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - G R Abecasis
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - M A Ferreira
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
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22
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Sidore C, Orrù V, Cocco E, Steri M, Inshaw JR, Pitzalis M, Mulas A, McGurnaghan S, Frau J, Porcu E, Busonero F, Dei M, Lai S, Sole G, Virdis F, Serra V, Poddie F, Delitala A, Marongiu M, Deidda F, Pala M, Floris M, Masala M, Onengut-Gumuscu S, Robertson CC, Leoni L, Frongia A, Ricciardi MR, Chessa M, Olla N, Lovicu M, Loizedda A, Maschio A, Mereu L, Ferrigno P, Curreli N, Balaci L, Loi F, Ferreli LA, Pilia MG, Pani A, Marrosu MG, Abecasis GR, Rich SS, Colhoun H, Todd JA, Schlessinger D, Fiorillo E, Cucca F, Zoledziewska M. PRF1 mutation alters immune system activation, inflammation, and risk of autoimmunity. Mult Scler 2021; 27:1332-1340. [PMID: 33566725 DOI: 10.1177/1352458520963937] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Defective alleles within the PRF1 gene, encoding the pore-forming protein perforin, in combination with environmental factors, cause familial type 2 hemophagocytic lymphohistiocytosis (FHL2), a rare, severe autosomal recessive childhood disorder characterized by massive release of cytokines-cytokine storm. OBJECTIVE The aim of this study was to determine the function of hypomorph PRF1:p.A91V g.72360387 G > A on multiple sclerosis (MS) and type 1 diabetes (T1D). METHODS We cross-compare the association data for PRF1:p.A91V mutation derived from GWAS on adult MS and pediatric T1D in Sardinians. The novel association with T1D was replicated in metanalysis in 12,584 cases and 17,692 controls from Sardinia, the United Kingdom, and Scotland. To dissect this mutation function, we searched through the coincident association immunophenotypes in additional set of general population Sardinians. RESULTS We report that PRF1:p.A91V, is associated with increase of lymphocyte levels, especially within the cytotoxic memory T-cells, at general population level with reduced interleukin 7 receptor expression on these cells. The minor allele increased risk of MS, in 2903 cases and 2880 controls from Sardinia p = 2.06 × 10-4, odds ratio OR = 1.29, replicating a previous finding, whereas it protects from T1D p = 1.04 × 10-5, OR = 0.82. CONCLUSION Our results indicate opposing contributions of the cytotoxic T-cell compartment to MS and T1D pathogenesis.
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Affiliation(s)
- Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Eleonora Cocco
- Department of Medical Sciences and Public health, Multiple Sclerosis Centre, University of Cagliari, Cagliari, Italy
| | - Maristella Steri
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Jamie Rj Inshaw
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Oxford, UK/Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Maristella Pitzalis
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Antonella Mulas
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Stuart McGurnaghan
- Diabetes Medical Informatics and Epidemiology, The University of Edinburgh, Edinburgh, Scotland
| | - Jessica Frau
- Department of Medical Sciences and Public health, Multiple Sclerosis Centre, University of Cagliari, Cagliari, Italy
| | - Eleonora Porcu
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland/Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Fabio Busonero
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Mariano Dei
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Sandra Lai
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Gabriella Sole
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Francesca Virdis
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Valentina Serra
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Fausto Poddie
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Alessandro Delitala
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy/Department of Surgical, Medical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Michele Marongiu
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Francesca Deidda
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Mauro Pala
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Matteo Floris
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Marco Masala
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | | | - Lidia Leoni
- Center for Advanced Studies, Research and Development in Sardinia (CRS4), Parco Scientifico e Tecnologico della Sardegna, Pula, Italy
| | | | | | - Margherita Chessa
- Struttura Complessa di Pediatria, Azienda Ospedaliera G. Brotzu, Cagliari, Italy
| | - Nazario Olla
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Mario Lovicu
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Annalisa Loizedda
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Andrea Maschio
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Luisa Mereu
- Unità Operativa di Pediatria, Ospedale San Martino di Oristano, Oristano, Italy
| | - Paola Ferrigno
- Reparto di Neurologia, Azienda Ospedaliera G. Brotzu, Cagliari, Italy
| | - Nicolo Curreli
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Lenuta Balaci
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Francesco Loi
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Liana Ap Ferreli
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Maria Grazia Pilia
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Antonello Pani
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy/Struttura Complessa di Nefrologia e Dialisi, Azienda Ospedaliera G. Brotzu, Cagliari, Italy
| | - Maria Giovanna Marrosu
- Department of Medical Sciences and Public health, Multiple Sclerosis Centre, University of Cagliari, Cagliari, Italy
| | - Goncalo R Abecasis
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Helen Colhoun
- Diabetes Medical Informatics and Epidemiology, The University of Edinburgh, Edinburgh, Scotland
| | - John A Todd
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Oxford, UK/Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - David Schlessinger
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy/Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Magdalena Zoledziewska
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Monserrato, Monserrato, Italy
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Lagou V, Mägi R, Hottenga JJ, Grallert H, Perry JRB, Bouatia-Naji N, Marullo L, Rybin D, Jansen R, Min JL, Dimas AS, Ulrich A, Zudina L, Gådin JR, Jiang L, Faggian A, Bonnefond A, Fadista J, Stathopoulou MG, Isaacs A, Willems SM, Navarro P, Tanaka T, Jackson AU, Montasser ME, O'Connell JR, Bielak LF, Webster RJ, Saxena R, Stafford JM, Pourcain BS, Timpson NJ, Salo P, Shin SY, Amin N, Smith AV, Li G, Verweij N, Goel A, Ford I, Johnson PCD, Johnson T, Kapur K, Thorleifsson G, Strawbridge RJ, Rasmussen-Torvik LJ, Esko T, Mihailov E, Fall T, Fraser RM, Mahajan A, Kanoni S, Giedraitis V, Kleber ME, Silbernagel G, Meyer J, Müller-Nurasyid M, Ganna A, Sarin AP, Yengo L, Shungin D, Luan J, Horikoshi M, An P, Sanna S, Boettcher Y, Rayner NW, Nolte IM, Zemunik T, Iperen EV, Kovacs P, Hastie ND, Wild SH, McLachlan S, Campbell S, Polasek O, Carlson O, Egan J, Kiess W, Willemsen G, Kuusisto J, Laakso M, Dimitriou M, Hicks AA, Rauramaa R, Bandinelli S, Thorand B, Liu Y, Miljkovic I, Lind L, Doney A, Perola M, Hingorani A, Kivimaki M, Kumari M, Bennett AJ, Groves CJ, Herder C, Koistinen HA, Kinnunen L, Faire UD, Bakker SJL, Uusitupa M, Palmer CNA, Jukema JW, Sattar N, Pouta A, Snieder H, Boerwinkle E, Pankow JS, Magnusson PK, Krus U, Scapoli C, de Geus EJCN, Blüher M, Wolffenbuttel BHR, Province MA, Abecasis GR, Meigs JB, Hovingh GK, Lindström J, Wilson JF, Wright AF, Dedoussis GV, Bornstein SR, Schwarz PEH, Tönjes A, Winkelmann BR, Boehm BO, März W, Metspalu A, Price JF, Deloukas P, Körner A, Lakka TA, Keinanen-Kiukaanniemi SM, Saaristo TE, Bergman RN, Tuomilehto J, Wareham NJ, Langenberg C, Männistö S, Franks PW, Hayward C, Vitart V, Kaprio J, Visvikis-Siest S, Balkau B, Altshuler D, Rudan I, Stumvoll M, Campbell H, van Duijn CM, Gieger C, Illig T, Ferrucci L, Pedersen NL, Pramstaller PP, Boehnke M, Frayling TM, Shuldiner AR, Peyser PA, Kardia SLR, Palmer LJ, Penninx BW, Meneton P, Harris TB, Navis G, Harst PVD, Smith GD, Forouhi NG, Loos RJF, Salomaa V, Soranzo N, Boomsma DI, Groop L, Tuomi T, Hofman A, Munroe PB, Gudnason V, Siscovick DS, Watkins H, Lecoeur C, Vollenweider P, Franco-Cereceda A, Eriksson P, Jarvelin MR, Stefansson K, Hamsten A, Nicholson G, Karpe F, Dermitzakis ET, Lindgren CM, McCarthy MI, Froguel P, Kaakinen MA, Lyssenko V, Watanabe RM, Ingelsson E, Florez JC, Dupuis J, Barroso I, Morris AP, Prokopenko I. Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability. Nat Commun 2021; 12:24. [PMID: 33402679 PMCID: PMC7785747 DOI: 10.1038/s41467-020-19366-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022] Open
Abstract
Differences between sexes contribute to variation in the levels of fasting glucose and insulin. Epidemiological studies established a higher prevalence of impaired fasting glucose in men and impaired glucose tolerance in women, however, the genetic component underlying this phenomenon is not established. We assess sex-dimorphic (73,089/50,404 women and 67,506/47,806 men) and sex-combined (151,188/105,056 individuals) fasting glucose/fasting insulin genetic effects via genome-wide association study meta-analyses in individuals of European descent without diabetes. Here we report sex dimorphism in allelic effects on fasting insulin at IRS1 and ZNF12 loci, the latter showing higher RNA expression in whole blood in women compared to men. We also observe sex-homogeneous effects on fasting glucose at seven novel loci. Fasting insulin in women shows stronger genetic correlations than in men with waist-to-hip ratio and anorexia nervosa. Furthermore, waist-to-hip ratio is causally related to insulin resistance in women, but not in men. These results position dissection of metabolic and glycemic health sex dimorphism as a steppingstone for understanding differences in genetic effects between women and men in related phenotypes.
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Affiliation(s)
- Vasiliki Lagou
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Microbiology and Immunology, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jouke- Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, VU University medical center, Amsterdam, the Netherlands
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD, München-Neuherberg, Germany
| | - John R B Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Nabila Bouatia-Naji
- University of Lille Nord de France, Lille, France
- CNRS UMR8199, Institut Pasteur de Lille, Lille, France
- INSERM U970, Paris Cardiovascular Research Center PARCC, 75006, Paris, France
| | - Letizia Marullo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Denis Rybin
- Boston University Data Coordinating Center, Boston, MA, USA
| | - Rick Jansen
- Department of Psychiatry, VU University Medical Center, Amsterdam, the Netherlands
| | - Josine L Min
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Antigone S Dimas
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Greece
| | - Anna Ulrich
- Department of Medicine, Imperial College London, London, UK
| | | | - Jesper R Gådin
- Cardiovascular Medicine Unit, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Longda Jiang
- Department of Medicine, Imperial College London, London, UK
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Amélie Bonnefond
- University of Lille Nord de France, Lille, France
- CNRS UMR8199, Institut Pasteur de Lille, Lille, France
- Department of Medicine, Imperial College London, London, UK
| | - Joao Fadista
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Aaron Isaacs
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- CARIM School for Cardiovascular Diseases and Maastricht Centre for Systems Biology (MaCSBio, Maastricht University, Maastricht, the Netherlands
- Department of Physiology, Maastricht University, Maastricht, the Netherlands
| | - Sara M Willems
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Pau Navarro
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Toshiko Tanaka
- Translational Gerontology Branch, Longitudinal Study Section, National Institute on Aging, Baltimore, MD, USA
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - May E Montasser
- Division of Endocrinology, Diabetes, and Nutrition, Department of Medicine, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Jeff R O'Connell
- Division of Endocrinology, Diabetes, and Nutrition, Department of Medicine, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Rebecca J Webster
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, University of Western Australia Centre for Medical Research, Nedlands, WA, Australia
| | - Richa Saxena
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Departmentartment of Anesthesia, Critical Care and Pain Medicine, MGH, Boston, MA, USA
| | - Jeanette M Stafford
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Beate St Pourcain
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Perttu Salo
- Public Health Genomics Unit, Department of Chronic Disease Prevention, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - So-Youn Shin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Najaf Amin
- Department of Epidemiology Erasmus MC, Rotterdam, the Netherlands
| | - Albert V Smith
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Guo Li
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anuj Goel
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ian Ford
- Robertson Centre for Biostatistics, University of Glasgow, Glasgow, UK
| | - Paul C D Johnson
- Robertson Centre for Biostatistics, University of Glasgow, Glasgow, UK
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Toby Johnson
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Unit, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Karen Kapur
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | | | - Rona J Strawbridge
- Cardiovascular Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska University Hospital Solna, Stockholm, Sweden
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Evelin Mihailov
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tove Fall
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ross M Fraser
- Usher Institute, University of Edinburgh, Edinburgh, UK
- Synpromics Ltd, Roslin Innovation Centre, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Genentech, 340 Point San Bruno Boulevard, South San Francisco, CA, 94080, USA
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Uppsala Universitet, Uppsala, Sweden
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Günther Silbernagel
- Division of Angiology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Julia Meyer
- Institute of Genetic Epidemiology,Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology,Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology and Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-University, Munich, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI, University Medical Center, Johannes Gutenberg University, 55101, Mainz, Germany
| | - Andrea Ganna
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Loic Yengo
- University of Lille Nord de France, Lille, France
- CNRS UMR8199, Institut Pasteur de Lille, Lille, France
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Dmitry Shungin
- Department of Public Health & Clinical Medicine, Umeå University, Umeå, Sweden
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Skåne University Hospital Malmö, Malmö, Sweden
- Department of Odontology, Umeå University, Umeå, Sweden
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Momoko Horikoshi
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- RIKEN, Center for Integrative Medical Sciences, Laboratory for Endocrinology, Metabolism and Kidney Disease, Yokohama, Japan
| | - Ping An
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Serena Sanna
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Italy
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Yvonne Boettcher
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | - N William Rayner
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Erik van Iperen
- Department of Clinical Epidemiology and Biostatistics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Peter Kovacs
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | - Nicholas D Hastie
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Sarah H Wild
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | | | - Susan Campbell
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Olga Carlson
- Laboratory of Clinical Investigation, National Institute of Aging, Baltimore, MD, USA
| | - Josephine Egan
- Laboratory of Clinical Investigation, National Institute of Aging, Baltimore, MD, USA
| | - Wieland Kiess
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Pediatric Research Center, Department of Women's & Child Health, University of Leipzig, Leipzig, Germany
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Maria Dimitriou
- Department of Dietetics-Nutrition, Harokopio University, Athens, Greece
| | - Andrew A Hicks
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC) (Affiliated Institute of the University of LübeckLübeckGermany), Bolzano, Italy
| | - Rainer Rauramaa
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | | | - Barbara Thorand
- German Center for Diabetes Research (DZD, München-Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Iva Miljkovic
- Department of Epidemiology, Center for Aging and Population Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Akademiska sjukhuset, Uppsala, Sweden
| | - Alex Doney
- Pat McPherson Centre for Pharmacogenetics and Pharmacogenomics, Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Markus Perola
- Public Health Genomics Unit, Department of Chronic Disease Prevention, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Aroon Hingorani
- Department of Epidemiology and Public Health, University College London, London, UK
| | - Mika Kivimaki
- Department of Epidemiology and Public Health, University College London, London, UK
| | - Meena Kumari
- Department of Epidemiology and Public Health, University College London, London, UK
- University of Essex, Wivenhoe Park, Colchester, Essex, UK
| | - Amanda J Bennett
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Christopher J Groves
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Christian Herder
- German Center for Diabetes Research (DZD, München-Neuherberg, Germany
- Institute of Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Heikki A Koistinen
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
- Department of Medicine, University of Helsinki and Helsinki University Central Hospital, P.O. Box 340, Haartmaninkatu 4, Helsinki, FI-00029, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum 2U, Tukholmankatu 8, Helsinki, FI-00290, Finland
| | - Leena Kinnunen
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
| | - Ulf de Faire
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Stephan J L Bakker
- Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Matti Uusitupa
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Colin N A Palmer
- Pat McPherson Centre for Pharmacogenetics and Pharmacogenomics, Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - J Wouter Jukema
- Dept of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Netherlands Heart Institute, Utrecht, the Netherlands
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Anneli Pouta
- Department of Government Services, Finnish Institute for Health and Welfare, Helsinki, Finland
- PEDEGO Research Unit, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eric Boerwinkle
- IMM Center for Human Genetics, University of Texas Health Science Center at Houston, Houston, TX, USA
- Division of Epidemiology, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MiI, USA
| | - Patrik K Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ulrika Krus
- Department of Clinical Sciences, Diabetes and Endocrinology Research Unit, University Hospital Malmö, Lund University, Malmö, Sweden
| | - Chiara Scapoli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Eco J C N de Geus
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, VU University medical center, Amsterdam, the Netherlands
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig, Germany
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Bruce H R Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Michael A Province
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - James B Meigs
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- General Medicine Division, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - G Kees Hovingh
- Department of Vascular Medicine, Amsterdam UMC, Amsterdam, the Netherlands
- Novo Nordisk A/S, Copenhagen, Denmark
| | - Jaana Lindström
- Finnish Institute for Health and Welfare, Diabetes Prevention Unit, Helsinki, Finland
| | - James F Wilson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Alan F Wright
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | | | - Stefan R Bornstein
- Department of Medicine, Division for Prevention and Care of Diabetes, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Peter E H Schwarz
- Department for Prevention and Care of Diabetes, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine, TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | | | - Bernhard O Boehm
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore and Imperial College London, Singapore, Singapore
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim, Germany
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Antje Körner
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Diabetes Research Center, Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Timo A Lakka
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
| | - Sirkka M Keinanen-Kiukaanniemi
- Faculty of Medicine, Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Unit of General Practice, Oulu University Hospital, Oulu, Finland
| | - Timo E Saaristo
- Finnish Diabetes Association, Tampere, Finland
- Pirkanmaa Hospital District, Tampere, Finland
| | - Richard N Bergman
- Diabetes and Obesity Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jaakko Tuomilehto
- Department of Chronic Disease Prevention, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Centre for Vascular Prevention, Danube-University Krems, Krems, Austria
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Satu Männistö
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
| | - Paul W Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Skåne University Hospital Malmö, Malmö, Sweden
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
- Department of Public Health & Clinical Medicine, Units of Medicine and Nutritional Research, Umeå University, Umeå, Sweden
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | | | - Beverley Balkau
- Inserm, CESP Center for Research in Epidemiology and Public Health, U1018, Villejuif, France
- Univ Paris-Saclay, Univ Paris Sud, UVSQ, UMRS 1018, UMRS 1018, Villejuif, France
| | - David Altshuler
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Igor Rudan
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | | | - Cornelia M van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Centre for Medical Systems Biology, Leiden, the Netherlands
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD, München-Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Luigi Ferrucci
- Clinical Research Branch, National Institute on Aging, Baltimore, Maryland, USA
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter P Pramstaller
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC) (Affiliated Institute of the University of LübeckLübeckGermany), Bolzano, Italy
- Department of Neurology, General Central Hospital, Bolzano, Italy
- Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Timothy M Frayling
- Genetics of Complex Traits, Peninsula Medical School, University of Exeter, Exeter, UK
| | - Alan R Shuldiner
- Division of Endocrinology, Diabetes, and Nutrition, Department of Medicine, University of Maryland, School of Medicine, Baltimore, MD, USA
- The Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Lyle J Palmer
- School of Public Health, University of Adelaide, Adelaide, Australia
| | - Brenda W Penninx
- Department of Psychiatry, VU University Medical Center, Amsterdam, the Netherlands
| | - Pierre Meneton
- U872 Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, 75006, Paris, France
| | - Tamara B Harris
- Geriatric Epidemiology Section, Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Bethesda, MD, USA
| | - Gerjan Navis
- Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
| | - Nita G Forouhi
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Ruth J F Loos
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Nicole Soranzo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Leif Groop
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Department of Clinical Sciences, Diabetes and Endocrinology Research Unit, University Hospital Malmö, Lund University, Malmö, Sweden
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Department of Clinical Sciences, Diabetes and Endocrinology Research Unit, University Hospital Malmö, Lund University, Malmö, Sweden
- Endocrinology, Abdominal Centre, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland
| | - Albert Hofman
- Department of Epidemiology Erasmus MC, Rotterdam, the Netherlands
- Netherlands Consortium for healthy ageing, the Hague, the Netherlands
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Patricia B Munroe
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Unit, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine University of Iceland, Reykjavik, Iceland
| | - David S Siscovick
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Hugh Watkins
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Cecile Lecoeur
- University of Lille Nord de France, Lille, France
- CNRS UMR8199, Institut Pasteur de Lille, Lille, France
| | - Peter Vollenweider
- Department of Medicine, University Hospital Lausanne, Lausanne, Switzerland
| | - Anders Franco-Cereceda
- Cardiothoracic Surgery Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Per Eriksson
- Cardiovascular Medicine Unit, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics and HPA-MRC Center, School of Public Health, Imperial College London, London, UK
- Institue of Health Sciences, University of Oulu, Oulu, Finland
| | - Kari Stefansson
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Anders Hamsten
- Cardiovascular Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska University Hospital Solna, Stockholm, Sweden
- Department of Cardiology, Karolinska University Hospital Solna, Stockholm, Sweden
| | | | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Cecilia M Lindgren
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Oxford, UK
- Genentech, 340 Point San Bruno Boulevard, South San Francisco, CA, 94080, USA
| | - Philippe Froguel
- University of Lille Nord de France, Lille, France
- CNRS UMR8199, Institut Pasteur de Lille, Lille, France
- Department of Medicine, Imperial College London, London, UK
| | - Marika A Kaakinen
- Department of Medicine, Imperial College London, London, UK
- School of Biosciences and Medicine, Department of Clinical and Experimental Medicine, University of Surrey, Guildford, UK
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology Research Unit, University Hospital Malmö, Lund University, Malmö, Sweden
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Richard M Watanabe
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
- Department of Physiology & Neuroscience, Keck School of Medicine of USC, Los Angeles, CA, USA
- USC Diabetes and Obesity Research Institute, Los Angeles, CA, USA
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, 94305, USA
| | - Jose C Florez
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Research Center, Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, UK
- Exeter Centre of ExcEllence in Diabetes (ExCEED), University of Exeter Medical School, Exeter, UK
| | - Andrew P Morris
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Inga Prokopenko
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
- Department of Medicine, Imperial College London, London, UK.
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK.
- School of Biosciences and Medicine, Department of Clinical and Experimental Medicine, University of Surrey, Guildford, UK.
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre Russian Academy of Sciences, Ufa, Russian Federation.
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24
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Nielsen JB, Rom O, Surakka I, Graham SE, Zhou W, Roychowdhury T, Fritsche LG, Gagliano Taliun SA, Sidore C, Liu Y, Gabrielsen ME, Skogholt AH, Wolford B, Overton W, Zhao Y, Chen J, Zhang H, Hornsby WE, Acheampong A, Grooms A, Schaefer A, Zajac GJM, Villacorta L, Zhang J, Brumpton B, Løset M, Rai V, Lundegaard PR, Olesen MS, Taylor KD, Palmer ND, Chen YD, Choi SH, Lubitz SA, Ellinor PT, Barnes KC, Daya M, Rafaels N, Weiss ST, Lasky-Su J, Tracy RP, Vasan RS, Cupples LA, Mathias RA, Yanek LR, Becker LC, Peyser PA, Bielak LF, Smith JA, Aslibekyan S, Hidalgo BA, Arnett DK, Irvin MR, Wilson JG, Musani SK, Correa A, Rich SS, Guo X, Rotter JI, Konkle BA, Johnsen JM, Ashley-Koch AE, Telen MJ, Sheehan VA, Blangero J, Curran JE, Peralta JM, Montgomery C, Sheu WHH, Chung RH, Schwander K, Nouraie SM, Gordeuk VR, Zhang Y, Kooperberg C, Reiner AP, Jackson RD, Bleecker ER, Meyers DA, Li X, Das S, Yu K, LeFaive J, Smith A, Blackwell T, Taliun D, Zollner S, Forer L, Schoenherr S, Fuchsberger C, Pandit A, Zawistowski M, Kheterpal S, Brummett CM, Natarajan P, Schlessinger D, Lee S, Kang HM, Cucca F, Holmen OL, Åsvold BO, Boehnke M, Kathiresan S, Abecasis GR, Chen YE, Willer CJ, Hveem K. Loss-of-function genomic variants highlight potential therapeutic targets for cardiovascular disease. Nat Commun 2020; 11:6417. [PMID: 33339817 PMCID: PMC7749177 DOI: 10.1038/s41467-020-20086-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022] Open
Abstract
Pharmaceutical drugs targeting dyslipidemia and cardiovascular disease (CVD) may increase the risk of fatty liver disease and other metabolic disorders. To identify potential novel CVD drug targets without these adverse effects, we perform genome-wide analyses of participants in the HUNT Study in Norway (n = 69,479) to search for protein-altering variants with beneficial impact on quantitative blood traits related to cardiovascular disease, but without detrimental impact on liver function. We identify 76 (11 previously unreported) presumed causal protein-altering variants associated with one or more CVD- or liver-related blood traits. Nine of the variants are predicted to result in loss-of-function of the protein. This includes ZNF529:p.K405X, which is associated with decreased low-density-lipoprotein (LDL) cholesterol (P = 1.3 × 10-8) without being associated with liver enzymes or non-fasting blood glucose. Silencing of ZNF529 in human hepatoma cells results in upregulation of LDL receptor and increased LDL uptake in the cells. This suggests that inhibition of ZNF529 or its gene product should be prioritized as a novel candidate drug target for treating dyslipidemia and associated CVD.
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Affiliation(s)
- Jonas B Nielsen
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA.
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Trondheim, Norway.
| | - Oren Rom
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Ida Surakka
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Sarah E Graham
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Tanmoy Roychowdhury
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Lars G Fritsche
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Sarah A Gagliano Taliun
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Yuhao Liu
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Maiken E Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - Anne Heidi Skogholt
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - Brooke Wolford
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - William Overton
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Ying Zhao
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Jin Chen
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - He Zhang
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Whitney E Hornsby
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Akua Acheampong
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Austen Grooms
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Amanda Schaefer
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Gregory J M Zajac
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Luis Villacorta
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Jifeng Zhang
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Ben Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - Mari Løset
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
- Department of Dermatology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Vivek Rai
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Pia R Lundegaard
- Laboratory for Molecular Cardiology, Department of Cardiology, Centre for Cardiac, Vascular, Pulmonary and Infectious Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten S Olesen
- Laboratory for Molecular Cardiology, Department of Cardiology, Centre for Cardiac, Vascular, Pulmonary and Infectious Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics and Los Angeles Biomedical Research Institute, Harbor-UCLA, Torrance, CA, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yii-Der Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics and Los Angeles Biomedical Research Institute, Harbor-UCLA, Torrance, CA, USA
| | - Seung H Choi
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Steven A Lubitz
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick T Ellinor
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Kathleen C Barnes
- Colorado Center for Personalized Medicine, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Michelle Daya
- Colorado Center for Personalized Medicine, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Nicholas Rafaels
- Colorado Center for Personalized Medicine, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Ramachandran S Vasan
- Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
- Framingham Heart Study, Framingham, MA, USA
| | - L Adrienne Cupples
- Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Rasika A Mathias
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Lewis C Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Stella Aslibekyan
- The University of Alabama at Birmingham, Birmingham, AL, USA
- 23andMe, Inc., Sunnyvale, CA, USA
| | | | - Donna K Arnett
- Deans Office, College of Public Health, University of Kentucky, Lexington, KY, USA
| | | | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
- Jackson Heart Study, Jackson, MS, USA
| | - Solomon K Musani
- Jackson Heart Study, Jackson, MS, USA
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Adolfo Correa
- Jackson Heart Study, Jackson, MS, USA
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics and Los Angeles Biomedical Research Institute, Harbor-UCLA, Torrance, CA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics and Los Angeles Biomedical Research Institute, Harbor-UCLA, Torrance, CA, USA
| | - Barbara A Konkle
- BloodWorks Northwest, University of Washington, Seattle, WA, USA
| | - Jill M Johnsen
- BloodWorks Northwest, University of Washington, Seattle, WA, USA
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Marilyn J Telen
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Vivien A Sheehan
- Department of Pediatrics, Division of Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Joanne E Curran
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Juan M Peralta
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Courtney Montgomery
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma, OK, USA
| | - Wayne H-H Sheu
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ren-Hua Chung
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Karen Schwander
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Seyed M Nouraie
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Yingze Zhang
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, Ohio State University, Columbus, OH, USA
| | | | - Deborah A Meyers
- Division of Pharmacogenomics University of Arizona, Tucson, AR, USA
| | - Xingnan Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AR, USA
| | - Sayantan Das
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Ketian Yu
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jonathon LeFaive
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Albert Smith
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Tom Blackwell
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Daniel Taliun
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Sebastian Zollner
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Lukas Forer
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AR, USA
| | - Sebastian Schoenherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christian Fuchsberger
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Anita Pandit
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Matthew Zawistowski
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Sachin Kheterpal
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, USA
| | - Chad M Brummett
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David Schlessinger
- Laboratory of Genetics, National Institute on Aging, US National Institutes of Health, Baltimore, MD, USA
| | - Seunggeun Lee
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Hyun Min Kang
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Oddgeir L Holmen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Levanger, Norway
| | - Bjørn O Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Levanger, Norway
- Department of Endocrinology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Michael Boehnke
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Sekar Kathiresan
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MD, USA
| | - Goncalo R Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Y Eugene Chen
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA.
| | - Cristen J Willer
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA.
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Trondheim, Norway.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Trondheim, Norway.
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Levanger, Norway.
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway.
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25
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Busonero F, Steri M, Orrù V, Sole G, Olla S, Marongiu M, Maschio A, Sidore C, Lai S, Mulas A, Zoledziewska M, Floris M, Pala M, Forabosco P, Asunis I, Pitzalis M, Deidda F, Masala M, Caria CA, Barella S, Abecasis GR, Schlessinger D, Sanna S, Fiorillo E, Cucca F. A Sardinian founder mutation in glycoprotein Ib platelet subunit beta (GP1BB) that impacts thrombocytopenia. Br J Haematol 2020; 191:e124-e128. [PMID: 33216977 DOI: 10.1111/bjh.17090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Fabio Busonero
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Maristella Steri
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Gabriella Sole
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Stefania Olla
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Michele Marongiu
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Andrea Maschio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Sandra Lai
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Antonella Mulas
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Magdalena Zoledziewska
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Matteo Floris
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy.,Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Mauro Pala
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Paola Forabosco
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Isadora Asunis
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Maristella Pitzalis
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Francesca Deidda
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Marco Masala
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Cristian Antonio Caria
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Susanna Barella
- Ospedale Pediatrico Microcitemico 'Antonio Cao' (A.O.Brotzu), Cagliari, Italy
| | - Goncalo R Abecasis
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - David Schlessinger
- Laboratory of Genetics and Genomics, National Institute on Aging, US National Institutes of Health, Baltimore, MD, USA
| | - Serena Sanna
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato (Cagliari), Italy.,Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
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26
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Surakka I, Fritsche LG, Zhou W, Backman J, Kosmicki JA, Lu H, Brumpton B, Nielsen JB, Gabrielsen ME, Skogholt AH, Wolford B, Graham SE, Chen YE, Lee S, Kang HM, Langhammer A, Forsmo S, Åsvold BO, Styrkarsdottir U, Holm H, Gudbjartsson D, Stefansson K, Baras A, Abecasis GR, Hveem K, Willer CJ. MEPE loss-of-function variant associates with decreased bone mineral density and increased fracture risk. Nat Commun 2020; 11:4093. [PMID: 33097703 PMCID: PMC7585430 DOI: 10.1038/s41467-020-17315-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 05/26/2020] [Indexed: 01/28/2023] Open
Abstract
A major challenge in genetic association studies is that most associated variants fall in the non-coding part of the human genome. We searched for variants associated with bone mineral density (BMD) after enriching the discovery cohort for loss-of-function (LoF) mutations by sequencing a subset of the Nord-Trøndelag Health Study, followed by imputation in the remaining sample (N = 19,705), and identified ten known BMD loci. However, one previously unreported variant, LoF mutation in MEPE, p.(Lys70IlefsTer26, minor allele frequency [MAF] = 0.8%), was associated with decreased ultradistal forearm BMD (P-value = 2.1 × 10−18), and increased osteoporosis (P-value = 4.2 × 10−5) and fracture risk (P-value = 1.6 × 10−5). The MEPE LoF association with BMD and fractures was further evaluated in 279,435 UK (MAF = 0.05%, heel bone estimated BMD P-value = 1.2 × 10−16, any fracture P-value = 0.05) and 375,984 Icelandic samples (MAF = 0.03%, arm BMD P-value = 0.12, forearm fracture P-value = 0.005). Screening for the MEPE LoF mutations before adulthood could potentially prevent osteoporosis and fractures due to the lifelong effect on BMD observed in the study. A key implication for precision medicine is that high-impact functional variants missing from the publicly available cosmopolitan panels could be clinically more relevant than polygenic risk scores. Bone mineral density (BMD) is associated with fracture risk and many genetic loci with small effect sizes have been discovered by genome-wide association studies (GWAS). Here, the authors discover a large-effect rare loss-of-function genetic variant for BMD in the MEPE gene in the Norwegian HUNT study which replicates in the UK Biobank.
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Affiliation(s)
- Ida Surakka
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, MI, 48109, USA
| | - Lars G Fritsche
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, MI, 48109, USA.,Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, 1415 Washington Heights, 1700 SPH I, Ann Arbor, MI, 48109, USA
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Palmer Commons, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Joshua Backman
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Jack A Kosmicki
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Haocheng Lu
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, MI, 48109, USA
| | - Ben Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway.,MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.,Clinic of Thoracic and Occupational Medicine, St. Olavs Hospital, Trondheim University Hospital, Prinsesse Kristinas gate 3, 7030, Trondheim, Norway
| | - Jonas B Nielsen
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, MI, 48109, USA
| | - Maiken E Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway
| | - Anne Heidi Skogholt
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway
| | - Brooke Wolford
- Department of Computational Medicine and Bioinformatics, University of Michigan, Palmer Commons, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Sarah E Graham
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, MI, 48109, USA
| | - Y Eugene Chen
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, MI, 48109, USA
| | - Seunggeun Lee
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, 1415 Washington Heights, 1700 SPH I, Ann Arbor, MI, 48109, USA
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, 1415 Washington Heights, 1700 SPH I, Ann Arbor, MI, 48109, USA
| | - Arnulf Langhammer
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Postboks 8905, N-7491, Levanger, Norway
| | - Siri Forsmo
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Postboks 8905, N-7491, Levanger, Norway
| | - Bjørn O Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway.,HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Postboks 8905, N-7491, Levanger, Norway.,Department of Endocrinology, St. Olavs Hospital, Trondheim University Hospital, Prinsesse Kristinas gate 3, 7030, Trondheim, Norway
| | | | - Hilma Holm
- deCODE genetics/Amgen, Inc., Sturlugata 8, 101, Reykjavik, Iceland
| | - Daniel Gudbjartsson
- deCODE genetics/Amgen, Inc., Sturlugata 8, 101, Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Sturlugata 7, 101, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Sturlugata 8, 101, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmýrarvegur 16, 101, Reykjavik, Iceland
| | - Aris Baras
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | | | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, 1415 Washington Heights, 1700 SPH I, Ann Arbor, MI, 48109, USA.,Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway. .,HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Postboks 8905, N-7491, Levanger, Norway.
| | - Cristen J Willer
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, 1500 E. Medical Center Dr., Ann Arbor, MI, 48109, USA. .,Department of Computational Medicine and Bioinformatics, University of Michigan, Palmer Commons, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA. .,K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway. .,Department of Human Genetics, University of Michigan, 4909 Buhl Building, 1241 E. Catherine St, Ann Arbor, MI, 48109, USA.
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27
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Zhao X, Qiao D, Yang C, Kasela S, Kim W, Ma Y, Shrine N, Batini C, Sofer T, Taliun SAG, Sakornsakolpat P, Balte PP, Prokopenko D, Yu B, Lange LA, Dupuis J, Cade BE, Lee J, Gharib SA, Daya M, Laurie CA, Ruczinski I, Cupples LA, Loehr LR, Bartz TM, Morrison AC, Psaty BM, Vasan RS, Wilson JG, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy RP, Ardlie KG, Aguet F, VanDenBerg DJ, Papanicolaou GJ, Rotter JI, Barnes KC, Jain D, Nickerson DA, Muzny DM, Metcalf GA, Doddapaneni H, Dugan-Perez S, Gupta N, Gabriel S, Rich SS, O'Connor GT, Redline S, Reed RM, Laurie CC, Daviglus ML, Preudhomme LK, Burkart KM, Kaplan RC, Wain LV, Tobin MD, London SJ, Lappalainen T, Oelsner EC, Abecasis GR, Silverman EK, Barr RG, Cho MH, Manichaikul A. Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants. Nat Commun 2020; 11:5182. [PMID: 33057025 PMCID: PMC7598941 DOI: 10.1038/s41467-020-18334-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/19/2020] [Indexed: 12/14/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD), diagnosed by reduced lung function, is a leading cause of morbidity and mortality. We performed whole genome sequence (WGS) analysis of lung function and COPD in a multi-ethnic sample of 11,497 participants from population- and family-based studies, and 8499 individuals from COPD-enriched studies in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program. We identify at genome-wide significance 10 known GWAS loci and 22 distinct, previously unreported loci, including two common variant signals from stratified analysis of African Americans. Four novel common variants within the regions of PIAS1, RGN (two variants) and FTO show evidence of replication in the UK Biobank (European ancestry n ~ 320,000), while colocalization analyses leveraging multi-omic data from GTEx and TOPMed identify potential molecular mechanisms underlying four of the 22 novel loci. Our study demonstrates the value of performing WGS analyses and multi-omic follow-up in cohorts of diverse ancestry.
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Affiliation(s)
- Xutong Zhao
- Center for Statistical Genetics, and Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Chaojie Yang
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Silva Kasela
- New York Genome Center, New York, NY, 10013, USA
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Yanlin Ma
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Chiara Batini
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Tamar Sofer
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sarah A Gagliano Taliun
- Center for Statistical Genetics, and Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Pallavi P Balte
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Bing Yu
- Department of Epidemiology, Human Genetics & Environmental Sciences, UTHealth School of Public Health, Houston, TX, 77030, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Brian E Cade
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Jiwon Lee
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sina A Gharib
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Michelle Daya
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
- Boston University and the National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Laura R Loehr
- Department of Medicine, UNC School of Medicine, Chapel Hill, NC, 27599, USA
| | - Traci M Bartz
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, 98101, USA
| | - Ramachandran S Vasan
- Boston University and the National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
- Department of Preventive Medicine and Epidemiology, Boston University School of Medicine and Public Health, Boston, MA, 02118, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, The Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Peter Durda
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Elaine Cornell
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, The Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Yongmei Liu
- Department of Medicine, Division of Cardiology, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, 27701, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | | | - François Aguet
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - David J VanDenBerg
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - George J Papanicolaou
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, The Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Donna M Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ginger A Metcalf
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Shannon Dugan-Perez
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - George T O'Connor
- Boston University School Of Medicine, Pulmonary Center, Boston, MA, 02118, USA
| | - Susan Redline
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Robert M Reed
- Division of Pulmonary and Critical Care Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | | | - Kristin M Burkart
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, NY, 10461, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Louise V Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Martin D Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Durham, NC, 27709, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, 10013, USA
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Elizabeth C Oelsner
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Goncalo R Abecasis
- Center for Statistical Genetics, and Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - R Graham Barr
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA.
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Erzurumluoglu AM, Liu M, Jackson VE, Barnes DR, Datta G, Melbourne CA, Young R, Batini C, Surendran P, Jiang T, Adnan SD, Afaq S, Agrawal A, Altmaier E, Antoniou AC, Asselbergs FW, Baumbach C, Bierut L, Bertelsen S, Boehnke M, Bots ML, Brazel DM, Chambers JC, Chang-Claude J, Chen C, Corley J, Chou YL, David SP, de Boer RA, de Leeuw CA, Dennis JG, Dominiczak AF, Dunning AM, Easton DF, Eaton C, Elliott P, Evangelou E, Faul JD, Foroud T, Goate A, Gong J, Grabe HJ, Haessler J, Haiman C, Hallmans G, Hammerschlag AR, Harris SE, Hattersley A, Heath A, Hsu C, Iacono WG, Kanoni S, Kapoor M, Kaprio J, Kardia SL, Karpe F, Kontto J, Kooner JS, Kooperberg C, Kuulasmaa K, Laakso M, Lai D, Langenberg C, Le N, Lettre G, Loukola A, Luan J, Madden PAF, Mangino M, Marioni RE, Marouli E, Marten J, Martin NG, McGue M, Michailidou K, Mihailov E, Moayyeri A, Moitry M, Müller-Nurasyid M, Naheed A, Nauck M, Neville MJ, Nielsen SF, North K, Perola M, Pharoah PDP, Pistis G, Polderman TJ, Posthuma D, Poulter N, Qaiser B, Rasheed A, Reiner A, Renström F, Rice J, Rohde R, Rolandsson O, Samani NJ, Samuel M, Schlessinger D, Scholte SH, Scott RA, Sever P, Shao Y, Shrine N, Smith JA, Starr JM, Stirrups K, Stram D, Stringham HM, Tachmazidou I, Tardif JC, Thompson DJ, Tindle HA, Tragante V, Trompet S, Turcot V, Tyrrell J, Vaartjes I, van der Leij AR, van der Meer P, Varga TV, Verweij N, Völzke H, Wareham NJ, Warren HR, Weir DR, Weiss S, Wetherill L, Yaghootkar H, Yavas E, Jiang Y, Chen F, Zhan X, Zhang W, Zhao W, Zhao W, Zhou K, Amouyel P, Blankenberg S, Caulfield MJ, Chowdhury R, Cucca F, Deary IJ, Deloukas P, Di Angelantonio E, Ferrario M, Ferrières J, Franks PW, Frayling TM, Frossard P, Hall IP, Hayward C, Jansson JH, Jukema JW, Kee F, Männistö S, Metspalu A, Munroe PB, Nordestgaard BG, Palmer CNA, Salomaa V, Sattar N, Spector T, Strachan DP, van der Harst P, Zeggini E, Saleheen D, Butterworth AS, Wain LV, Abecasis GR, Danesh J, Tobin MD, Vrieze S, Liu DJ, Howson JMM. Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci. Mol Psychiatry 2020; 25:2392-2409. [PMID: 30617275 PMCID: PMC7515840 DOI: 10.1038/s41380-018-0313-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 09/30/2018] [Accepted: 11/14/2018] [Indexed: 02/02/2023]
Abstract
Smoking is a major heritable and modifiable risk factor for many diseases, including cancer, common respiratory disorders and cardiovascular diseases. Fourteen genetic loci have previously been associated with smoking behaviour-related traits. We tested up to 235,116 single nucleotide variants (SNVs) on the exome-array for association with smoking initiation, cigarettes per day, pack-years, and smoking cessation in a fixed effects meta-analysis of up to 61 studies (up to 346,813 participants). In a subset of 112,811 participants, a further one million SNVs were also genotyped and tested for association with the four smoking behaviour traits. SNV-trait associations with P < 5 × 10-8 in either analysis were taken forward for replication in up to 275,596 independent participants from UK Biobank. Lastly, a meta-analysis of the discovery and replication studies was performed. Sixteen SNVs were associated with at least one of the smoking behaviour traits (P < 5 × 10-8) in the discovery samples. Ten novel SNVs, including rs12616219 near TMEM182, were followed-up and five of them (rs462779 in REV3L, rs12780116 in CNNM2, rs1190736 in GPR101, rs11539157 in PJA1, and rs12616219 near TMEM182) replicated at a Bonferroni significance threshold (P < 4.5 × 10-3) with consistent direction of effect. A further 35 SNVs were associated with smoking behaviour traits in the discovery plus replication meta-analysis (up to 622,409 participants) including a rare SNV, rs150493199, in CCDC141 and two low-frequency SNVs in CEP350 and HDGFRP2. Functional follow-up implied that decreased expression of REV3L may lower the probability of smoking initiation. The novel loci will facilitate understanding the genetic aetiology of smoking behaviour and may lead to the identification of potential drug targets for smoking prevention and/or cessation.
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Affiliation(s)
| | - Mengzhen Liu
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Victoria E Jackson
- Department of Health Sciences, University of Leicester, Leicester, UK
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, 3052, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, 3010, Parkville, Australia
| | - Daniel R Barnes
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Gargi Datta
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Robin Young
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Chiara Batini
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Praveen Surendran
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Tao Jiang
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Sheikh Daud Adnan
- National Institute of Cardiovascular Diseases, Sher-e-Bangla Nagar, Dhaka, Bangladesh
| | - Saima Afaq
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
| | - Arpana Agrawal
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Elisabeth Altmaier
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
- Durrer Center for Cardiovascular Research, Netherlands Heart Institute, Utrecht, The Netherlands
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK
- Farr Institute of Health Informatics Research and Institute of Health Informatics, University College London, London, UK
| | - Clemens Baumbach
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Laura Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Sarah Bertelsen
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Michiel L Bots
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3508GA, Utrecht, The Netherlands
- Center for Circulatory Health, University Medical Center Utrecht, 3508GA, Utrecht, The Netherlands
| | - David M Brazel
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- Department of Cardiology, Ealing Hospital, Middlesex, UB1 3HW, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg, Germany
| | - Chu Chen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Janie Corley
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Yi-Ling Chou
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Sean P David
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Rudolf A de Boer
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Christiaan A de Leeuw
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, Netherlands
| | - Joe G Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Anna F Dominiczak
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge Centre, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge Centre, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Charles Eaton
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, W2 1PG, UK
- National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare NHS Trust and Imperial College London, London, UK
- UK Dementia Research Institute (UK DRI) at Imperial College London, London, UK
| | - Evangelos Evangelou
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Alison Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jian Gong
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475, Greifswald, Germany
| | - Jeff Haessler
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Göran Hallmans
- Department of Public Health and Clinical Medicine, Nutritional research, Umeå University, Umeå, Sweden
| | - Anke R Hammerschlag
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, Netherlands
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrew Hattersley
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, UK
| | - Andrew Heath
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Chris Hsu
- University of Southern California, California, CA, USA
| | - William G Iacono
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Centre for Genomic Health, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Manav Kapoor
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Sharon L Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Oxford National Institute for Health Research, Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Jukka Kontto
- Department of Public Health Solutions, National Institute for Health and Welfare, FI-00271, Helsinki, Finland
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, Middlesex, UB1 3HW, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, W2 1PG, UK
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington School of Medicine, Seattle, WA, USA
| | - Kari Kuulasmaa
- Department of Public Health Solutions, National Institute for Health and Welfare, FI-00271, Helsinki, Finland
| | | | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Nhung Le
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montreal, Quebec, H1T 1C8, Canada
- Department of Medicine, Faculty of Medicine, Universite de Montreal, Montreal, Quebec, H3T 1J4, Canada
| | - Anu Loukola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | | | - Massimo Mangino
- NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, SE1 9RT, UK
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, SE1 7EH, UK
| | - Riccardo E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Eirini Marouli
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Centre for Genomic Health, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Jonathan Marten
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, 1683, Nicosia, Cyprus
| | | | - Alireza Moayyeri
- Institute of Health Informatics, University College London, London, UK
| | - Marie Moitry
- Department of Epidemiology and Public health, University Hospital of Strasbourg, Strasbourg, France
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Medicine I, Ludwig-Maximilians-University Munich, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Aliya Naheed
- Initiative for Noncommunicable Diseases, Health Systems and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b) International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, Greifswald, Germany
| | - Matthew J Neville
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Oxford National Institute for Health Research, Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Sune Fallgaard Nielsen
- Department of Clinical Biochemistry Herlev Hospital, Copenhagen University Hospital, Herlev Ringvej 74, DK-2730, Herlev, Denmark
| | - Kari North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Markus Perola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health Solutions, National Institute for Health and Welfare, FI-00271, Helsinki, Finland
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge Centre, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Giorgio Pistis
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Tinca J Polderman
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, Netherlands
- Department of Clinical Genetics, VU University Medical Centre Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Neil Poulter
- International Centre for Circulatory Health, Imperial College London, London, UK
| | - Beenish Qaiser
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Asif Rasheed
- Centre for Non-Communicable Diseases, Karachi, Pakistan
| | - Alex Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Frida Renström
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Skåne University Hospital, Lund University, SE-214 28, Malmö, Sweden
- Department of Biobank Research, Umeå University, SE-901 87, Umeå, Sweden
| | - John Rice
- Departments of Psychiatry and Mathematics, Washington University St. Louis, St. Louis, MO, USA
| | | | - Olov Rolandsson
- Department of Public Health & Clinical Medicine, Section for Family Medicine, Umeå universitet, SE, 90185, Umeå, Sweden
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Cardiovascular Research Centre, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Maria Samuel
- Centre for Non-Communicable Diseases, Karachi, Pakistan
| | - David Schlessinger
- National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Steven H Scholte
- Department of Psychology, University of Amsterdam & Amsterdam Brain and Cognition, University of Amsterdam, Amsterdam, Netherlands
| | - Robert A Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Peter Sever
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
- International Centre for Circulatory Health, Imperial College London, London, UK
| | - Yaming Shao
- University of North Carolina, Chapel Hill, NC, USA
| | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Alzheimer Scotland Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Kathleen Stirrups
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0PT, UK
| | - Danielle Stram
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Heather M Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Jean-Claude Tardif
- Montreal Heart Institute, Montreal, Quebec, H1T 1C8, Canada
- Department of Medicine, Faculty of Medicine, Universite de Montreal, Montreal, Quebec, H3T 1J4, Canada
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Hilary A Tindle
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Vinicius Tragante
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, 3508GA, Utrecht, The Netherlands
| | - Stella Trompet
- Department of gerontology and geriatrics, Leiden University Medical Center, Leiden, The Netherlands
- Department of cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Valerie Turcot
- Montreal Heart Institute, Montreal, Quebec, H1T 1C8, Canada
| | - Jessica Tyrrell
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, UK
| | - Ilonca Vaartjes
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3508GA, Utrecht, The Netherlands
- Center for Circulatory Health, University Medical Center Utrecht, 3508GA, Utrecht, The Netherlands
| | - Andries R van der Leij
- Department of Psychology, University of Amsterdam & Amsterdam Brain and Cognition, University of Amsterdam, Amsterdam, Netherlands
| | - Peter van der Meer
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Tibor V Varga
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Skåne University Hospital, Lund University, SE-214 28, Malmö, Sweden
| | - Niek Verweij
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 301 Binney Street, Cambridge, MA, 02142, USA
| | - Henry Völzke
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, 17475, Greifswald, Germany
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Helen R Warren
- Clinical Pharmacology, William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Stefan Weiss
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt-University Greifswald, 17475, Greifswald, Germany
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Hanieh Yaghootkar
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, UK
| | - Ersin Yavas
- Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania, PA, 16802, USA
| | - Yu Jiang
- Institute of Personalized Medicine, Penn State College of Medicine, Hershey, PA, USA
| | - Fang Chen
- Institute of Personalized Medicine, Penn State College of Medicine, Hershey, PA, USA
| | - Xiaowei Zhan
- Department of Clinical Science, Center for Genetics of Host Defense, University of Texas Southwestern, Dallas, TX, USA
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Middlesex, UB1 3HW, UK
| | - Wei Zhao
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Pennsylvania, PA, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Kaixin Zhou
- School of Medicine, University of Dundee, Dundee, UK
| | - Philippe Amouyel
- Department of Epidemiology and Public Health, Institut Pasteur de Lille, Lille, France
| | - Stefan Blankenberg
- Department of General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
- University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Mark J Caulfield
- Clinical Pharmacology, William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Rajiv Chowdhury
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Emanuele Di Angelantonio
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Marco Ferrario
- EPIMED Research Centre, Department of Medicine and Surgery, University of Insubria at Varese, Varese, Italy
| | - Jean Ferrières
- Department of Epidemiology, UMR 1027- INSERM, Toulouse University-CHU Toulouse, Toulouse, France
| | - Paul W Franks
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Skåne University Hospital, Lund University, SE-214 28, Malmö, Sweden
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Tim M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, UK
| | | | - Ian P Hall
- Division of Respiratory Medicine and NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jan-Håkan Jansson
- Department of Public Health and Clinical Medicine, Skellefteå Research Unit, Umeå University, Umeå, Sweden
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- The Interuniversity Cardiology Institute of the Netherlands, Utrecht, The Netherlands
| | - Frank Kee
- UKCRC Centre of Excellence for Public Health, Queens, University, Belfast, Belfast, UK
| | - Satu Männistö
- Department of Public Health Solutions, National Institute for Health and Welfare, FI-00271, Helsinki, Finland
| | | | - Patricia B Munroe
- Clinical Pharmacology, William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Børge Grønne Nordestgaard
- Department of Clinical Biochemistry Herlev Hospital, Copenhagen University Hospital, Herlev Ringvej 74, DK-2730, Herlev, Denmark
| | - Colin N A Palmer
- Medical Research Institute, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Veikko Salomaa
- Department of Public Health Solutions, National Institute for Health and Welfare, FI-00271, Helsinki, Finland
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Timothy Spector
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, SE1 7EH, UK
| | - David Peter Strachan
- Population Health Research Institute, St George!s, University of London, London, SW17 0RE, UK
| | - Pim van der Harst
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Danish Saleheen
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, USA
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Dajiang J Liu
- Institute of Personalized Medicine, Penn State College of Medicine, Hershey, PA, USA.
| | - Joanna M M Howson
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.
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29
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Zhou W, Zhao Z, Nielsen JB, Fritsche LG, LeFaive J, Gagliano Taliun SA, Bi W, Gabrielsen ME, Daly MJ, Neale BM, Hveem K, Abecasis GR, Willer CJ, Lee S. Scalable generalized linear mixed model for region-based association tests in large biobanks and cohorts. Nat Genet 2020; 52:634-639. [PMID: 32424355 PMCID: PMC7871731 DOI: 10.1038/s41588-020-0621-6] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 03/31/2020] [Indexed: 12/13/2022]
Abstract
With very large sample sizes, biobanks provide an exciting opportunity to identify genetic components of complex traits. To analyze rare variants, region-based multiple-variant aggregate tests are commonly used to increase power for association tests. However, because of the substantial computational cost, existing region-based tests cannot analyze hundreds of thousands of samples while accounting for confounders such as population stratification and sample relatedness. Here we propose a scalable generalized mixed-model region-based association test, SAIGE-GENE, that is applicable to exome-wide and genome-wide region-based analysis for hundreds of thousands of samples and can account for unbalanced case-control ratios for binary traits. Through extensive simulation studies and analysis of the HUNT study with 69,716 Norwegian samples and the UK Biobank data with 408,910 White British samples, we show that SAIGE-GENE can efficiently analyze large-sample data (N > 400,000) with type I error rates well controlled.
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Affiliation(s)
- Wei Zhou
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Zhangchen Zhao
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jonas B Nielsen
- Division of Cardiology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lars G Fritsche
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jonathon LeFaive
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Sarah A Gagliano Taliun
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Wenjian Bi
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Maiken E Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology (NTNU), Levanger, Norway
| | - Goncalo R Abecasis
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Cristen J Willer
- Division of Cardiology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Seunggeun Lee
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA.
- Graduate School of Data Science, Seoul National University, Seoul, Republic of Korea.
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30
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Jiang Y, Chen S, Wang X, Liu M, Iacono WG, Hewitt JK, Hokanson JE, Krauter K, Laakso M, Li KW, Lutz SM, McGue M, Pandit A, Zajac GJ, Boehnke M, Abecasis GR, Vrieze SI, Jiang B, Zhan X, Liu DJ. Association Analysis and Meta-Analysis of Multi-Allelic Variants for Large-Scale Sequence Data. Genes (Basel) 2020; 11:genes11050586. [PMID: 32466134 PMCID: PMC7288273 DOI: 10.3390/genes11050586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 11/16/2022] Open
Abstract
There is great interest in understanding the impact of rare variants in human diseases using large sequence datasets. In deep sequence datasets of >10,000 samples, ~10% of the variant sites are observed to be multi-allelic. Many of the multi-allelic variants have been shown to be functional and disease-relevant. Proper analysis of multi-allelic variants is critical to the success of a sequencing study, but existing methods do not properly handle multi-allelic variants and can produce highly misleading association results. We discuss practical issues and methods to encode multi-allelic sites, conduct single-variant and gene-level association analyses, and perform meta-analysis for multi-allelic variants. We evaluated these methods through extensive simulations and the study of a large meta-analysis of ~18,000 samples on the cigarettes-per-day phenotype. We showed that our joint modeling approach provided an unbiased estimate of genetic effects, greatly improved the power of single-variant association tests among methods that can properly estimate allele effects, and enhanced gene-level tests over existing approaches. Software packages implementing these methods are available online.
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Affiliation(s)
- Yu Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA; (Y.J.); (X.W.); (D.J.L.)
| | - Sai Chen
- Illumina Inc., 5200 Illuminay Way, San Diego, CA 92122, USA;
| | - Xingyan Wang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA; (Y.J.); (X.W.); (D.J.L.)
| | - Mengzhen Liu
- Department of Psychology, University of Minnesota, Minneapolis, MN 55454, USA; (M.L.); (M.M.); (S.I.V.)
| | - William G. Iacono
- Department of Psychiatry, University of Minnesota, Minneapolis, MN 55454, USA;
| | - John K. Hewitt
- Institute for Behavioral Genetics, University of Colorado Boulder, Aurora, CO 80045, USA; (J.K.H.); (K.K.)
| | - John E. Hokanson
- Department of Epidemiology, School of Public Health, University of Colorado Denver, Aurora, CO 80045, USA;
| | - Kenneth Krauter
- Institute for Behavioral Genetics, University of Colorado Boulder, Aurora, CO 80045, USA; (J.K.H.); (K.K.)
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, 70211 Kuopio, Finland;
| | - Kevin W. Li
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; (K.W.L.); (A.P.); (G.J.M.Z.); (M.B.); (G.R.A.)
| | - Sharon M. Lutz
- Department of Biostatistics and Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA;
| | - Matthew McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN 55454, USA; (M.L.); (M.M.); (S.I.V.)
| | - Anita Pandit
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; (K.W.L.); (A.P.); (G.J.M.Z.); (M.B.); (G.R.A.)
| | - Gregory J.M. Zajac
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; (K.W.L.); (A.P.); (G.J.M.Z.); (M.B.); (G.R.A.)
| | - Michael Boehnke
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; (K.W.L.); (A.P.); (G.J.M.Z.); (M.B.); (G.R.A.)
| | - Goncalo R. Abecasis
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; (K.W.L.); (A.P.); (G.J.M.Z.); (M.B.); (G.R.A.)
| | - Scott I. Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN 55454, USA; (M.L.); (M.M.); (S.I.V.)
| | - Bibo Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA; (Y.J.); (X.W.); (D.J.L.)
- Correspondence: (B.J.); (X.Z.)
| | - Xiaowei Zhan
- Department of Clinical Science, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Correspondence: (B.J.); (X.Z.)
| | - Dajiang J. Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA; (Y.J.); (X.W.); (D.J.L.)
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31
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Damask A, Steg PG, Schwartz GG, Szarek M, Hagström E, Badimon L, Chapman MJ, Boileau C, Tsimikas S, Ginsberg HN, Banerjee P, Manvelian G, Pordy R, Hess S, Overton JD, Lotta LA, Yancopoulos GD, Abecasis GR, Baras A, Paulding C. Patients With High Genome-Wide Polygenic Risk Scores for Coronary Artery Disease May Receive Greater Clinical Benefit From Alirocumab Treatment in the ODYSSEY OUTCOMES Trial. Circulation 2019; 141:624-636. [PMID: 31707832 DOI: 10.1161/circulationaha.119.044434] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Alirocumab, an antibody that blocks PCSK9 (proprotein convertase subtilisin/kexin type 9), was associated with reduced major adverse cardiovascular events (MACE) and death in the ODYSSEY OUTCOMES trial (Evaluation of Cardiovascular Outcomes After an Acute Coronary Syndrome During Treatment With Alirocumab). In this study, higher baseline levels of low-density lipoprotein cholesterol (LDL-C) predicted greater benefit from alirocumab treatment. Recent studies indicate high polygenic risk scores (PRS) for coronary artery disease (CAD) identify individuals at higher risk who derive increased benefit from statins. We performed post hoc analyses to determine whether high PRS for CAD identifies higher-risk individuals, independent of baseline LDL-C and other known risk factors, who might derive greater benefit from alirocumab treatment. METHODS ODYSSEY OUTCOMES was a randomized, double-blind, placebo-controlled trial comparing alirocumab or placebo in 18 924 patients with acute coronary syndrome and elevated atherogenic lipoproteins despite optimized statin treatment. The primary endpoint (MACE) comprised death of CAD, nonfatal myocardial infarction, ischemic stroke, or unstable angina requiring hospitalization. A genome-wide PRS for CAD comprising 6 579 025 genetic variants was evaluated in 11 953 patients with available DNA samples. Analysis of MACE risk was performed in placebo-treated patients, whereas treatment benefit analysis was performed in all patients. RESULTS The incidence of MACE in the placebo group was related to PRS for CAD: 17.0% for high PRS patients (>90th percentile) and 11.4% for lower PRS patients (≤90th percentile; P<0.001); this PRS relationship was not explained by baseline LDL-C or other established risk factors. Both the absolute and relative reduction of MACE by alirocumab compared with placebo was greater in high versus low PRS patients. There was an absolute reduction by alirocumab in high versus low PRS groups of 6.0% and 1.5%, respectively, and a relative risk reduction by alirocumab of 37% in the high PRS group (hazard ratio, 0.63 [95% CI, 0.46-0.86]; P=0.004) versus a 13% reduction in the low PRS group (hazard ratio, 0.87 [95% CI, 0.78-0.98]; P=0.022; interaction P=0.04). CONCLUSIONS A high PRS for CAD is associated with elevated risk for recurrent MACE after acute coronary syndrome and a larger absolute and relative risk reduction with alirocumab treatment, providing an independent tool for risk stratification and precision medicine.
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Affiliation(s)
- Amy Damask
- Regeneron Pharmaceuticals Inc, Tarrytown, NY (A.D., P.B., G.M., R.P., J.D.O., L.A.L., G.D.Y., G.R.A., A.B., C.P.)
| | - P Gabriel Steg
- Université de Paris, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, INSERM U1148, France (P.G.S.)
| | | | - Michael Szarek
- Department of Biostatistics and Epidemiology, SUNY Downstate School of Public Health, Brooklyn, NY (M.S.)
| | - Emil Hagström
- Department of Medical Sciences, Cardiology, Uppsala University, Sweden (E.H.)
| | - Lina Badimon
- Cardiovascular Program-ICCC, CiberCV, IR-Hospital de la Santa Creu i Sant Pau, Barcelona, Spain (L.B.)
| | - M John Chapman
- Endocrinology Metabolism Division, Pitie-Salpetriere University Hospital, Sorbonne University and National Institute for Health and Medical Research (INSERM), Paris, France (M.J.C.)
| | - Catherine Boileau
- Université de Paris, INSERM U1148 and Genetics Department, APHP-Hospital Bichat-Claude Bernard, France (C.B.)
| | - Sotirios Tsimikas
- Sulpizio Cardiovascular Center, Division of Cardiovascular Medicine, University of California San Diego, La Jolla (S.T.)
| | - Henry N Ginsberg
- Irving Institute for Clinical and Translational Research, Columbia University, New York (H.N.G.)
| | - Poulabi Banerjee
- Regeneron Pharmaceuticals Inc, Tarrytown, NY (A.D., P.B., G.M., R.P., J.D.O., L.A.L., G.D.Y., G.R.A., A.B., C.P.)
| | - Garen Manvelian
- Regeneron Pharmaceuticals Inc, Tarrytown, NY (A.D., P.B., G.M., R.P., J.D.O., L.A.L., G.D.Y., G.R.A., A.B., C.P.)
| | - Robert Pordy
- Regeneron Pharmaceuticals Inc, Tarrytown, NY (A.D., P.B., G.M., R.P., J.D.O., L.A.L., G.D.Y., G.R.A., A.B., C.P.)
| | - Sibylle Hess
- Sanofi Aventis Deutschland GmbH, Translational Medicine and Early Development, Biomarkers and Clinical Bioanalyses, Frankfurt, Germany (S.H.)
| | - John D Overton
- Regeneron Pharmaceuticals Inc, Tarrytown, NY (A.D., P.B., G.M., R.P., J.D.O., L.A.L., G.D.Y., G.R.A., A.B., C.P.)
| | - Luca A Lotta
- Regeneron Pharmaceuticals Inc, Tarrytown, NY (A.D., P.B., G.M., R.P., J.D.O., L.A.L., G.D.Y., G.R.A., A.B., C.P.)
| | - George D Yancopoulos
- Regeneron Pharmaceuticals Inc, Tarrytown, NY (A.D., P.B., G.M., R.P., J.D.O., L.A.L., G.D.Y., G.R.A., A.B., C.P.)
| | - Goncalo R Abecasis
- Regeneron Pharmaceuticals Inc, Tarrytown, NY (A.D., P.B., G.M., R.P., J.D.O., L.A.L., G.D.Y., G.R.A., A.B., C.P.)
| | - Aris Baras
- Regeneron Pharmaceuticals Inc, Tarrytown, NY (A.D., P.B., G.M., R.P., J.D.O., L.A.L., G.D.Y., G.R.A., A.B., C.P.)
| | - Charles Paulding
- Regeneron Pharmaceuticals Inc, Tarrytown, NY (A.D., P.B., G.M., R.P., J.D.O., L.A.L., G.D.Y., G.R.A., A.B., C.P.)
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32
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Graham SE, Nielsen JB, Zawistowski M, Zhou W, Fritsche LG, Gabrielsen ME, Skogholt AH, Surakka I, Hornsby WE, Fermin D, Larach DB, Kheterpal S, Brummett CM, Lee S, Kang HM, Abecasis GR, Romundstad S, Hallan S, Sampson MG, Hveem K, Willer CJ. Sex-specific and pleiotropic effects underlying kidney function identified from GWAS meta-analysis. Nat Commun 2019; 10:1847. [PMID: 31015462 PMCID: PMC6478837 DOI: 10.1038/s41467-019-09861-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 04/03/2019] [Indexed: 12/19/2022] Open
Abstract
Chronic kidney disease (CKD) is a growing health burden currently affecting 10–15% of adults worldwide. Estimated glomerular filtration rate (eGFR) as a marker of kidney function is commonly used to diagnose CKD. We analyze eGFR data from the Nord-Trøndelag Health Study and Michigan Genomics Initiative and perform a GWAS meta-analysis with public summary statistics, more than doubling the sample size of previous meta-analyses. We identify 147 loci (53 novel) associated with eGFR, including genes involved in transcriptional regulation, kidney development, cellular signaling, metabolism, and solute transport. Additionally, sex-stratified analysis identifies one locus with more significant effects in women than men. Using genetic risk scores constructed from these eGFR meta-analysis results, we show that associated variants are generally predictive of CKD with only modest improvements in detection compared with other known clinical risk factors. Collectively, these results yield additional insight into the genetic factors underlying kidney function and progression to CKD. Estimated glomerular filtration rate (eGFR) is a measure of kidney function and used to characterize chronic kidney disease. Here, Graham et al. identify 53 novel loci for eGFR in a GWAS meta-analysis, a subset of which are associated with other common diseases, such as diabetes and hypertension, based on PheWAS.
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Affiliation(s)
- Sarah E Graham
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Jonas B Nielsen
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Matthew Zawistowski
- Department of Biostatistics: Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Lars G Fritsche
- Department of Biostatistics: Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Maiken E Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway.,Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | - Anne Heidi Skogholt
- K.G. Jebsen Center for Genetic Epidemiology, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway.,Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway.,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | - Ida Surakka
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Whitney E Hornsby
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Damian Fermin
- Department of Pediatrics: Pediatric Nephrology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Daniel B Larach
- Department of Anesthesiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Sachin Kheterpal
- Department of Anesthesiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Chad M Brummett
- Department of Anesthesiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Seunggeun Lee
- Department of Biostatistics: Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Hyun Min Kang
- Department of Biostatistics: Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Goncalo R Abecasis
- Department of Biostatistics: Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Solfrid Romundstad
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway.,Department of Internal Medicine, Levanger Hospital, Health Trust Nord-Trøndelag, Levanger, 7600, Norway
| | - Stein Hallan
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway.,Department of Nephrology, St Olav Hospital, Trondheim, 7491, Norway
| | - Matthew G Sampson
- Department of Pediatrics: Pediatric Nephrology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway. .,Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway. .,HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, 7600, Norway.
| | - Cristen J Willer
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, 48109, MI, USA. .,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, MI, USA. .,Department of Human Genetics, University of Michigan, Ann Arbor, 48109, MI, USA.
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33
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Bien SA, Su YR, Conti DV, Harrison TA, Qu C, Guo X, Lu Y, Albanes D, Auer PL, Banbury BL, Berndt SI, Bézieau S, Brenner H, Buchanan DD, Caan BJ, Campbell PT, Carlson CS, Chan AT, Chang-Claude J, Chen S, Connolly CM, Easton DF, Feskens EJM, Gallinger S, Giles GG, Gunter MJ, Hampe J, Huyghe JR, Hoffmeister M, Hudson TJ, Jacobs EJ, Jenkins MA, Kampman E, Kang HM, Kühn T, Küry S, Lejbkowicz F, Le Marchand L, Milne RL, Li L, Li CI, Lindblom A, Lindor NM, Martín V, McNeil CE, Melas M, Moreno V, Newcomb PA, Offit K, Pharaoh PDP, Potter JD, Qu C, Riboli E, Rennert G, Sala N, Schafmayer C, Scacheri PC, Schmit SL, Severi G, Slattery ML, Smith JD, Trichopoulou A, Tumino R, Ulrich CM, van Duijnhoven FJB, Van Guelpen B, Weinstein SJ, White E, Wolk A, Woods MO, Wu AH, Abecasis GR, Casey G, Nickerson DA, Gruber SB, Hsu L, Zheng W, Peters U. Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer. Hum Genet 2019; 138:307-326. [PMID: 30820706 PMCID: PMC6483948 DOI: 10.1007/s00439-019-01989-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/20/2019] [Indexed: 02/02/2023]
Abstract
Genome-wide association studies have reported 56 independently associated colorectal cancer (CRC) risk variants, most of which are non-coding and believed to exert their effects by modulating gene expression. The computational method PrediXcan uses cis-regulatory variant predictors to impute expression and perform gene-level association tests in GWAS without directly measured transcriptomes. In this study, we used reference datasets from colon (n = 169) and whole blood (n = 922) transcriptomes to test CRC association with genetically determined expression levels in a genome-wide analysis of 12,186 cases and 14,718 controls. Three novel associations were discovered from colon transverse models at FDR ≤ 0.2 and further evaluated in an independent replication including 32,825 cases and 39,933 controls. After adjusting for multiple comparisons, we found statistically significant associations using colon transcriptome models with TRIM4 (discovery P = 2.2 × 10- 4, replication P = 0.01), and PYGL (discovery P = 2.3 × 10- 4, replication P = 6.7 × 10- 4). Interestingly, both genes encode proteins that influence redox homeostasis and are related to cellular metabolic reprogramming in tumors, implicating a novel CRC pathway linked to cell growth and proliferation. Defining CRC risk regions as one megabase up- and downstream of one of the 56 independent risk variants, we defined 44 non-overlapping CRC-risk regions. Among these risk regions, we identified genes associated with CRC (P < 0.05) in 34/44 CRC-risk regions. Importantly, CRC association was found for two genes in the previously reported 2q25 locus, CXCR1 and CXCR2, which are potential cancer therapeutic targets. These findings provide strong candidate genes to prioritize for subsequent laboratory follow-up of GWAS loci. This study is the first to implement PrediXcan in a large colorectal cancer study and findings highlight the utility of integrating transcriptome data in GWAS for discovery of, and biological insight into, risk loci.
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Affiliation(s)
- Stephanie A Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
| | - Yu-Ru Su
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - David V Conti
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Tabitha A Harrison
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Conghui Qu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Xingyi Guo
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Yingchang Lu
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, 53205, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Barbara L Banbury
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Stéphane Bézieau
- Centre Hospitalier Universitaire Hotel-Dieu, 44093, Nantes, France
- Service de Génétique Médiczle, Centre Hospitalier Universitaire (CHU), 44093, Nantes, France
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Colorectal Oncogenomics Group, Department of Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia
- Genetic Medicine and Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, VIC, 3010, Australia
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program of Northern California, Oakland, CA, 94612, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Peter T Campbell
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30329-4251, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Christopher S Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jenny Chang-Claude
- Unit of Genetic Epidemiology, Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Genetic Tumour Epidemiology Group, University Medical Center Hamburg-Eppendorf, University Cancer Center Hamburg, 20246, Hamburg, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Sai Chen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Charles M Connolly
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care School of Clinical Medicine, University of Cambridge, Cambridge, England, 01223, UK
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Edith J M Feskens
- Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, 1X5, Canada
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, 3004, Australia
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Marc J Gunter
- Section for Epidemiology, Department of Public Health, Aarhus University, Aarhus, Denmark
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, TU Dresden, 01307, Dresden, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jeroen R Huyghe
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- AbbVie Inc, 1500 Seaport Blvd, Redwood City, CA, 94063, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Eric J Jacobs
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30329-4251, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Ellen Kampman
- Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Hyun Min Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Tilman Kühn
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Sébastien Küry
- Centre Hospitalier Universitaire Hotel-Dieu, 44093, Nantes, France
- Service de Génétique Médiczle, Centre Hospitalier Universitaire (CHU), 44093, Nantes, France
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Flavio Lejbkowicz
- Clalit Health Services National Israeli Cancer Control Center, 34361, Haifa, Israel
- Department of Community Medicine and Epidemiology, Carmel Medical Center, 34361, Haifa, Israel
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Loic Le Marchand
- University of Hawai'i Cancer Center, Honolulu, Hawaii, 96813, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, 3004, Australia
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Li Li
- Department of Family Medicine and Community Health, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Christopher I Li
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital Solna, 171 77, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet Solna, 171 77, Stockholm, Sweden
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, AZ, 85259, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Vicente Martín
- Biomedicine Institute (IBIOMED), University of León, León, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Caroline E McNeil
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Marilena Melas
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Victor Moreno
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), 08028, Barcelona, Spain
- University of Barcelona, 08007, Barcelona, Spain
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Polly A Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Kenneth Offit
- Department of Medicine, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Paul D P Pharaoh
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB2 1TN, UK
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - John D Potter
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Chenxu Qu
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Gad Rennert
- Clalit Health Services National Israeli Cancer Control Center, 34361, Haifa, Israel
- Department of Community Medicine and Epidemiology, Carmel Medical Center, 34361, Haifa, Israel
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Núria Sala
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Molecular Epidemiology Group, Translational Research Laboratory, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Clemens Schafmayer
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein, Campus Kiel, 24118, Kiel, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Inc, Tampa, FL, 33612, USA
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Inc, Tampa, FL, 33612, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Gianluca Severi
- Centre for Research in Epidemiology and Population Health, Institut de Cancérologie Gustave Roussy, Villejuif, France
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Joshua D Smith
- Department Genome Sciences, University of Washington, 98195, Seattle, WA, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Antonia Trichopoulou
- Hellenic Health Foundation, 13 Kaisareias & Alexandroupoleos, 115 27, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Mikras Asias 75, 115 27, Athens, Greece
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Rosario Tumino
- Affiliation Cancer Registry, Department of Prevention, Azienda Sanitaria Provinciale di Ragusa, Ragusa, Italy
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Cornelia M Ulrich
- Population Sciences, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Fränzel J B van Duijnhoven
- Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Bethany Van Guelpen
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet Solna, 17177, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, 75121, Uppsala, Sweden
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Michael O Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, Saint John's, NL, A1B 3V6, Canada
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Anna H Wu
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Goncalo R Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Graham Casey
- Centre for Research in Epidemiology and Population Health, Institut de Cancérologie Gustave Roussy, Villejuif, France
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Deborah A Nickerson
- Department Genome Sciences, University of Washington, 98195, Seattle, WA, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Stephen B Gruber
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Li Hsu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, 37232, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
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Huyghe JR, Bien SA, Harrison TA, Kang HM, Chen S, Schmit SL, Conti DV, Qu C, Jeon J, Edlund CK, Greenside P, Wainberg M, Schumacher FR, Smith JD, Levine DM, Nelson SC, Sinnott-Armstrong NA, Albanes D, Alonso MH, Anderson K, Arnau-Collell C, Arndt V, Bamia C, Banbury BL, Baron JA, Berndt SI, Bézieau S, Bishop DT, Boehm J, Boeing H, Brenner H, Brezina S, Buch S, Buchanan DD, Burnett-Hartman A, Butterbach K, Caan BJ, Campbell PT, Carlson CS, Castellví-Bel S, Chan AT, Chang-Claude J, Chanock SJ, Chirlaque MD, Cho SH, Connolly CM, Cross AJ, Cuk K, Curtis KR, de la Chapelle A, Doheny KF, Duggan D, Easton DF, Elias SG, Elliott F, English DR, Feskens EJM, Figueiredo JC, Fischer R, FitzGerald LM, Forman D, Gala M, Gallinger S, Gauderman WJ, Giles GG, Gillanders E, Gong J, Goodman PJ, Grady WM, Grove JS, Gsur A, Gunter MJ, Haile RW, Hampe J, Hampel H, Harlid S, Hayes RB, Hofer P, Hoffmeister M, Hopper JL, Hsu WL, Huang WY, Hudson TJ, Hunter DJ, Ibañez-Sanz G, Idos GE, Ingersoll R, Jackson RD, Jacobs EJ, Jenkins MA, Joshi AD, Joshu CE, Keku TO, Key TJ, Kim HR, Kobayashi E, Kolonel LN, Kooperberg C, Kühn T, Küry S, Kweon SS, Larsson SC, Laurie CA, Le Marchand L, Leal SM, Lee SC, Lejbkowicz F, Lemire M, Li CI, Li L, Lieb W, Lin Y, Lindblom A, Lindor NM, Ling H, Louie TL, Männistö S, Markowitz SD, Martín V, Masala G, McNeil CE, Melas M, Milne RL, Moreno L, Murphy N, Myte R, Naccarati A, Newcomb PA, Offit K, Ogino S, Onland-Moret NC, Pardini B, Parfrey PS, Pearlman R, Perduca V, Pharoah PDP, Pinchev M, Platz EA, Prentice RL, Pugh E, Raskin L, Rennert G, Rennert HS, Riboli E, Rodríguez-Barranco M, Romm J, Sakoda LC, Schafmayer C, Schoen RE, Seminara D, Shah M, Shelford T, Shin MH, Shulman K, Sieri S, Slattery ML, Southey MC, Stadler ZK, Stegmaier C, Su YR, Tangen CM, Thibodeau SN, Thomas DC, Thomas SS, Toland AE, Trichopoulou A, Ulrich CM, Van Den Berg DJ, van Duijnhoven FJB, Van Guelpen B, van Kranen H, Vijai J, Visvanathan K, Vodicka P, Vodickova L, Vymetalkova V, Weigl K, Weinstein SJ, White E, Win AK, Wolf CR, Wolk A, Woods MO, Wu AH, Zaidi SH, Zanke BW, Zhang Q, Zheng W, Scacheri PC, Potter JD, Bassik MC, Kundaje A, Casey G, Moreno V, Abecasis GR, Nickerson DA, Gruber SB, Hsu L, Peters U. Discovery of common and rare genetic risk variants for colorectal cancer. Nat Genet 2019; 51:76-87. [PMID: 30510241 PMCID: PMC6358437 DOI: 10.1038/s41588-018-0286-6] [Citation(s) in RCA: 293] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/22/2018] [Indexed: 12/17/2022]
Abstract
To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 × 10-8, bringing the number of known independent signals for CRC to ~100. New signals implicate lower-frequency variants, Krüppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.
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Affiliation(s)
- Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Sai Chen
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - David V Conti
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jihyoun Jeon
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Christopher K Edlund
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Peyton Greenside
- Biomedical Informatics Program, Stanford University, Stanford, CA, USA
| | - Michael Wainberg
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Joshua D Smith
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David M Levine
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Sarah C Nelson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - M Henar Alonso
- Cancer Prevention and Control Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Kristin Anderson
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Coral Arnau-Collell
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christina Bamia
- Hellenic Health Foundation, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Barbara L Banbury
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John A Baron
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes, France
| | - D Timothy Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Juergen Boehm
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition (DIfE), Potsdam-Rehbrücke, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | | | - Katja Butterbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program, Oakland, CA, USA
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Christopher S Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria-Dolores Chirlaque
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Epidemiology, Regional Health Council, IMIB-Arrixaca, Murcia University, Murcia, Spain
| | - Sang Hee Cho
- Department of Hematology-Oncology, Chonnam National University Hospital, Hwasun, South Korea
| | - Charles M Connolly
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Amanda J Cross
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Katarina Cuk
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Keith R Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Kimberly F Doheny
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David Duggan
- Translational Genomics Research Institute - An Affiliate of City of Hope, Phoenix, AZ, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Sjoerd G Elias
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Faye Elliott
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Dallas R English
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Edith J M Feskens
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, The Netherlands
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rocky Fischer
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI, USA
| | - Liesel M FitzGerald
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - David Forman
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - W James Gauderman
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Elizabeth Gillanders
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, USA
| | - Jian Gong
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John S Grove
- University of Hawaii Cancer Research Center, Honolulu, HI, USA
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Robert W Haile
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Philipp Hofer
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Epidemiology, School of Public Health and Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Wan-Ling Hsu
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Gemma Ibañez-Sanz
- Cancer Prevention and Control Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Gastroenterology Department, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Gregory E Idos
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Roxann Ingersoll
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Rebecca D Jackson
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, OH, USA
| | - Eric J Jacobs
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Corinne E Joshu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA
| | - Timothy J Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Hyeong Rok Kim
- Department of Surgery, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | - Emiko Kobayashi
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Laurence N Kolonel
- Office of Public Health Studies, University of Hawaii Manoa, Honolulu, HI, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tilman Kühn
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sébastien Küry
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes, France
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Korea
- Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Susanna C Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Soo Chin Lee
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Flavio Lejbkowicz
- The Clalit Health Services, Personalized Genomic Service, Carmel, Haifa, Israel
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Li Li
- Center for Community Health Integration and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Wolfgang Lieb
- Institute of Epidemiology, PopGen Biobank, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, AZ, USA
| | - Hua Ling
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Tin L Louie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Satu Männistö
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Sanford D Markowitz
- Departments of Medicine and Genetics, Case Comprehensive Cancer Center, Case Western Reserve University, and University Hospitals of Cleveland, Cleveland, OH, USA
| | - Vicente Martín
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Biomedicine Institute (IBIOMED), University of León, León, Spain
| | - Giovanna Masala
- Cancer Risk Factors and Life-Style Epidemiology Unit, Institute of Cancer Research, Prevention and Clinical Network - ISPRO, Florence, Italy
| | - Caroline E McNeil
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Marilena Melas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Lorena Moreno
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Neil Murphy
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Robin Myte
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Alessio Naccarati
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Shuji Ogino
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - N Charlotte Onland-Moret
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Patrick S Parfrey
- The Clinical Epidemiology Unit, Memorial University Medical School, Newfoundland, Canada
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Vittorio Perduca
- Laboratoire de Mathématiques Appliquées MAP5 (UMR CNRS 8145), Université Paris Descartes, Paris, France
- CESP (Inserm U1018), Facultés de Medicine Université Paris-Sud, UVSQ, Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Mila Pinchev
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ross L Prentice
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elizabeth Pugh
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Leon Raskin
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hedy S Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
| | - Miguel Rodríguez-Barranco
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Escuela Andaluza de Salud Pública. Instituto de Investigación Biosanitaria ibs.GRANADA, Hospitales Universitarios de Granada, Universidad de Granada, Granada, Spain
| | - Jane Romm
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Clemens Schafmayer
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, USA
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Tameka Shelford
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Korea
| | | | - Sabina Sieri
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yu-Ru Su
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Duncan C Thomas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sushma S Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Amanda E Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Antonia Trichopoulou
- Hellenic Health Foundation, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - David J Van Den Berg
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Henk van Kranen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Korbinian Weigl
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Aung Ko Win
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - C Roland Wolf
- School of Medicine, University of Dundee, Dundee, Scotland, UK
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St. John's, Newfoundland, Canada
| | - Anna H Wu
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Brent W Zanke
- Division of Hematology, University of Toronto, Toronto, Ontario, Canada
| | - Qing Zhang
- Genomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Epidemiology, University of Washington, Seattle, WA, USA.
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Sivakumaran TA, Igo RP, Kidd JM, Itsara A, Kopplin LJ, Chen W, Hagstrom SA, Peachey NS, Francis PJ, Klein ML, Chew EY, Ramprasad VL, Tay WT, Mitchell P, Seielstad M, Stambolian DE, Edwards AO, Lee KE, Leontiev DV, Jun G, Wang Y, Tian L, Qiu F, Henning AK, LaFramboise T, Sen P, Aarthi M, George R, Raman R, Das MK, Vijaya L, Kumaramanickavel G, Wong TY, Swaroop A, Abecasis GR, Klein R, Klein BEK, Nickerson DA, Eichler EE, Iyengar SK. Correction: A 32 kb Critical Region Excluding Y402H in CFH Mediates Risk for Age-Related Macular Degeneration. PLoS One 2018; 13:e0209943. [PMID: 30571798 PMCID: PMC6301675 DOI: 10.1371/journal.pone.0209943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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36
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Regier AA, Farjoun Y, Larson DE, Krasheninina O, Kang HM, Howrigan DP, Chen BJ, Kher M, Banks E, Ames DC, English AC, Li H, Xing J, Zhang Y, Matise T, Abecasis GR, Salerno W, Zody MC, Neale BM, Hall IM. Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects. Nat Commun 2018; 9:4038. [PMID: 30279509 PMCID: PMC6168605 DOI: 10.1038/s41467-018-06159-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/16/2018] [Indexed: 12/30/2022] Open
Abstract
Hundreds of thousands of human whole genome sequencing (WGS) datasets will be generated over the next few years. These data are more valuable in aggregate: joint analysis of genomes from many sources increases sample size and statistical power. A central challenge for joint analysis is that different WGS data processing pipelines cause substantial differences in variant calling in combined datasets, necessitating computationally expensive reprocessing. This approach is no longer tenable given the scale of current studies and data volumes. Here, we define WGS data processing standards that allow different groups to produce functionally equivalent (FE) results, yet still innovate on data processing pipelines. We present initial FE pipelines developed at five genome centers and show that they yield similar variant calling results and produce significantly less variability than sequencing replicates. This work alleviates a key technical bottleneck for genome aggregation and helps lay the foundation for community-wide human genetics studies. Sharing of whole genome sequencing (WGS) data improves study scale and power, but data from different groups are often incompatible. Here, US genome centers and NIH programs define WGS data processing standards and a flexible validation method, facilitating collaboration in human genetics research.
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Affiliation(s)
- Allison A Regier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA
| | - Yossi Farjoun
- Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA
| | - David E Larson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA
| | - Olga Krasheninina
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, 77030, TX, USA
| | - Hyun Min Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, 48109, MI, USA
| | | | - Bo-Juen Chen
- New York Genome Center, New York, 10013, NY, USA.,Google, New York, 10011, NY, USA
| | - Manisha Kher
- New York Genome Center, New York, 10013, NY, USA
| | - Eric Banks
- Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA
| | | | | | - Heng Li
- Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers University, Piscataway, 08854, NJ, USA
| | - Yeting Zhang
- Department of Genetics, Rutgers University, Piscataway, 08854, NJ, USA
| | - Tara Matise
- Department of Genetics, Rutgers University, Piscataway, 08854, NJ, USA
| | - Goncalo R Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Will Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, 77030, TX, USA
| | | | - Benjamin M Neale
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, 02114, MA, USA
| | - Ira M Hall
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA.
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37
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Jiang Y, Chen S, McGuire D, Chen F, Liu M, Iacono WG, Hewitt JK, Hokanson JE, Krauter K, Laakso M, Li KW, Lutz SM, McGue M, Pandit A, Zajac GJM, Boehnke M, Abecasis GR, Vrieze SI, Zhan X, Jiang B, Liu DJ. Proper conditional analysis in the presence of missing data: Application to large scale meta-analysis of tobacco use phenotypes. PLoS Genet 2018; 14:e1007452. [PMID: 30016313 PMCID: PMC6063450 DOI: 10.1371/journal.pgen.1007452] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 07/27/2018] [Accepted: 05/25/2018] [Indexed: 11/19/2022] Open
Abstract
Meta-analysis of genetic association studies increases sample size and the power for mapping complex traits. Existing methods are mostly developed for datasets without missing values, i.e. the summary association statistics are measured for all variants in contributing studies. In practice, genotype imputation is not always effective. This may be the case when targeted genotyping/sequencing assays are used or when the un-typed genetic variant is rare. Therefore, contributed summary statistics often contain missing values. Existing methods for imputing missing summary association statistics and using imputed values in meta-analysis, approximate conditional analysis, or simple strategies such as complete case analysis all have theoretical limitations. Applying these approaches can bias genetic effect estimates and lead to seriously inflated type-I or type-II errors in conditional analysis, which is a critical tool for identifying independently associated variants. To address this challenge and complement imputation methods, we developed a method to combine summary statistics across participating studies and consistently estimate joint effects, even when the contributed summary statistics contain large amounts of missing values. Based on this estimator, we proposed a score statistic called PCBS (partial correlation based score statistic) for conditional analysis of single-variant and gene-level associations. Through extensive analysis of simulated and real data, we showed that the new method produces well-calibrated type-I errors and is substantially more powerful than existing approaches. We applied the proposed approach to one of the largest meta-analyses to date for the cigarettes-per-day phenotype. Using the new method, we identified multiple novel independently associated variants at known loci for tobacco use, which were otherwise missed by alternative methods. Together, the phenotypic variance explained by these variants was 1.1%, improving that of previously reported associations by 71%. These findings illustrate the extent of locus allelic heterogeneity and can help pinpoint causal variants. It is of great interest to estimate the joint effects of multiple variants from large scale meta-analyses, in order to fine-map causal variants and understand the genetic architecture for complex traits. The summary association statistics from participating studies in a meta-analysis often contain missing values at some variant sites, as the imputation methods may not work well and the variants with low imputation quality will be filtered out. Missingness is especially likely when the underlying genetic variant is rare or the participating studies use targeted genotyping array that is not suitable for imputation. Existing methods for conditional meta-analysis do not properly handle missing data, and can incorrectly estimate correlations between score statistics. As a result, they can produce highly inflated type-I errors for conditional analysis, which will result in overestimated phenotypic variance explained and incorrect identification of causal variants. We systematically evaluated this bias and proposed a novel partial correlation based score statistic. The new statistic has valid type-I errors for conditional analysis and much higher power than the existing methods, even when the contributed summary statistics contain a large fraction of missing values. We expect this method to be highly useful in the sequencing age for complex trait genetics.
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Affiliation(s)
- Yu Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania, United States of America
| | - Sai Chen
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Daniel McGuire
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania, United States of America
| | - Fang Chen
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania, United States of America
| | - Mengzhen Liu
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - William G. Iacono
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - John K. Hewitt
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - John E. Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Kenneth Krauter
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Kevin W. Li
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sharon M. Lutz
- Department of Biostatistics and Informatics, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Matthew McGue
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Anita Pandit
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gregory J. M. Zajac
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Michael Boehnke
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Goncalo R. Abecasis
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Scott I. Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Xiaowei Zhan
- Department of Clinical Science, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Bibo Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania, United States of America
- * E-mail: (DJL); (BJ)
| | - Dajiang J. Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania, United States of America
- * E-mail: (DJL); (BJ)
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38
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Gusarova V, O'Dushlaine C, Teslovich TM, Benotti PN, Mirshahi T, Gottesman O, Van Hout CV, Murray MF, Mahajan A, Nielsen JB, Fritsche L, Wulff AB, Gudbjartsson DF, Sjögren M, Emdin CA, Scott RA, Lee WJ, Small A, Kwee LC, Dwivedi OP, Prasad RB, Bruse S, Lopez AE, Penn J, Marcketta A, Leader JB, Still CD, Kirchner HL, Mirshahi UL, Wardeh AH, Hartle CM, Habegger L, Fetterolf SN, Tusie-Luna T, Morris AP, Holm H, Steinthorsdottir V, Sulem P, Thorsteinsdottir U, Rotter JI, Chuang LM, Damrauer S, Birtwell D, Brummett CM, Khera AV, Natarajan P, Orho-Melander M, Flannick J, Lotta LA, Willer CJ, Holmen OL, Ritchie MD, Ledbetter DH, Murphy AJ, Borecki IB, Reid JG, Overton JD, Hansson O, Groop L, Shah SH, Kraus WE, Rader DJ, Chen YDI, Hveem K, Wareham NJ, Kathiresan S, Melander O, Stefansson K, Nordestgaard BG, Tybjærg-Hansen A, Abecasis GR, Altshuler D, Florez JC, Boehnke M, McCarthy MI, Yancopoulos GD, Carey DJ, Shuldiner AR, Baras A, Dewey FE, Gromada J. Genetic inactivation of ANGPTL4 improves glucose homeostasis and is associated with reduced risk of diabetes. Nat Commun 2018; 9:2252. [PMID: 29899519 PMCID: PMC5997992 DOI: 10.1038/s41467-018-04611-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/10/2018] [Indexed: 01/05/2023] Open
Abstract
Angiopoietin-like 4 (ANGPTL4) is an endogenous inhibitor of lipoprotein lipase that modulates lipid levels, coronary atherosclerosis risk, and nutrient partitioning. We hypothesize that loss of ANGPTL4 function might improve glucose homeostasis and decrease risk of type 2 diabetes (T2D). We investigate protein-altering variants in ANGPTL4 among 58,124 participants in the DiscovEHR human genetics study, with follow-up studies in 82,766 T2D cases and 498,761 controls. Carriers of p.E40K, a variant that abolishes ANGPTL4 ability to inhibit lipoprotein lipase, have lower odds of T2D (odds ratio 0.89, 95% confidence interval 0.85–0.92, p = 6.3 × 10−10), lower fasting glucose, and greater insulin sensitivity. Predicted loss-of-function variants are associated with lower odds of T2D among 32,015 cases and 84,006 controls (odds ratio 0.71, 95% confidence interval 0.49–0.99, p = 0.041). Functional studies in Angptl4-deficient mice confirm improved insulin sensitivity and glucose homeostasis. In conclusion, genetic inactivation of ANGPTL4 is associated with improved glucose homeostasis and reduced risk of T2D. Genetic variation in ANGPTL4 is associated with lipid traits. Here, the authors find that predicted loss-of-function variants in ANGPTL4 are associated with glucose homeostasis and reduced risk of type 2 diabetes and that Angptl4−/− mice on a high-fat diet show improved insulin sensitivity.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Jonas B Nielsen
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, University of Michigan, Ann Arbor, 48109, MI, USA.,Department of Human Genetics, University of Michigan, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Lars Fritsche
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Anders Berg Wulff
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen, 2100, Denmark
| | | | - Marketa Sjögren
- Department of Clinical Sciences, Malmö, Lund University, Malmö, 221, Sweden
| | - Connor A Emdin
- Program in Medical and Population Genetics, Broad Institute, Cambridge, 02142, MA, USA
| | - Robert A Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, 40705, Taiwan.,Department of Social Work, Tunghai University, Taichung, 40704, Taiwan
| | - Aeron Small
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, PA, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, USA
| | - Lydia C Kwee
- Division of Cardiology, Department of Medicine; Molecular Physiology Institute, School of Medicine, Duke University, Durham, 27710, NC, USA
| | - Om Prakash Dwivedi
- Finnish Institute of Molecular Medicine (FIMM), Helsinki University, Helsinki, 00170, Finland
| | - Rashmi B Prasad
- Department of Clinical Sciences, Clinical Research Centre, Lund University, Malmö, 221, Sweden
| | - Shannon Bruse
- Regeneron Genetics Center, Tarrytown, 10591, NY, USA
| | | | - John Penn
- Regeneron Genetics Center, Tarrytown, 10591, NY, USA
| | | | | | | | | | | | | | | | | | | | - Teresa Tusie-Luna
- Instituto de Investigaciones Biomédicas, UNAM, Coyoacán, 04510, Mexico City, Mexico.,Unidad de Biología Molecular y Medicina Genómica, UNAM/INCMNSZ Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, 14080, Mexico
| | - Andrew P Morris
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,Department of Biostatistics, University of Liverpool, Liverpool, L69 7ZX, UK.,Estonian Genome Center, University of Tartu, Tartu, 50090, Estonia
| | - Hilma Holm
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
| | | | - Patrick Sulem
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
| | | | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, LABioMed at Harbor-UCLA Medical Center, Torrance, 90502, CA, USA
| | - Lee-Ming Chuang
- Division of Endocrinology & Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, 10617, Taiwan.,Institute of Preventive Medicine, School of Public Health, National Taiwan University, Taipei, 10617, Taiwan
| | - Scott Damrauer
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, PA, USA.,Department of Surgery, Corporal Michael Crescenz VA Medical Center, Philadelphia, 19104, PA, USA
| | - David Birtwell
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, PA, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, USA
| | - Chad M Brummett
- Department of Anesthesiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Amit V Khera
- Program in Medical and Population Genetics, Broad Institute, Cambridge, 02142, MA, USA.,Center for Human Genetic Research, Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, 02114, MA, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute, Cambridge, 02142, MA, USA.,Center for Human Genetic Research, Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, 02114, MA, USA
| | | | - Jason Flannick
- Program in Medical and Population Genetics, Broad Institute, Cambridge, 02142, MA, USA.,Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, 02114, MA, USA
| | - Luca A Lotta
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, University of Michigan, Ann Arbor, 48109, MI, USA.,Department of Human Genetics, University of Michigan, University of Michigan, Ann Arbor, 48109, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Oddgeir L Holmen
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, 7601, Norway
| | | | | | | | | | | | | | - Ola Hansson
- Finnish Institute of Molecular Medicine (FIMM), Helsinki University, Helsinki, 00170, Finland.,Department of Clinical Sciences, Clinical Research Centre, Lund University, Malmö, 221, Sweden
| | - Leif Groop
- Finnish Institute of Molecular Medicine (FIMM), Helsinki University, Helsinki, 00170, Finland.,Department of Clinical Sciences, Clinical Research Centre, Lund University, Malmö, 221, Sweden
| | - Svati H Shah
- Division of Cardiology, Department of Medicine; Molecular Physiology Institute, School of Medicine, Duke University, Durham, 27710, NC, USA
| | - William E Kraus
- Division of Cardiology, Department of Medicine; Molecular Physiology Institute, School of Medicine, Duke University, Durham, 27710, NC, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, PA, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, USA
| | - Yii-Der I Chen
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, LABioMed at Harbor-UCLA Medical Center, Torrance, 90502, CA, USA
| | - Kristian Hveem
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, 7601, Norway.,K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health, Norwegian University of Science and Technology, Trondheim, 7491, Norway.,Department of Medicine, Levanger Hospital, Nord-Trøndelag Health Trust, Levanger, 7601, Norway
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Sekar Kathiresan
- Center for Human Genetic Research, Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, 02114, MA, USA
| | - Olle Melander
- Department of Clinical Sciences, Malmö, Lund University, Malmö, 221, Sweden
| | | | - Børge G Nordestgaard
- The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, 2730, Denmark.,Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, 2730, Denmark.,The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen University Hospital, Copenhagen, 2400, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Anne Tybjærg-Hansen
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen, 2100, Denmark.,The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, 2730, Denmark.,The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen University Hospital, Copenhagen, 2400, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - David Altshuler
- Program in Medical and Population Genetics, Broad Institute, Cambridge, 02142, MA, USA.,Department of Molecular Biology, Diabetes Unit, and Center for Human Genetic Research, Massachusetts General Hospital, Boston, 02114, MA, USA.,Departments of Genetics and Medicine, Harvard Medical School, Boston, 02115, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, MA, USA
| | - Jose C Florez
- Diabetes Unit and Center for Human Genetic Research, Massachusetts General Hospital, Boston, 02115, MA, USA.,Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, 02142, MA, USA.,Department of Medicine, Harvard Medical School, Boston, 02115, MA, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, OX3 7LE, UK.,Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, OX4 2PG, UK
| | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, 10591, NY, USA.
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39
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Raffield LM, Ulirsch JC, Naik RP, Lessard S, Handsaker RE, Jain D, Kang HM, Pankratz N, Auer PL, Bao EL, Smith JD, Lange LA, Lange EM, Li Y, Thornton TA, Young BA, Abecasis GR, Laurie CC, Nickerson DA, McCarroll SA, Correa A, Wilson JG, Lettre G, Sankaran VG, Reiner AP. Common α-globin variants modify hematologic and other clinical phenotypes in sickle cell trait and disease. PLoS Genet 2018; 14:e1007293. [PMID: 29590102 PMCID: PMC5891078 DOI: 10.1371/journal.pgen.1007293] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/09/2018] [Accepted: 03/06/2018] [Indexed: 11/18/2022] Open
Abstract
Co-inheritance of α-thalassemia has a significant protective effect on the severity of complications of sickle cell disease (SCD), including stroke. However, little information exists on the association and interactions for the common African ancestral α-thalassemia mutation (-α3.7 deletion) and β-globin traits (HbS trait [SCT] and HbC trait) on important clinical phenotypes such as red blood cell parameters, anemia, and chronic kidney disease (CKD). In a community-based cohort of 2,916 African Americans from the Jackson Heart Study, we confirmed the expected associations between SCT, HbC trait, and the -α3.7 deletion with lower mean corpuscular volume/mean corpuscular hemoglobin and higher red blood cell count and red cell distribution width. In addition to the recently recognized association of SCT with lower estimated glomerular filtration rate and glycated hemoglobin (HbA1c), we observed a novel association of the -α3.7 deletion with higher HbA1c levels. Co-inheritance of each additional copy of the -α3.7 deletion significantly lowered the risk of anemia and chronic kidney disease among individuals with SCT (P-interaction = 0.031 and 0.019, respectively). Furthermore, co-inheritance of a novel α-globin regulatory variant was associated with normalization of red cell parameters in individuals with the -α3.7 deletion and significantly negated the protective effect of α-thalassemia on stroke in 1,139 patients with sickle cell anemia from the Cooperative Study of Sickle Cell Disease (CSSCD) (P-interaction = 0.0049). Functional assays determined that rs11865131, located in the major alpha-globin enhancer MCS-R2, was the most likely causal variant. These findings suggest that common α- and β-globin variants interact to influence hematologic and clinical phenotypes in African Americans, with potential implications for risk-stratification and counseling of individuals with SCD and SCT.
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Affiliation(s)
- Laura M. Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jacob C. Ulirsch
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Rakhi P. Naik
- Hematology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Samuel Lessard
- Department of Medicine, Université de Montréal, Montréal, Quebec, Canada
- Montreal Heart Institute, Montréal, Quebec, Canada
| | - Robert E. Handsaker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Hyun M. Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nathan Pankratz
- Department of Laboratory Medicine & Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Paul L. Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Erik L. Bao
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Joshua D. Smith
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Leslie A. Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Ethan M. Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Timothy A. Thornton
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Bessie A. Young
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Seattle Epidemiologic Research and Information Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington, United States of America
| | - Goncalo R. Abecasis
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Cathy C. Laurie
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Steven A. McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | | | - Guillaume Lettre
- Department of Medicine, Université de Montréal, Montréal, Quebec, Canada
- Montreal Heart Institute, Montréal, Quebec, Canada
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (APR); (VGS)
| | - Alex P. Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (APR); (VGS)
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Scott RA, Scott LJ, Mägi R, Marullo L, Gaulton KJ, Kaakinen M, Pervjakova N, Pers TH, Johnson AD, Eicher JD, Jackson AU, Ferreira T, Lee Y, Ma C, Steinthorsdottir V, Thorleifsson G, Qi L, Van Zuydam NR, Mahajan A, Chen H, Almgren P, Voight BF, Grallert H, Müller-Nurasyid M, Ried JS, Rayner NW, Robertson N, Karssen LC, van Leeuwen EM, Willems SM, Fuchsberger C, Kwan P, Teslovich TM, Chanda P, Li M, Lu Y, Dina C, Thuillier D, Yengo L, Jiang L, Sparso T, Kestler HA, Chheda H, Eisele L, Gustafsson S, Frånberg M, Strawbridge RJ, Benediktsson R, Hreidarsson AB, Kong A, Sigurðsson G, Kerrison ND, Luan J, Liang L, Meitinger T, Roden M, Thorand B, Esko T, Mihailov E, Fox C, Liu CT, Rybin D, Isomaa B, Lyssenko V, Tuomi T, Couper DJ, Pankow JS, Grarup N, Have CT, Jørgensen ME, Jørgensen T, Linneberg A, Cornelis MC, van Dam RM, Hunter DJ, Kraft P, Sun Q, Edkins S, Owen KR, Perry JRB, Wood AR, Zeggini E, Tajes-Fernandes J, Abecasis GR, Bonnycastle LL, Chines PS, Stringham HM, Koistinen HA, Kinnunen L, Sennblad B, Mühleisen TW, Nöthen MM, Pechlivanis S, Baldassarre D, Gertow K, Humphries SE, Tremoli E, Klopp N, Meyer J, Steinbach G, Wennauer R, Eriksson JG, Mӓnnistö S, Peltonen L, Tikkanen E, Charpentier G, Eury E, Lobbens S, Gigante B, Leander K, McLeod O, Bottinger EP, Gottesman O, Ruderfer D, Blüher M, Kovacs P, Tonjes A, Maruthur NM, Scapoli C, Erbel R, Jöckel KH, Moebus S, de Faire U, Hamsten A, Stumvoll M, Deloukas P, Donnelly PJ, Frayling TM, Hattersley AT, Ripatti S, Salomaa V, Pedersen NL, Boehm BO, Bergman RN, Collins FS, Mohlke KL, Tuomilehto J, Hansen T, Pedersen O, Barroso I, Lannfelt L, Ingelsson E, Lind L, Lindgren CM, Cauchi S, Froguel P, Loos RJF, Balkau B, Boeing H, Franks PW, Barricarte Gurrea A, Palli D, van der Schouw YT, Altshuler D, Groop LC, Langenberg C, Wareham NJ, Sijbrands E, van Duijn CM, Florez JC, Meigs JB, Boerwinkle E, Gieger C, Strauch K, Metspalu A, Morris AD, Palmer CNA, Hu FB, Thorsteinsdottir U, Stefansson K, Dupuis J, Morris AP, Boehnke M, McCarthy MI, Prokopenko I. An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans. Diabetes 2017; 66:2888-2902. [PMID: 28566273 PMCID: PMC5652602 DOI: 10.2337/db16-1253] [Citation(s) in RCA: 456] [Impact Index Per Article: 65.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 05/21/2017] [Indexed: 12/12/2022]
Abstract
To characterize type 2 diabetes (T2D)-associated variation across the allele frequency spectrum, we conducted a meta-analysis of genome-wide association data from 26,676 T2D case and 132,532 control subjects of European ancestry after imputation using the 1000 Genomes multiethnic reference panel. Promising association signals were followed up in additional data sets (of 14,545 or 7,397 T2D case and 38,994 or 71,604 control subjects). We identified 13 novel T2D-associated loci (P < 5 × 10-8), including variants near the GLP2R, GIP, and HLA-DQA1 genes. Our analysis brought the total number of independent T2D associations to 128 distinct signals at 113 loci. Despite substantially increased sample size and more complete coverage of low-frequency variation, all novel associations were driven by common single nucleotide variants. Credible sets of potentially causal variants were generally larger than those based on imputation with earlier reference panels, consistent with resolution of causal signals to common risk haplotypes. Stratification of T2D-associated loci based on T2D-related quantitative trait associations revealed tissue-specific enrichment of regulatory annotations in pancreatic islet enhancers for loci influencing insulin secretion and in adipocytes, monocytes, and hepatocytes for insulin action-associated loci. These findings highlight the predominant role played by common variants of modest effect and the diversity of biological mechanisms influencing T2D pathophysiology.
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Affiliation(s)
- Robert A Scott
- MRC Epidemiology Unit, University of Cambridge, Cambridge, U.K
| | - Laura J Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Letizia Marullo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Kyle J Gaulton
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Department of Genetics, Stanford University, Stanford, CA
| | - Marika Kaakinen
- Department of Genomics of Common Disease, Imperial College London, London, U.K
| | | | - Tune H Pers
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Andrew D Johnson
- Framingham Heart Study, Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Framingham, MA
| | - John D Eicher
- Framingham Heart Study, Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Framingham, MA
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Teresa Ferreira
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
| | - Yeji Lee
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Clement Ma
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | | | | | - Lu Qi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Natalie R Van Zuydam
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics and Biomedical Research Institute, Ninewells Hospital, University of Dundee, Dundee, U.K
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
| | - Han Chen
- Human Genetics Center and Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
- Center for Precision Health, School Biomedical Informatics, and School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Peter Almgren
- Lund University Diabetes Centre and Department of Clinical Sciences Malmö, University Hospital Scania, Lund University, Malmö, Sweden
| | - Ben F Voight
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, Munich, Germany
- Genetic Epidemiology, Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Munich Heart Alliance, German Centre for Cardiovascular Disease, Munich, Germany
| | - Janina S Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nigel W Rayner
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, U.K
- Wellcome Trust Sanger Institute, Hinxton, U.K
| | - Neil Robertson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, U.K
| | - Lennart C Karssen
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- PolyOmica, 's-Hertogenbosch, the Netherlands
| | | | - Sara M Willems
- MRC Epidemiology Unit, University of Cambridge, Cambridge, U.K
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Christian Fuchsberger
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Phoenix Kwan
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Tanya M Teslovich
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Pritam Chanda
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Man Li
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Christian Dina
- l'institut du thorax, INSERM, CNRS, Centre Hospitalier Universitaire de Nantes, Université de Nantes, Nantes, France
| | - Dorothee Thuillier
- Lille Institute of Biology, European Genomics Institute of Diabetes, Lille, France
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Loic Yengo
- Lille Institute of Biology, European Genomics Institute of Diabetes, Lille, France
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Longda Jiang
- Department of Genomics of Common Disease, Imperial College London, London, U.K
| | - Thomas Sparso
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans A Kestler
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Himanshu Chheda
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Lewin Eisele
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, Essen, Germany
| | - Stefan Gustafsson
- Molecular Epidemiology, Department of Medical Sciences, and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mattias Frånberg
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
- Department for Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden
| | - Rona J Strawbridge
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Rafn Benediktsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Landspítali University Hospital, Reykjavik, Iceland
| | | | | | - Gunnar Sigurðsson
- Landspítali University Hospital, Reykjavik, Iceland
- Icelandic Heart Association, Kópavogur, Iceland
| | | | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge, Cambridge, U.K
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Thomas Meitinger
- Munich Heart Alliance, German Centre for Cardiovascular Disease, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Michael Roden
- German Center for Diabetes Research, Neuherberg, Germany
- Department of Endocrinology and Diabetology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Institute for Diabetes Research at Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Barbara Thorand
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Division of Genetics and Endocrinology, Boston Children's Hospital, Boston, MA
| | | | - Caroline Fox
- Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Denis Rybin
- Data Coordinating Center, Boston University School of Public Health, Boston, MA
| | - Bo Isomaa
- Folkhälsan Research Center, Helsinki, Finland
- Department of Social Services and Health Care, Jakobstad, Finland
| | - Valeriya Lyssenko
- Lund University Diabetes Centre and Department of Clinical Sciences Malmö, University Hospital Scania, Lund University, Malmö, Sweden
| | - Tiinamaija Tuomi
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medicine, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - David J Couper
- Collaborative Studies Coordinating Center, Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - James S Pankow
- Division of Epidemiology & Community Health, University of Minnesota, Minneapolis, MN
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian T Have
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Torben Jørgensen
- Research Centre for Prevention and Health, Capital Region of Denmark, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Medicine, Aalborg University, Aalborg, Denmark
| | - Allan Linneberg
- Research Centre for Prevention and Health, Capital Region of Denmark, Copenhagen, Denmark
- Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Marilyn C Cornelis
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Rob M van Dam
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Qi Sun
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | | | - Katharine R Owen
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, U.K
- National Institute for Health Research Oxford Biomedical Research Centre, Churchill Hospital, Oxford, U.K
| | - John R B Perry
- MRC Epidemiology Unit, University of Cambridge, Cambridge, U.K
| | - Andrew R Wood
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | | | | | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Lori L Bonnycastle
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Peter S Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Heather M Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Heikki A Koistinen
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
- Endocrinology, Department of Medicine and Abdominal Center, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum Helsinki 2U, Helsinki, Finland
| | - Leena Kinnunen
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
- Endocrinology, Department of Medicine and Abdominal Center, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum Helsinki 2U, Helsinki, Finland
| | - Bengt Sennblad
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Thomas W Mühleisen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Sonali Pechlivanis
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, Essen, Germany
| | - Damiano Baldassarre
- Centro Cardiologico Monzino, Istituto di Ricovero e Cura a Carattere Scientifico, Milan, Italy
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università di Milano, Milan, Italy
| | - Karl Gertow
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Steve E Humphries
- Cardiovascular Genetics, BHF Laboratories, Institute Cardiovascular Sciences, University College London, London, U.K
| | - Elena Tremoli
- Centro Cardiologico Monzino, Istituto di Ricovero e Cura a Carattere Scientifico, Milan, Italy
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università di Milano, Milan, Italy
| | - Norman Klopp
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Julia Meyer
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Gerald Steinbach
- Department of Clinical Chemistry and Central Laboratory, University of Ulm, Ulm, Germany
| | - Roman Wennauer
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Johan G Eriksson
- Folkhälsan Research Center, Helsinki, Finland
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland
- Unit of General Practice, Helsinki University Central Hospital, Helsinki, Finland
| | - Satu Mӓnnistö
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Leena Peltonen
- Wellcome Trust Sanger Institute, Hinxton, U.K
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Emmi Tikkanen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki, Finland
| | | | - Elodie Eury
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Stéphane Lobbens
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Bruna Gigante
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Karin Leander
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Olga McLeod
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Omri Gottesman
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Douglas Ruderfer
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Matthias Blüher
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Peter Kovacs
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Anke Tonjes
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Nisa M Maruthur
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins Bloomberg School of Medicine, Baltimore, MD
- The Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins University, Baltimore, MD
| | - Chiara Scapoli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Raimund Erbel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, Essen, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, Essen, Germany
| | - Susanne Moebus
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, Essen, Germany
| | - Ulf de Faire
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anders Hamsten
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Michael Stumvoll
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Panagiotis Deloukas
- Wellcome Trust Sanger Institute, Hinxton, U.K
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, U.K
| | - Peter J Donnelly
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Department of Statistics, University of Oxford, Oxford, U.K
| | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, U.K
| | - Samuli Ripatti
- Wellcome Trust Sanger Institute, Hinxton, U.K
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Bernhard O Boehm
- Division of Endocrinology and Diabetes, Department of Internal Medicine, University Medical Centre Ulm, Ulm, Germany
- Lee Kong Chian School of Medicine, Imperial College London and Nanyang Technological University, Singapore, Singapore
| | - Richard N Bergman
- Diabetes and Obesity Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Francis S Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - Jaakko Tuomilehto
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
- Dasman Diabetes Institute, Dasman, Kuwait
- Centre for Vascular Prevention, Danube University Krems, Krems, Austria
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Hinxton, U.K
- University of Cambridge Metabolic Research Laboratories and National Institute for Health Research Cambridge Biomedical Research Centre, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital Cambridge, Cambridge, U.K
| | - Lars Lannfelt
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Erik Ingelsson
- Molecular Epidemiology, Department of Medical Sciences, and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Lars Lind
- Cardiovascular Epidemiology, Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden
| | - Cecilia M Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Stephane Cauchi
- Lille Institute of Biology, European Genomics Institute of Diabetes, Lille, France
| | - Philippe Froguel
- Department of Genomics of Common Disease, Imperial College London, London, U.K
- Lille Institute of Biology, European Genomics Institute of Diabetes, Lille, France
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Beverley Balkau
- INSERM, CESP, UMR 1018, Villejuif, France
- University of Paris-Sud, UMR 1018, Villejuif, France
| | - Heiner Boeing
- German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Paul W Franks
- Lund University, Malmö, Sweden
- Umeå University, Umeå, Sweden
| | - Aurelio Barricarte Gurrea
- Navarra Public Health Institute, Pamplona, Spain
- Navarra Institute for Health Research, Pamplona, Spain
- CIBER Epidemiology and Public Health, Madrid, Spain
| | - Domenico Palli
- Cancer Research and Prevention Institute, Florence, Italy
| | | | - David Altshuler
- Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Department of Genetics, Harvard Medical School, Boston, MA
- Department of Molecular Biology, Harvard Medical School, Boston, MA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA
| | - Leif C Groop
- Lund University Diabetes Centre and Department of Clinical Sciences Malmö, University Hospital Scania, Lund University, Malmö, Sweden
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | | | | | - Eric Sijbrands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Netherlands Genomics Initiative, Netherlands Consortium for Healthy Ageing and Center for Medical Systems Biology, Rotterdam, the Netherlands
| | - Jose C Florez
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Diabetes Unit and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - James B Meigs
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- General Medicine Division, Massachusetts General Hospital, Boston, MA
| | - Eric Boerwinkle
- Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Genetic Epidemiology, Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Andrew D Morris
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, U.K
| | - Colin N A Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics and Biomedical Research Institute, Ninewells Hospital, University of Dundee, Dundee, U.K
- Cardiovascular and Diabetes Medicine, Biomedical Research Institute, Ninewells Hospital, University of Dundee, Dundee, U.K
| | - Frank B Hu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Unnur Thorsteinsdottir
- deCODE genetics, Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics, Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Josée Dupuis
- Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Andrew P Morris
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Department of Biostatistics, University of Liverpool, Liverpool, U.K
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, U.K
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K.
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, U.K
- National Institute for Health Research Oxford Biomedical Research Centre, Churchill Hospital, Oxford, U.K
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K.
- Department of Genomics of Common Disease, Imperial College London, London, U.K
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, U.K
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Dand N, Mucha S, Tsoi LC, Mahil SK, Stuart PE, Arnold A, Baurecht H, Burden AD, Callis Duffin K, Chandran V, Curtis CJ, Das S, Ellinghaus D, Ellinghaus E, Enerback C, Esko T, Gladman DD, Griffiths CEM, Gudjonsson JE, Hoffman P, Homuth G, Hüffmeier U, Krueger GG, Laudes M, Lee SH, Lieb W, Lim HW, Löhr S, Mrowietz U, Müller-Nurayid M, Nöthen M, Peters A, Rahman P, Reis A, Reynolds NJ, Rodriguez E, Schmidt CO, Spain SL, Strauch K, Tejasvi T, Voorhees JJ, Warren RB, Weichenthal M, Weidinger S, Zawistowski M, Nair RP, Capon F, Smith CH, Trembath RC, Abecasis GR, Elder JT, Franke A, Simpson MA, Barker JN. Exome-wide association study reveals novel psoriasis susceptibility locus at TNFSF15 and rare protective alleles in genes contributing to type I IFN signalling. Hum Mol Genet 2017; 26:4301-4313. [PMID: 28973304 PMCID: PMC5886170 DOI: 10.1093/hmg/ddx328] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 08/15/2017] [Accepted: 08/18/2017] [Indexed: 02/06/2023] Open
Abstract
Psoriasis is a common inflammatory skin disorder for which multiple genetic susceptibility loci have been identified, but few resolved to specific functional variants. In this study, we sought to identify common and rare psoriasis-associated gene-centric variation. Using exome arrays we genotyped four independent cohorts, totalling 11 861 psoriasis cases and 28 610 controls, aggregating the dataset through statistical meta-analysis. Single variant analysis detected a previously unreported risk locus at TNFSF15 (rs6478108; P = 1.50 × 10-8, OR = 1.10), and association of common protein-altering variants at 11 loci previously implicated in psoriasis susceptibility. We validate previous reports of protective low-frequency protein-altering variants within IFIH1 (encoding an innate antiviral receptor) and TYK2 (encoding a Janus kinase), in each case establishing a further series of protective rare variants (minor allele frequency < 0.01) via gene-wide aggregation testing (IFIH1: pburden = 2.53 × 10-7, OR = 0.707; TYK2: pburden = 6.17 × 10-4, OR = 0.744). Both genes play significant roles in type I interferon (IFN) production and signalling. Several of the protective rare and low-frequency variants in IFIH1 and TYK2 disrupt conserved protein domains, highlighting potential mechanisms through which their effect may be exerted.
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Affiliation(s)
- Nick Dand
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Sören Mucha
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Lam C Tsoi
- Department of Dermatology
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Satveer K Mahil
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | | | - Andreas Arnold
- Clinic and Polyclinic of Dermatology, University Medicine Greifswald, Greifswald, Germany
| | - Hansjörg Baurecht
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - A David Burden
- Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | | | - Vinod Chandran
- Department of Medicine
- Department of Laboratory Medicine and Pathobiology
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Charles J Curtis
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Sayantan Das
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Charlotta Enerback
- Division of Cell Biology and Dermatology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Tõnu Esko
- Estonian Biobank, Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Dafna D Gladman
- Department of Medicine
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Christopher E M Griffiths
- Dermatology Centre, Salford Royal Hospital, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | | | - Per Hoffman
- Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Ulrike Hüffmeier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Gerald G Krueger
- Department of Dermatology, University of Utah, Salt Lake City, UT, USA
| | | | - Sang Hyuck Lee
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank PopGen, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Henry W Lim
- Department of Dermatology, Henry Ford Hospital, Detroit, MI, USA
| | - Sabine Löhr
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ulrich Mrowietz
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | | | - Markus Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Annette Peters
- Institute of Genetic Epidemiology, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Proton Rahman
- Memorial University of Newfoundland, St. John's, NL, Canada
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nick J Reynolds
- Dermatological Sciences, Institute of Cellular Medicine, Newcastle University Medical School, Newcastle upon Tyne, UK
- Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Elke Rodriguez
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Carsten O Schmidt
- Institute for Community Medicine, Study of Health in Pomerania/KEF, University Medicine Greifswald, Greifswald, Germany
| | - Sarah L Spain
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum Munich, Neuherberg, Germany
| | | | | | - Richard B Warren
- Dermatology Centre, Salford Road NHS Foundation Trust, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Michael Weichenthal
- Department of Dermatology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Matthew Zawistowski
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - Francesca Capon
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Catherine H Smith
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Richard C Trembath
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Goncalo R Abecasis
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - James T Elder
- Department of Dermatology
- Ann Arbor Veterans Hospital, Ann Arbor, MI, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Michael A Simpson
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Jonathan N Barker
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
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42
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Zhou W, Fritsche LG, Das S, Zhang H, Nielsen JB, Holmen OL, Chen J, Lin M, Elvestad MB, Hveem K, Abecasis GR, Kang HM, Willer CJ. Improving power of association tests using multiple sets of imputed genotypes from distributed reference panels. Genet Epidemiol 2017; 41:744-755. [PMID: 28861891 DOI: 10.1002/gepi.22067] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/16/2017] [Accepted: 07/10/2017] [Indexed: 11/09/2022]
Abstract
The accuracy of genotype imputation depends upon two factors: the sample size of the reference panel and the genetic similarity between the reference panel and the target samples. When multiple reference panels are not consented to combine together, it is unclear how to combine the imputation results to optimize the power of genetic association studies. We compared the accuracy of 9,265 Norwegian genomes imputed from three reference panels-1000 Genomes phase 3 (1000G), Haplotype Reference Consortium (HRC), and a reference panel containing 2,201 Norwegian participants from the population-based Nord Trøndelag Health Study (HUNT) from low-pass genome sequencing. We observed that the population-matched reference panel allowed for imputation of more population-specific variants with lower frequency (minor allele frequency (MAF) between 0.05% and 0.5%). The overall imputation accuracy from the population-specific panel was substantially higher than 1000G and was comparable with HRC, despite HRC being 15-fold larger. These results recapitulate the value of population-specific reference panels for genotype imputation. We also evaluated different strategies to utilize multiple sets of imputed genotypes to increase the power of association studies. We observed that testing association for all variants imputed from any panel results in higher power to detect association than the alternative strategy of including only one version of each genetic variant, selected for having the highest imputation quality metric. This was particularly true for lower frequency variants (MAF < 1%), even after adjusting for the additional multiple testing burden.
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Affiliation(s)
- Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lars G Fritsche
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Sayantan Das
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - He Zhang
- Department of Internal Medicine, Division of Cardiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jonas B Nielsen
- Department of Internal Medicine, Division of Cardiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Oddgeir L Holmen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway.,St. Olav Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jin Chen
- Department of Internal Medicine, Division of Cardiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Maoxuan Lin
- Department of Internal Medicine, Division of Cardiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Maiken B Elvestad
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kristian Hveem
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway.,Department of Medicine, Levanger Hospital, Nord-Trøndelag Health Trust, Levanger, Norway
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Cristen J Willer
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America.,Department of Internal Medicine, Division of Cardiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.,Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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43
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Dey R, Schmidt EM, Abecasis GR, Lee S. A Fast and Accurate Algorithm to Test for Binary Phenotypes and Its Application to PheWAS. Am J Hum Genet 2017; 101:37-49. [PMID: 28602423 DOI: 10.1016/j.ajhg.2017.05.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/17/2017] [Indexed: 12/19/2022] Open
Abstract
The availability of electronic health record (EHR)-based phenotypes allows for genome-wide association analyses in thousands of traits and has great potential to enable identification of genetic variants associated with clinical phenotypes. We can interpret the phenome-wide association study (PheWAS) result for a single genetic variant by observing its association across a landscape of phenotypes. Because a PheWAS can test thousands of binary phenotypes, and most of them have unbalanced or often extremely unbalanced case-control ratios (1:10 or 1:600, respectively), existing methods cannot provide an accurate and scalable way to test for associations. Here, we propose a computationally fast score-test-based method that estimates the distribution of the test statistic by using the saddlepoint approximation. Our method is much (∼100 times) faster than the state-of-the-art Firth's test. It can also adjust for covariates and control type I error rates even when the case-control ratio is extremely unbalanced. Through application to PheWAS data from the Michigan Genomics Initiative, we show that the proposed method can control type I error rates while replicating previously known association signals even for traits with a very small number of cases and a large number of controls.
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Affiliation(s)
- Rounak Dey
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ellen M Schmidt
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Goncalo R Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seunggeun Lee
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
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44
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Nomura A, Won HH, Khera AV, Takeuchi F, Ito K, McCarthy S, Emdin CA, Klarin D, Natarajan P, Zekavat SM, Gupta N, Peloso GM, Borecki IB, Teslovich TM, Asselta R, Duga S, Merlini PA, Correa A, Kessler T, Wilson JG, Bown MJ, Hall AS, Braund PS, Carey DJ, Murray MF, Kirchner HL, Leader JB, Lavage DR, Manus JN, Hartze DN, Samani NJ, Schunkert H, Marrugat J, Elosua R, McPherson R, Farrall M, Watkins H, Juang JMJ, Hsiung CA, Lin SY, Wang JS, Tada H, Kawashiri MA, Inazu A, Yamagishi M, Katsuya T, Nakashima E, Nakatochi M, Yamamoto K, Yokota M, Momozawa Y, Rotter JI, Lander ES, Rader DJ, Danesh J, Ardissino D, Gabriel S, Willer CJ, Abecasis GR, Saleheen D, Kubo M, Kato N, Ida Chen YD, Dewey FE, Kathiresan S. Protein-Truncating Variants at the Cholesteryl Ester Transfer Protein Gene and Risk for Coronary Heart Disease. Circ Res 2017; 121:81-88. [PMID: 28506971 PMCID: PMC5523940 DOI: 10.1161/circresaha.117.311145] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 04/28/2017] [Accepted: 05/12/2017] [Indexed: 12/30/2022]
Abstract
RATIONALE Therapies that inhibit CETP (cholesteryl ester transfer protein) have failed to demonstrate a reduction in risk for coronary heart disease (CHD). Human DNA sequence variants that truncate the CETP gene may provide insight into the efficacy of CETP inhibition. OBJECTIVE To test whether protein-truncating variants (PTVs) at the CETP gene were associated with plasma lipid levels and CHD. METHODS AND RESULTS We sequenced the exons of the CETP gene in 58 469 participants from 12 case-control studies (18 817 CHD cases, 39 652 CHD-free controls). We defined PTV as those that lead to a premature stop, disrupt canonical splice sites, or lead to insertions/deletions that shift frame. We also genotyped 1 Japanese-specific PTV in 27561 participants from 3 case-control studies (14 286 CHD cases, 13 275 CHD-free controls). We tested association of CETP PTV carrier status with both plasma lipids and CHD. Among 58 469 participants with CETP gene-sequencing data available, average age was 51.5 years and 43% were women; 1 in 975 participants carried a PTV at the CETP gene. Compared with noncarriers, carriers of PTV at CETP had higher high-density lipoprotein cholesterol (effect size, 22.6 mg/dL; 95% confidence interval, 18-27; P<1.0×10-4), lower low-density lipoprotein cholesterol (-12.2 mg/dL; 95% confidence interval, -23 to -0.98; P=0.033), and lower triglycerides (-6.3%; 95% confidence interval, -12 to -0.22; P=0.043). CETP PTV carrier status was associated with reduced risk for CHD (summary odds ratio, 0.70; 95% confidence interval, 0.54-0.90; P=5.1×10-3). CONCLUSIONS Compared with noncarriers, carriers of PTV at CETP displayed higher high-density lipoprotein cholesterol, lower low-density lipoprotein cholesterol, lower triglycerides, and lower risk for CHD.
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45
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Abstract
With the increasing focus of genetic association on the identification of trait-associated rare variants through sequencing, it is important to identify the most cost-effective sequencing strategies for these studies. Deep sequencing will accurately detect and genotype the most rare variants per individual, but may limit sample size. Low pass sequencing will miss some variants in each individual but has been shown to provide a cost-effective alternative for studies of common variants. Here, we investigate the impact of sequencing depth on studies of rare variants, focusing on singletons—the variants that are sampled in a single individual and are hardest to detect at low sequencing depths. We first estimate the sensitivity to detect singleton variants in both simulated data and in down-sampled deep genome and exome sequence data. We then explore the power of association studies comparing burden of singleton variants in cases and controls under a variety of conditions. We show that the power to detect singletons increases with coverage, typically plateauing for coverage > ~25x. Next, we show that, when total sequencing capacity is fixed, the power of association studies focused on singletons is typically maximized for coverage of 15-20x, independent of relative risk, disease prevalence, singleton burden, and case-control ratio. Our results suggest sequencing depth of 15-20x as an appropriate compromise of singleton detection power and sample size for studies of rare variants in complex disease. Genetic studies of rare variants can help us understand the biology of human disease. With modern techniques and sufficient effort, it is possible to very accurately resolve any human genome, identifying most of its unique features. When funding is limited, applying these techniques to study human disease often involves a trade-off between examining more samples, at reduced accuracy per sample, or fewer samples, each at greater accuracy. We evaluate these trade-offs for studies of very rare variants, using both simulation and real data. We propose cost effective strategies for increasing our understanding of human disease.
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Affiliation(s)
- Sara Rashkin
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (SR); (GRA)
| | - Goo Jun
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Sai Chen
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Goncalo R. Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (SR); (GRA)
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Ried JS, Jeff M. J, Chu AY, Bragg-Gresham JL, van Dongen J, Huffman JE, Ahluwalia TS, Cadby G, Eklund N, Eriksson J, Esko T, Feitosa MF, Goel A, Gorski M, Hayward C, Heard-Costa NL, Jackson AU, Jokinen E, Kanoni S, Kristiansson K, Kutalik Z, Lahti J, Luan J, Mägi R, Mahajan A, Mangino M, Medina-Gomez C, Monda KL, Nolte IM, Pérusse L, Prokopenko I, Qi L, Rose LM, Salvi E, Smith MT, Snieder H, Stančáková A, Ju Sung Y, Tachmazidou I, Teumer A, Thorleifsson G, van der Harst P, Walker RW, Wang SR, Wild SH, Willems SM, Wong A, Zhang W, Albrecht E, Couto Alves A, Bakker SJL, Barlassina C, Bartz TM, Beilby J, Bellis C, Bergman RN, Bergmann S, Blangero J, Blüher M, Boerwinkle E, Bonnycastle LL, Bornstein SR, Bruinenberg M, Campbell H, Chen YDI, Chiang CWK, Chines PS, Collins FS, Cucca F, Cupples LA, D'Avila F, de Geus EJ.C, Dedoussis G, Dimitriou M, Döring A, Eriksson JG, Farmaki AE, Farrall M, Ferreira T, Fischer K, Forouhi NG, Friedrich N, Gjesing AP, Glorioso N, Graff M, Grallert H, Grarup N, Gräßler J, Grewal J, Hamsten A, Harder MN, Hartman CA, Hassinen M, Hastie N, Hattersley AT, Havulinna AS, Heliövaara M, Hillege H, Hofman A, Holmen O, Homuth G, Hottenga JJ, Hui J, Husemoen LL, Hysi PG, Isaacs A, Ittermann T, Jalilzadeh S, James AL, Jørgensen T, Jousilahti P, Jula A, Marie Justesen J, Justice AE, Kähönen M, Karaleftheri M, Tee Khaw K, Keinanen-Kiukaanniemi SM, Kinnunen L, Knekt PB, Koistinen HA, Kolcic I, Kooner IK, Koskinen S, Kovacs P, Kyriakou T, Laitinen T, Langenberg C, Lewin AM, Lichtner P, Lindgren CM, Lindström J, Linneberg A, Lorbeer R, Lorentzon M, Luben R, Lyssenko V, Männistö S, Manunta P, Leach IM, McArdle WL, Mcknight B, Mohlke KL, Mihailov E, Milani L, Mills R, Montasser ME, Morris AP, Müller G, Musk AW, Narisu N, Ong KK, Oostra BA, Osmond C, Palotie A, Pankow JS, Paternoster L, Penninx BW, Pichler I, Pilia MG, Polašek O, Pramstaller PP, Raitakari OT, Rankinen T, Rao DC, Rayner NW, Ribel-Madsen R, Rice TK, Richards M, Ridker PM, Rivadeneira F, Ryan KA, Sanna S, Sarzynski MA, Scholtens S, Scott RA, Sebert S, Southam L, Sparsø TH, Steinthorsdottir V, Stirrups K, Stolk RP, Strauch K, Stringham HM, Swertz MA, Swift AJ, Tönjes A, Tsafantakis E, van der Most PJ, Van Vliet-Ostaptchouk JV, Vandenput L, Vartiainen E, Venturini C, Verweij N, Viikari JS, Vitart V, Vohl MC, Vonk JM, Waeber G, Widén E, Willemsen G, Wilsgaard T, Winkler TW, Wright AF, Yerges-Armstrong LM, Hua Zhao J, Carola Zillikens M, Boomsma DI, Bouchard C, Chambers JC, Chasman DI, Cusi D, Gansevoort RT, Gieger C, Hansen T, Hicks AA, Hu F, Hveem K, Jarvelin MR, Kajantie E, Kooner JS, Kuh D, Kuusisto J, Laakso M, Lakka TA, Lehtimäki T, Metspalu A, Njølstad I, Ohlsson C, Oldehinkel AJ, Palmer LJ, Pedersen O, Perola M, Peters A, Psaty BM, Puolijoki H, Rauramaa R, Rudan I, Salomaa V, Schwarz PEH, Shudiner AR, Smit JH, Sørensen TIA, Spector TD, Stefansson K, Stumvoll M, Tremblay A, Tuomilehto J, Uitterlinden AG, Uusitupa M, Völker U, Vollenweider P, Wareham NJ, Watkins H, Wilson JF, Zeggini E, Abecasis GR, Boehnke M, Borecki IB, Deloukas P, van Duijn CM, Fox C, Groop LC, Heid IM, Hunter DJ, Kaplan RC, McCarthy MI, North KE, O'Connell JR, Schlessinger D, Thorsteinsdottir U, Strachan DP, Frayling T, Hirschhorn JN, Müller-Nurasyid M, Loos RJF. A principal component meta-analysis on multiple anthropometric traits identifies novel loci for body shape. Nat Commun 2016; 7:13357. [PMID: 27876822 PMCID: PMC5114527 DOI: 10.1038/ncomms13357] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 09/21/2016] [Indexed: 01/15/2023] Open
Abstract
Large consortia have revealed hundreds of genetic loci associated with anthropometric traits, one trait at a time. We examined whether genetic variants affect body shape as a composite phenotype that is represented by a combination of anthropometric traits. We developed an approach that calculates averaged PCs (AvPCs) representing body shape derived from six anthropometric traits (body mass index, height, weight, waist and hip circumference, waist-to-hip ratio). The first four AvPCs explain >99% of the variability, are heritable, and associate with cardiometabolic outcomes. We performed genome-wide association analyses for each body shape composite phenotype across 65 studies and meta-analysed summary statistics. We identify six novel loci: LEMD2 and CD47 for AvPC1, RPS6KA5/C14orf159 and GANAB for AvPC3, and ARL15 and ANP32 for AvPC4. Our findings highlight the value of using multiple traits to define complex phenotypes for discovery, which are not captured by single-trait analyses, and may shed light onto new pathways.
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Affiliation(s)
- Janina S. Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Janina Jeff M.
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Audrey Y. Chu
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02215, USA
| | - Jennifer L. Bragg-Gresham
- Kidney Epidemiology and Cost Center, Internal Medicine-Nephrology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jenny van Dongen
- Department of Biological Psychology, VU University, 1081BT Amsterdam, The Netherlands
| | - Jennifer E. Huffman
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, Scotland
| | - Tarunveer S. Ahluwalia
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
- Steno Diabetes Center A/S, DK-2820 Gentofte, Denmark
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Allé 34, DK-2820 Copenhagen, Denmark
| | - Gemma Cadby
- Centre for Genetic Origins of Health and Disease, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Niina Eklund
- Department of Health, National Institute for Health and Welfare (THL), FI-00271 Helsinki, Finland
| | - Joel Eriksson
- Department of Internal Medicine and Clinical Nutrition, Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Tõnu Esko
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 2142, USA
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mary F. Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Anuj Goel
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Mathias Gorski
- Department of Nephrology, University Hospital Regensburg, 93042 Regensburg, Germany
- Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, 93053 Regensburg, Germany
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, Scotland
| | - Nancy L. Heard-Costa
- National Heart, Lung, and Blood Institute, the Framingham Heart Study, Framingham, Massachusetts 01702, USA
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Anne U. Jackson
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Eero Jokinen
- Hospital for Children and Adolescents, University of Helsinki, FI-00290 Helsinki, Finland
| | - Stavroula Kanoni
- Wellcome Trust Sanger Institute, Human Genetics, Hinxton, Cambridge CB10 1SA, UK
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Kati Kristiansson
- Department of Health, National Institute for Health and Welfare (THL), FI-00271 Helsinki, Finland
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00290 Helsinki, Finland
| | - Zoltán Kutalik
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Department of Medical Genetics, University of Lausanne, Lausanne, 1005, Switzerland
- Institute of Social and Preventive Medicine, University Hospital Lausanne (CHUV), 1010 Lausanne, Switzerland
| | - Jari Lahti
- Folkhälsan Research Centre, FI-00290 Helsinki, Finland
- Institute of Behavioural Sciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Carolina Medina-Gomez
- Department of Epidemiology, Erasmus Medical Center, 3015GE Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, 3015GE Rotterdam, The Netherlands
| | - Keri L. Monda
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- The Center for Observational Research, Amgen Inc., Thousand Oaks, California 91320-1799, USA
| | - Ilja M. Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | - Louis Pérusse
- Department of Kinesiology, Laval University, Québec, Québec, Canada G1V 0A6
- Institute of Nutrition and Functional Foods, Laval University, Québec, Québec, Canada G1V 0A6
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London W12 0NN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
| | - Lu Qi
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Lynda M. Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02215, USA
| | - Erika Salvi
- Department of Health Sciences, University of Milano at San Paolo Hospital, 20139 Milano, Italy
- Filarete Foundation, Genomic and Bioinformatics Unit, Milano 20139, Italy
| | - Megan T. Smith
- Department of Biostatistics, University of Washington, Seattle, Washington 98195, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | - Alena Stančáková
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Yun Ju Sung
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Ioanna Tachmazidou
- Wellcome Trust Sanger Institute, Human Genetics, Hinxton, Cambridge CB10 1SA, UK
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | | | - Pim van der Harst
- Durrer Center for Cardiogenetic Research, Interuniversity Cardiology Institute Netherlands-Netherlands Heart Institute, 3501 DG Utrecht, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, Netherlands
| | - Ryan W. Walker
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- The Department of Preventive Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Sophie R. Wang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Division of Endocrinology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Divisions of Genetics and Endocrinology and Program in Genomics, Boston's Children's Hospital, Boston, Massachusetts 02115, USA
| | - Sarah H. Wild
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, EH8 9AG Teviot Place, Edinburgh, Scotland
| | - Sara M. Willems
- Department of Epidemiology, Genetic Epidemiology Unit, Erasmus University Medical Center, 3015GE Rotterdam, The Netherlands
| | - Andrew Wong
- MRC Unit for Lifelong Health & Ageing at UCL, London WC1B 5JU, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London W2 1PG, UK
- Ealing Hospital NHS Trust, Middlesex UB1 3HW, UK
| | - Eva Albrecht
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Alexessander Couto Alves
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPA) Centre for Environment and Health, School of Public Health, Imperial College, London W12 0NN, UK
| | - Stephan J. L. Bakker
- Department of Medicine, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, Netherlands
| | - Cristina Barlassina
- Department of Health Sciences, University of Milano at San Paolo Hospital, 20139 Milano, Italy
- Filarete Foundation, Genomic and Bioinformatics Unit, Milano 20139, Italy
| | - Traci M. Bartz
- Department of Biostatistics, University of Washington, Seattle, Washington 98195, USA
- Department of Medicine, University of Washington, Seattle, Washington 98101, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington 98101, USA
| | - John Beilby
- Pathwest Laboratory Medicine of Western Australia, Nedlands, Western Australia 6009, Australia
- School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands, Western Australia 6009, Australia
| | - Claire Bellis
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research of Singapore, Singapore 138672, Singapore
| | - Richard N. Bergman
- Diabetes and Obesity Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Sven Bergmann
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Department of Medical Genetics, University of Lausanne, Lausanne, 1005, Switzerland
| | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
| | - Matthias Blüher
- University of Leipzig, IFB Adiposity Diseases, 04103 Leipzig, Germany
- Department of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Eric Boerwinkle
- Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Lori L. Bonnycastle
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA
| | - Stefan R. Bornstein
- Medical Faculty Carl Gustav Carus, Department of Medicine III, University of Dresden, 01307 Dresden, Germany
| | - Marcel Bruinenberg
- University of Groningen, University Medical Center Groningen, The LifeLines Cohort Study, 9700 RB Groningen, The Netherlands
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, EH8 9AG Teviot Place, Edinburgh, Scotland
| | - Yii-Der Ida Chen
- Los Angeles BioMedical Resesarch Institute at Harbor-UCLA Medical Center, Torrance, California 90502, USA
| | | | - Peter S. Chines
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA
| | - Francis S Collins
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA
| | | | - L Adrienne Cupples
- National Heart, Lung, and Blood Institute, the Framingham Heart Study, Framingham, Massachusetts 01702, USA
| | - Francesca D'Avila
- Department of Health Sciences, University of Milano at San Paolo Hospital, 20139 Milano, Italy
- Filarete Foundation, Genomic and Bioinformatics Unit, Milano 20139, Italy
| | - Eco J .C. de Geus
- Department of Biological Psychology, VU University, 1081BT Amsterdam, The Netherlands
- EMGO Institute for Health and Care Research, VU University Medical Center, 1081 BT Amsterdam, The Netherlands
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, 17671 Athens, Greece
| | - Maria Dimitriou
- Wellcome Trust Sanger Institute, Human Genetics, Hinxton, Cambridge CB10 1SA, UK
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, 17671 Athens, Greece
| | - Angela Döring
- Institute of Epidemiology I, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Johan G. Eriksson
- Folkhälsan Research Centre, FI-00290 Helsinki, Finland
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, FI-00271 Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki, FI-00014 Helsinki, Finland
| | - Aliki-Eleni Farmaki
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, 17671 Athens, Greece
| | - Martin Farrall
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Teresa Ferreira
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Krista Fischer
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Nita G. Forouhi
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Anette Prior Gjesing
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Nicola Glorioso
- Hypertension and Related Disease Centre, AOU-University of Sassari, 7100 Sassari, Italy
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Harald Grallert
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Niels Grarup
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jürgen Gräßler
- Department of Medicine III, Pathobiochemistry, Technische Universitaet, 01307 Dresden, Germany
| | - Jagvir Grewal
- Department of Epidemiology and Biostatistics, Imperial College London, London W2 1PG, UK
- Ealing Hospital NHS Trust, Middlesex UB1 3HW, UK
| | - Anders Hamsten
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Medicine Solna, Atherosclerosis Research Unit, Karolinska Institutet, 17176 Stockholm 17176, Sweden
- Center for Molecular Medicine, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Marie Neergaard Harder
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Catharina A. Hartman
- University of Groningen, University Medical Center Groningen, Interdisciplinary Center Psychopathology and Emotion Regulation, 9700 RB Groningen, The Netherlands
| | - Maija Hassinen
- Kuopio Research Institute of Exercise Medicine, 70100 Kuopio, Finland
| | - Nicholas Hastie
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, Scotland
| | - Andrew Tym Hattersley
- Institue of Biomedical & Clinical Science, University of Exeter, Barrack Road, Exeter EX2 5DW, UK
| | - Aki S. Havulinna
- Department of Health, National Institute for Health and Welfare (THL), FI-00271 Helsinki, Finland
| | - Markku Heliövaara
- Department of Health, National Institute for Health and Welfare (THL), FI-00271 Helsinki, Finland
| | - Hans Hillege
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, 3015GE Rotterdam, The Netherlands
| | - Oddgeir Holmen
- Department of Public Health and General Practice, Norwegian University of Science and Technology, 7489 Trondheim, Norway
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, VU University, 1081BT Amsterdam, The Netherlands
| | - Jennie Hui
- Pathwest Laboratory Medicine of Western Australia, Nedlands, Western Australia 6009, Australia
- School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands, Western Australia 6009, Australia
- School of Population Health, University of Western Australia, Nedlands, Western Australia 6009, Australia
| | - Lise Lotte Husemoen
- Research Centre for Prevention and Health, Glostrup Hospital, 2600 Glostrup, Denmark
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Aaron Isaacs
- Department of Epidemiology, Genetic Epidemiology Unit, Erasmus University Medical Center, 3015GE Rotterdam, The Netherlands
| | - Till Ittermann
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Shapour Jalilzadeh
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Alan L. James
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia 6009, Australia
| | - Torben Jørgensen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Faculty of Medicine, University of Aalborg, 9220 Aalborg, Denmark
- Research Centre for Prevention and Health, Capital Region of Denmark, DK2600 Glostrup, Denmark
| | - Pekka Jousilahti
- Department of Health, National Institute for Health and Welfare (THL), FI-00271 Helsinki, Finland
| | - Antti Jula
- Department of Health, National Institute for Health and Welfare (THL), FI-00271 Helsinki, Finland
| | - Johanne Marie Justesen
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Anne E. Justice
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, FI-33521 Tampere, Finland
- Department of Clinical Physiology, University of Tampere School of Medicine, FI-33014 Tampere, Finland
| | | | - Kay Tee Khaw
- Clinical Gerontology Unit, Box 251, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - Sirkka M. Keinanen-Kiukaanniemi
- Faculty of Medicine, Institute of Health Sciences, University of Oulu, Oulu F1-90014, Finland
- Unit of General Practice, Oulu University Hospital, Oulu FI-90029, Finland
| | - Leena Kinnunen
- National Institute for Health and Welfare, FI-00271 Helsinki, Finland
| | - Paul B. Knekt
- Department of Health, National Institute for Health and Welfare (THL), FI-00271 Helsinki, Finland
| | - Heikki A. Koistinen
- National Institute for Health and Welfare, FI-00271 Helsinki, Finland
- Department of Medicine and Abdominal Center: Endocrinology, University of Helsinki and Helsinki University Central Hospital,, 00029 Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
| | - Ivana Kolcic
- Department of Public Health, Faculty of Medicine, University of Split, 21000 Split, Croatia
| | | | - Seppo Koskinen
- Department of Health, National Institute for Health and Welfare (THL), FI-00271 Helsinki, Finland
| | - Peter Kovacs
- University of Leipzig, IFB Adiposity Diseases, 04103 Leipzig, Germany
| | - Theodosios Kyriakou
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Tomi Laitinen
- Kuopio University Hospital, 70029 Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Epidemiology and Public Health, UCL, London WC1E 6BT, UK
| | - Alexandra M. Lewin
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPA) Centre for Environment and Health, School of Public Health, Imperial College, London W12 0NN, UK
| | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Cecilia M. Lindgren
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 2142, USA
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- The Big Data Institute, University of Oxford, Oxford OX3 7LJ, UK
| | - Jaana Lindström
- Department of Health, National Institute for Health and Welfare (THL), FI-00271 Helsinki, Finland
| | - Allan Linneberg
- Research Centre for Prevention and Health, Glostrup Hospital, 2600 Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, 2600 Glostrup, Denmark
| | - Roberto Lorbeer
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Mattias Lorentzon
- Department of Internal Medicine and Clinical Nutrition, Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Robert Luben
- Strangeways Research Laboratory Wort's Causeway, Cambridge CB1 8RN, UK
| | - Valeriya Lyssenko
- Steno Diabetes Center A/S, DK-2820 Gentofte, Denmark
- Lund University Diabetes Centre and Department of Clinical Science, Diabetes & Endocrinology Unit, Lund University, 221 00 Malmö, Sweden
| | - Satu Männistö
- Department of Health, National Institute for Health and Welfare (THL), FI-00271 Helsinki, Finland
| | - Paolo Manunta
- Chair of Nephrology, Università Vita Salute San Raffaele and Genomics of Renal Diseases and Hypertension Unit, IRCCS San Raffaele Scientific Institute, Milan 20139, Italy
| | - Irene Mateo Leach
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, Netherlands
| | - Wendy L. McArdle
- School of Social and Community Medicine, University of Bristol, Bristol BS82BN, UK
| | - Barbara Mcknight
- Department of Biostatistics, University of Washington, Seattle, Washington 98195, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington 98101, USA
- Divison of Public Health Sciences, Program in Biostatistics and Biomathematics, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | | | - May E. Montasser
- Division of Endocrinology, Diabetes & Nutrition, Department of Medicine, Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Biostatistics, University of Liverpool, Liverpool L69 3GA, UK
| | - Gabriele Müller
- Center for Evidence Based Healthcare, University of Dresden, Medical Faculty Carl Gustav Carus, Dresden, 01307, Germany
| | - Arthur W. Musk
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, West Australia 6009, Australia
| | - Narisu Narisu
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA
| | - Ken K. Ong
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- MRC Unit for Lifelong Health & Ageing at UCL, London WC1B 5JU, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Ben A. Oostra
- Department of Epidemiology, Genetic Epidemiology Unit, Erasmus University Medical Center, 3015GE Rotterdam, The Netherlands
| | - Clive Osmond
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00290 Helsinki, Finland
- Massachusetts General Hospital, Center for Human Genetic Research, Psychiatric and Neurodevelopmental Genetics Unit, Boston, Massachusetts 02114, USA
| | - James S. Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota 55455-0381, USA
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 1TH, UK
| | - Brenda W. Penninx
- Department of Psychiatry and EMGO Institute for Health and Care Research, VU University Medical Center, AJ Ernstraat 1887, 1081 HL Amsterdam, The Netherlands
| | - Irene Pichler
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), 39100 Bolzano, Italy
- Affiliated Institute of the University of Lübeck, 23562 Lübeck, Germany
| | - Maria G. Pilia
- Istituto di Ricerca Genetica e Biomedica, CNR, 9042 Monserrato, Italy
| | - Ozren Polašek
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, EH8 9AG Teviot Place, Edinburgh, Scotland
- Department of Public Health, Faculty of Medicine, University of Split, 21000 Split, Croatia
| | - Peter P. Pramstaller
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), 39100 Bolzano, Italy
- Affiliated Institute of the University of Lübeck, 23562 Lübeck, Germany
- Department of Neurology, University of Lübeck, 23562 Lübeck, Germany
- Department of Neurology, General Central Hospital, 39100 Bolzano, Italy
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, FI-20521 Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, FI-20520 Turku, Finland
| | - Tuomo Rankinen
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, Louisiana 70808, USA
| | - D. C. Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Nigel W. Rayner
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
- Wellcome Trust Sanger Institute, Human Genetics, Hinxton CB10 1HH, UK
| | - Rasmus Ribel-Madsen
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Treva K. Rice
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Marcus Richards
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
- MRC Unit for Lifelong Health & Ageing at UCL, London WC1B 5JU, UK
| | - Paul M. Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02215, USA
- Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, 3015GE Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, 3015GE Rotterdam, The Netherlands
| | - Kathy A. Ryan
- Division of Endocrinology, Diabetes & Nutrition, Department of Medicine, Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Serena Sanna
- Istituto di Ricerca Genetica e Biomedica, CNR, 9042 Monserrato, Italy
| | - Mark A. Sarzynski
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, Louisiana 70808, USA
| | - Salome Scholtens
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | - Robert A. Scott
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Sylvain Sebert
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London W12 0NN, UK
- Biocenter Oulu, University of Oulu, Oulu FI-90014, Finland
- Center For Life-Course Health Research, University of Oulu, FI-90014 Oulu, Finland
| | - Lorraine Southam
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Wellcome Trust Sanger Institute, Human Genetics, Hinxton, Cambridge CB10 1SA, UK
| | - Thomas Hempel Sparsø
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Kathleen Stirrups
- Wellcome Trust Sanger Institute, Human Genetics, Hinxton, Cambridge CB10 1SA, UK
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Ronald P. Stolk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | - Heather M. Stringham
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Morris A. Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | - Amy J. Swift
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | | | - Peter J. van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | - Jana V. Van Vliet-Ostaptchouk
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | - Liesbeth Vandenput
- Department of Internal Medicine and Clinical Nutrition, Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Erkki Vartiainen
- Department of Health, National Institute for Health and Welfare (THL), FI-00271 Helsinki, Finland
| | - Cristina Venturini
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, Netherlands
| | - Jorma S. Viikari
- Department of Medicine, University of Turku, FI-20521 Turku, Finland
- Division of Medicine, Turku University Hospital, Turku, Finland
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, Scotland
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods, Laval University, Québec, Québec, Canada G1V 0A6
- School of Nutrition, Laval University, Québec, Québec, Canada G1V 0A6
| | - Judith M. Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | - Gérard Waeber
- Department of Internal Medicine, University Hospital Lausanne (CHUV) and University of Lausanne, 1011 Lausanne, Switzerland
| | - Elisabeth Widén
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00290 Helsinki, Finland
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University, 1081BT Amsterdam, The Netherlands
| | - Tom Wilsgaard
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, 9037 Tromsø, Norway
| | - Thomas W. Winkler
- Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, 93053 Regensburg, Germany
| | - Alan F. Wright
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, Scotland
| | - Laura M. Yerges-Armstrong
- Division of Endocrinology, Diabetes & Nutrition, Department of Medicine, Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Jing Hua Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - M. Carola Zillikens
- Department of Internal Medicine, Erasmus Medical Center, 3015GE Rotterdam, The Netherlands
| | - Dorret I. Boomsma
- Department of Biological Psychology, VU University, 1081BT Amsterdam, The Netherlands
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, Louisiana 70808, USA
| | - John C. Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London W2 1PG, UK
- Ealing Hospital NHS Trust, Middlesex UB1 3HW, UK
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
| | - Daniel I. Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02215, USA
- Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Daniele Cusi
- Department of Health Sciences, University of Milano at San Paolo Hospital, 20139 Milano, Italy
- Filarete Foundation, Genomic and Bioinformatics Unit, Milano 20139, Italy
| | - Ron T. Gansevoort
- Department of Medicine, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, Netherlands
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Torben Hansen
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
- Faculty of Health Sciences, University of Southern Denmark, 5000 Odense, Denmark
| | - Andrew A. Hicks
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), 39100 Bolzano, Italy
- Affiliated Institute of the University of Lübeck, 23562 Lübeck, Germany
| | - Frank Hu
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Kristian Hveem
- Department of Public Health and General Practice, Norwegian University of Science and Technology, 7489 Trondheim, Norway
| | - Marjo-Riitta Jarvelin
- Biocenter Oulu, University of Oulu, Oulu FI-90014, Finland
- Unit of Primary Care, Oulu University Hospital, 90029 OYS Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC–PHE Centre for Environment & Health, School of Public Health, Imperial College London W12 0NN, UK
- Faculty of Medicine, Center for Life Course Epidemiology, University of Oulu, P.O.Box 5000, FI-90014 Oulu, Finland
| | - Eero Kajantie
- Department of Health, National Institute for Health and Welfare (THL), FI-00271 Helsinki, Finland
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, FI-00271 Helsinki, Finland
- Children's Hospital, Helsinki University Hospital and University of Helsinki, FI-00029 Helsinki, Finland
- Department of Obstetrics and Gynecology, MRC Oulu, Oulu University Hospital and University of Oulu, FI-90029 Oulu, Finland
| | - Jaspal S. Kooner
- Ealing Hospital NHS Trust, Middlesex UB1 3HW, UK
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK
| | - Diana Kuh
- MRC Unit for Lifelong Health & Ageing at UCL, London WC1B 5JU, UK
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Timo A. Lakka
- Kuopio Research Institute of Exercise Medicine, 70100 Kuopio, Finland
- Department of Physiology, Institute of Biomedicine, University of Eastern Finland, Kuopio Campus, 70210 Kuopio, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, University of Tampere School of Medicine, FI-33014 Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories and School of Medicine, University of Tampere, FI-33520 Tampere, Finland
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Inger Njølstad
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, 9037 Tromsø, Norway
- Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø, 9037 Tromsø, Norway
| | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Albertine J. Oldehinkel
- University of Groningen, University Medical Center Groningen, Interdisciplinary Center Psychopathology and Emotion Regulation, 9700 RB Groningen, The Netherlands
| | - Lyle J. Palmer
- School of Public Health, University of Adelaide, Adelaide, South Australia 5005, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Oluf Pedersen
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Markus Perola
- Department of Health, National Institute for Health and Welfare (THL), FI-00271 Helsinki, Finland
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00290 Helsinki, Finland
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
- DZHK (German Centre for Cardiovascular Research), partnersite Munich Heart Alliance, 80802 Munich, Germany
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington 98101, USA
- Department of Medicine, University of Washington, Seattle, Washington 98101, USA
- Departments of Epidemiology and Health Services, University of Washington, Seattle, Washington 98101, USA
- Group Health Research Institute, Group Health Cooperative, Seatte, Washington 98101, USA
| | - Hannu Puolijoki
- South Ostrobothnia Central Hospital, Seinäjoki Fi-60220, Finland
| | - Rainer Rauramaa
- Kuopio Research Institute of Exercise Medicine, 70100 Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, 70211 Kuopio, Finland
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, EH8 9AG Teviot Place, Edinburgh, Scotland
| | - Veikko Salomaa
- Department of Health, National Institute for Health and Welfare (THL), FI-00271 Helsinki, Finland
| | - Peter E. H. Schwarz
- Medical Faculty Carl Gustav Carus, Department of Medicine III, University of Dresden, 01307 Dresden, Germany
- Paul Langerhans Institute Dresden, German Center for Diabetes Research (DZD), Dresden 01307, Germany
| | - Alan R. Shudiner
- Division of Endocrinology, Diabetes & Nutrition, Department of Medicine, Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Geriatric Research and Education Clinical Center, Vetrans Administration Medical Center, Baltimore, Maryland 21042, USA
| | - Jan H. Smit
- Department of Psychiatry and EMGO Institute for Health and Care Research, VU University Medical Center, AJ Ernstraat 1887, 1081 HL Amsterdam, The Netherlands
| | - Thorkild I. A. Sørensen
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS82BN, UK
- Institute of Preventive Medicine, Bispebjerg and Frederiksberg Hospital, The Capital Region, 2000 Frederiksberg, Denmark
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Kari Stefansson
- deCODE Genetics, Amgen inc., 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Michael Stumvoll
- University of Leipzig, IFB Adiposity Diseases, 04103 Leipzig, Germany
- Department of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Angelo Tremblay
- Department of Kinesiology, Laval University, Québec, Québec, Canada G1V 0A6
| | - Jaakko Tuomilehto
- Diabetes Prevention Unit, National Institute for Health and Welfare, FI-00271 Helsinki, Finland
- Centre for Vascular Prevention, Danube-University Krems, 3500 Krems, Austria
- Diabetes Research Group, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, 3015GE Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, 3015GE Rotterdam, The Netherlands
| | - Matti Uusitupa
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland
- Research Unit, Kuopio University Hospital, 70029 Kuopio, Finland
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, 17475 Greifswald, Germany
| | - Peter Vollenweider
- Department of Internal Medicine, University Hospital Lausanne (CHUV) and University of Lausanne, 1011 Lausanne, Switzerland
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - James F. Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, Scotland
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, EH8 9AG Teviot Place, Edinburgh, Scotland
| | - Eleftheria Zeggini
- Wellcome Trust Sanger Institute, Human Genetics, Hinxton, Cambridge CB10 1SA, UK
| | - Goncalo R. Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Michael Boehnke
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Ingrid B. Borecki
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
- Wellcome Trust Sanger Institute, Human Genetics, Hinxton CB10 1HH, UK
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Cornelia M. van Duijn
- Department of Epidemiology, Genetic Epidemiology Unit, Erasmus University Medical Center, 3015GE Rotterdam, The Netherlands
- Center for Medical Systems Biology, 2300 Leiden, The Netherlands
| | - Caroline Fox
- National Heart, Lung, and Blood Institute, the Framingham Heart Study, Framingham, Massachusetts 01702, USA
- Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Leif C. Groop
- Lund University Diabetes Centre and Department of Clinical Science, Diabetes & Endocrinology Unit, Lund University, 221 00 Malmö, Sweden
- Finnish Institute for Molecular Medicine (FIMM), Helsinki University, 00014 Helsinki, Finland
| | - Iris M. Heid
- Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, 93053 Regensburg, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - David J. Hunter
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 2142, USA
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Robert C. Kaplan
- Department of Epidemiology and Popualtion Health, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
- Oxford NIHR Biomedical Research Centre, Oxford OX3 7LJ, UK
| | - Kari E. North
- Department of Epidemiology, Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7400, USA
| | - Jeffrey R. O'Connell
- Division of Endocrinology, Diabetes & Nutrition, Department of Medicine, Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - David Schlessinger
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Amgen inc., 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - David P. Strachan
- Population Health Research Institute, St George's, University of London, London SW17 0RE, UK
| | - Timothy Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter EX1 2LU, UK
| | - Joel N. Hirschhorn
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 2142, USA
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Division of Endocrinology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Divisions of Genetics and Endocrinology and Program in Genomics, Boston's Children's Hospital, Boston, Massachusetts 02115, USA
- Metabolism Initiative, Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, 81377 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partnersite Munich Heart Alliance, 80802 Munich, Germany
- Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- The Department of Preventive Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- The Mindich Child Health and Development Institute, The Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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Loh PR, Danecek P, Palamara PF, Fuchsberger C, A Reshef Y, K Finucane H, Schoenherr S, Forer L, McCarthy S, Abecasis GR, Durbin R, L Price A. Reference-based phasing using the Haplotype Reference Consortium panel. Nat Genet 2016; 48:1443-1448. [PMID: 27694958 PMCID: PMC5096458 DOI: 10.1038/ng.3679] [Citation(s) in RCA: 939] [Impact Index Per Article: 117.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/29/2016] [Indexed: 12/17/2022]
Abstract
Haplotype phasing is a fundamental problem in medical and population genetics. Phasing is generally performed via statistical phasing in a genotyped cohort, an approach that can yield high accuracy in very large cohorts but attains lower accuracy in smaller cohorts. Here we instead explore the paradigm of reference-based phasing. We introduce a new phasing algorithm, Eagle2, that attains high accuracy across a broad range of cohort sizes by efficiently leveraging information from large external reference panels (such as the Haplotype Reference Consortium; HRC) using a new data structure based on the positional Burrows-Wheeler transform. We demonstrate that Eagle2 attains a ∼20× speedup and ∼10% increase in accuracy compared to reference-based phasing using SHAPEIT2. On European-ancestry samples, Eagle2 with the HRC panel achieves >2× the accuracy of 1000 Genomes-based phasing. Eagle2 is open source and freely available for HRC-based phasing via the Sanger Imputation Service and the Michigan Imputation Server.
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Affiliation(s)
- Po-Ru Loh
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Petr Danecek
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Pier Francesco Palamara
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Christian Fuchsberger
- Center for Biomedicine, European Academy of Bozen/Bolzano (EURAC), affiliated with the University of Lübeck, Bolzano, Italy
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Yakir A Reshef
- Department of Computer Science, Harvard University, Cambridge, Massachusetts, USA
| | - Hilary K Finucane
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sebastian Schoenherr
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas Forer
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Shane McCarthy
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Goncalo R Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Alkes L Price
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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48
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Auer PL, Reiner AP, Wang G, Kang HM, Abecasis GR, Altshuler D, Bamshad MJ, Nickerson DA, Tracy RP, Rich SS, Leal SM, Leal SM. Guidelines for Large-Scale Sequence-Based Complex Trait Association Studies: Lessons Learned from the NHLBI Exome Sequencing Project. Am J Hum Genet 2016; 99:791-801. [PMID: 27666372 DOI: 10.1016/j.ajhg.2016.08.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 08/08/2016] [Indexed: 12/11/2022] Open
Abstract
Massively parallel whole-genome sequencing (WGS) data have ushered in a new era in human genetics. These data are now being used to understand the role of rare variants in complex traits and to advance the goals of precision medicine. The technological and computing advances that have enabled us to generate WGS data on thousands of individuals have also outpaced our ability to perform analyses in scientifically and statistically rigorous and thoughtful ways. The past several years have witnessed the application of whole-exome sequencing (WES) to complex traits and diseases. From our analysis of NHLBI Exome Sequencing Project (ESP) data, not only have a number of important disease and complex trait association findings emerged, but our collective experience offers some valuable lessons for WGS initiatives. These include caveats associated with generating automated pipelines for quality control and analysis of rare variants; the importance of studying minority populations; sample size requirements and efficient study designs for identifying rare-variant associations; and the significance of incidental findings in population-based genetic research. With the ESP as an example, we offer guidance and a framework on how to conduct a large-scale association study in the era of WGS.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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49
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Huyghe J, Chen S, Kang HM, Harrison TA, Berndt SI, Bézieau S, Brenner H, Casey G, Chan AT, Chang-Claude J, Steven GJ, Gruber SB, Gsur A, Hoffmeister M, Hudson TJ, Le Marchand L, Newcomb PA, Potter JD, Qu C, Slattery ML, Smith JD, White E, Hsu L, Abecasis GR, Nickerson DA, Peters U. Abstract 5230: Large scale whole genome sequencing with imputation into GWAS improves our understanding of the genetic architecture of colorectal cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-5230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Whole-genome sequencing (WGS) has started a new era in human genetics in which data can be used to more fully understand the role of genetic variation in common complex diseases, including the role of less frequent and rare variants and structural variation. To explore the impact of these variants on colorectal cancer risk we conducted the first large scale WGS study for colorectal cancer (CRC) including 1,961 CRC cases and 981 controls. These WGS data as well as those from the Haplotype Reference Consortium were imputed in 13,104 CRC cases and 15,521 controls with genome-wide association study (GWAS) data that are part of the Colorectal Cancer Family Registry (CCFR) and the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO). Focusing on rare and less frequent variants, insertions and deletions we observed potentially novel variants: a less frequent variant (MAF = 0.026) on chromosome 5 located in NREP/STARD4-AS1 (p = value 4E-08); and a novel rare multi-allelic variant (MAF = 0.003) on chromosome 9 near KLF9 and TRPM3 (p-value 2E-09; the other allele of this multi-allelic variant had a MAF of 0.0003 and p-value of 0.55). Furthermore, we observed an independent locus close to the known region 8q24 that was located upstream of GSDMC (MAF = 0.16, p-value 5E-08). Within the known region 8q23/EIF3H we identified several low frequency variants with similar MAF (0.0181 to 0.0204) including a 6bp deletion with p-values between 4E-08 and 1E-09 that were independent of the common variant signal in this region. In addition, we identified statistically significant (p<5E-08) deletions, insertions, and an essential splice site within known GWAS loci that present interesting candidates for functional studies. We will follow up these findings in independent samples from the Colorectal Cancer Transdisciplinary Study (CORECT) and CCFR, as well as additional samples currently genotyped in GECCO. In conclusion, next generation sequencing combined with imputation in large GWAS data sets has the potential to identify novel low frequency and rare genetic variants, aid fine-mapping of known CRC susceptibility loci and point to interesting functional candidates.
Citation Format: Jeroen Huyghe, Sai Chen, Hyun M. Kang, Tabitha A. Harrison, Sonja I. Berndt, Stephane Bézieau, Hermann Brenner, Graham Casey, Andrew T. Chan, Jenny Chang-Claude, Gallinger J. Steven, Stephen B. Gruber, Andrea Gsur, Michael Hoffmeister, Thomas J. Hudson, Loic Le Marchand, Polly A. Newcomb, John D. Potter, Conghui Qu, Martha L. Slattery, Joshua D. Smith, Emily White, Li Hsu, Goncalo R. Abecasis, Deborah A. Nickerson, Ulrike Peters. Large scale whole genome sequencing with imputation into GWAS improves our understanding of the genetic architecture of colorectal cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5230.
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Affiliation(s)
- Jeroen Huyghe
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Sai Chen
- 2University of Michigan, Ann Arbors, MI
| | | | | | | | | | | | - Graham Casey
- 6University of Southern California, Los Angeles, CA
| | | | | | | | | | - Andrea Gsur
- 9Medical University of Vienna, Vienna, Australia
| | | | - Thomas J. Hudson
- 10Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | | | | | - Conghui Qu
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | - Emily White
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Li Hsu
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | - Ulrike Peters
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
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50
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Bien SA, Harrison TA, Auer PL, Qu F, Huyghe J, Banbury B, Greenside P, Abecasis GR, Berndt SI, Bézieau S, Brenner H, Casey G, Chan AT, Chang-Claude J, Chen S, Smith JD, Le Marchand L, Carlson C, Newcomb PA, Fuchsberger C, Slattery ML, Kang HM, White E, Potter J, Gallinger SJ, Hoffmeister M, Gruber SB, Nickerson DA, Peters U, Kundaje A, Hsu L. Abstract 4489: Using functional data from Roadmap Epigenomics to inform analysis of rare variants linked to gene expression in a large colorectal cancer study. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
To investigate the role of low frequency and rare genetic variation in colorectal cancer (CRC) susceptibility, the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and the Colorectal Cancer Family Registry (CCFR) conducted whole genome sequencing and imputed into genome-wide association studies (GWAS) of 14,718 CRC cases and 12,186 controls. These data provide a unique opportunity to investigate rare variants, which contribute to the majority of the variation in the genome. To improve power for discovering rare CRC susceptibility variants (<1% MAF), Roadmap Epigenomics data were used to construct biologically relevant testing sets of enhancers, promoters and exons for gene-based association testing across the genome. Since enhancers exert their effects by impacting expression of target genes, we defined enhancer-gene networks by linking enhancer(s) to target gene expression using Roadmap chromatin state maps and gene expression. Variants in linked enhancers from digestive and immune tissues were aggregated together with variants in the promoter and non-synonymous coding variants in the target gene. We tested 9,884 variant sets for association with CRC risk using the Mixed effects Score Test (MiST). Our most significant findings are for acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain precursor-ACADS (p = 1×10−4), AlkB homologs, including AlkB homolog 1-ALKBH1 (p = 2×10−4), and SRA stem-loop interacting RNA binding protein-SLIRP (p = 2×10−4). We will replicate these findings within the Colorectal Cancer Transdisciplinary Study (CORECT), as well as additional samples currently genotyped in CCFR and GECCO (over 25,000 CRC cases and controls). Although the top findings are statistically non-significant in this initial dataset, each of these genes linked to molecular pathways implicated in CRC carcinogenesis (fatty acid metabolism, DNA/RNA repair, and Nuclear Receptor signaling pathway, which interacts with the Wnt, beta-catenin pathways to result in a diverse array of cellular effects including altered cellular adhesion, tissue morphogenesis, and oncogenesis). Our current findings suggest that although functional insight can improve power for novel discovery, even larger sample sizes and/or pathway-based analyses are necessary to understand the role of rare variants in CRC carcinogenesis.
Citation Format: Stephanie A. Bien, Tabitha A. Harrison, Paul L. Auer, Flora Qu, Jeroen Huyghe, Barbara Banbury, Peyton Greenside, Goncalo R. Abecasis, Sonja I. Berndt, Stephane Bézieau, Hermann Brenner, Graham Casey, Andrew T. Chan, Jenny Chang-Claude, Sai Chen, Joshua D. Smith, Loic Le Marchand, Christopher Carlson, Polly A. Newcomb, Christian Fuchsberger, Marty L. Slattery, Hyun M. Kang, Emily White, John Potter, Steven J. Gallinger, Michael Hoffmeister, Stephen B. Gruber, Deborah A. Nickerson, Ulrike Peters, Anshul Kundaje, Li Hsu. Using functional data from Roadmap Epigenomics to inform analysis of rare variants linked to gene expression in a large colorectal cancer study. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4489.
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Affiliation(s)
| | | | | | - Flora Qu
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jeroen Huyghe
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | - Sonja I. Berndt
- 5National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | | | - Graham Casey
- 8University of Southern California, Los Angeles, CA
| | | | | | - Sai Chen
- 4University of Michigan, Ann Arbor, MI
| | | | | | | | | | | | | | | | - Emily White
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | - John Potter
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | | | - Ulrike Peters
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Li Hsu
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
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