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Hu X, Logan JG, Kwon Y, Lima JAC, Jacobs DR, Duprez D, Brumback L, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy RP, Blackwell TW, Papanicolaou G, Mitchell GF, Rich SS, Rotter JI, Van Den Berg DJ, Chirinos JA, Hughes TM, Garrett-Bakelman FE, Manichaikul A. Multi-ancestry epigenome-wide analyses identify methylated sites associated with aortic augmentation index in TOPMed MESA. Sci Rep 2023; 13:17680. [PMID: 37848499 PMCID: PMC10582077 DOI: 10.1038/s41598-023-44806-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 06/29/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023] Open
Abstract
Despite the prognostic value of arterial stiffness (AS) and pulsatile hemodynamics (PH) for cardiovascular morbidity and mortality, epigenetic modifications that contribute to AS/PH remain unknown. To gain a better understanding of the link between epigenetics (DNA methylation) and AS/PH, we examined the relationship of eight measures of AS/PH with CpG sites and co-methylated regions using multi-ancestry participants from Trans-Omics for Precision Medicine (TOPMed) Multi-Ethnic Study of Atherosclerosis (MESA) with sample sizes ranging from 438 to 874. Epigenome-wide association analysis identified one genome-wide significant CpG (cg20711926-CYP1B1) associated with aortic augmentation index (AIx). Follow-up analyses, including gene set enrichment analysis, expression quantitative trait methylation analysis, and functional enrichment analysis on differentially methylated positions and regions, further prioritized three CpGs and their annotated genes (cg23800023-ETS1, cg08426368-TGFB3, and cg17350632-HLA-DPB1) for AIx. Among these, ETS1 and TGFB3 have been previously prioritized as candidate genes. Furthermore, both ETS1 and HLA-DPB1 have significant tissue correlations between Whole Blood and Aorta in GTEx, which suggests ETS1 and HLA-DPB1 could be potential biomarkers in understanding pathophysiology of AS/PH. Overall, our findings support the possible role of epigenetic regulation via DNA methylation of specific genes associated with AIx as well as identifying potential targets for regulation of AS/PH.
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Affiliation(s)
- Xiaowei Hu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jeongok G Logan
- School of Nursing, University of Virginia, Charlottesville, VA, USA
| | - Younghoon Kwon
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joao A C Lima
- Department of Internal Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David R Jacobs
- Division of Epidemiology, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Daniel Duprez
- Cardiovascular Division, University of Minnesota, Minneapolis, MN, USA
| | - Lyndia Brumback
- Department of Biostatistics, University of Washington, Seattle, WA, 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, USA
| | - Peter Durda
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Elaine Cornell
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, 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, USA
| | - Yongmei Liu
- Division of Cardiology, Department of Medicine, Duke University, Durham, NC, USA
| | - Russell P Tracy
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA
| | - Thomas W Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - George Papanicolaou
- Epidemiology Branch, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | | | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, 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, USA
| | - David J Van Den Berg
- Department of Preventive Medicine and Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Julio A Chirinos
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy M Hughes
- Department of Internal Medicine - Section of Gerontology and Geriatric Medicine, and Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Francine E Garrett-Bakelman
- Department of Biochemistry and Molecular Genetics, Department of Medicine, University of Virginia, 1340 Jefferson Park Ave., Pinn hall 6054, Charlottesville, VA, 22908, USA.
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA.
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2
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Berndt SI, Vijai J, Benavente Y, Camp NJ, Nieters A, Wang Z, Smedby KE, Kleinstern G, Hjalgrim H, Besson C, Skibola CF, Morton LM, Brooks-Wilson AR, Teras LR, Breeze C, Arias J, Adami HO, Albanes D, Anderson KC, Ansell SM, Bassig B, Becker N, Bhatti P, Birmann BM, Boffetta P, Bracci PM, Brennan P, Brown EE, Burdett L, Cannon-Albright LA, Chang ET, Chiu BCH, Chung CC, Clavel J, Cocco P, Colditz G, Conde L, Conti DV, Cox DG, Curtin K, Casabonne D, De Vivo I, Diepstra A, Diver WR, Dogan A, Edlund CK, Foretova L, Fraumeni JF, Gabbas A, Ghesquières H, Giles GG, Glaser S, Glenn M, Glimelius B, Gu J, Habermann TM, Haiman CA, Haioun C, Hofmann JN, Holford TR, Holly EA, Hutchinson A, Izhar A, Jackson RD, Jarrett RF, Kaaks R, Kane E, Kolonel LN, Kong Y, Kraft P, Kricker A, Lake A, Lan Q, Lawrence C, Li D, Liebow M, Link BK, Magnani C, Maynadie M, McKay J, Melbye M, Miligi L, Milne RL, Molina TJ, Monnereau A, Montalvan R, North KE, Novak AJ, Onel K, Purdue MP, Rand KA, Riboli E, Riby J, Roman E, Salles G, Sborov DW, Severson RK, Shanafelt TD, Smith MT, Smith A, Song KW, Song L, Southey MC, Spinelli JJ, Staines A, Stephens D, Sutherland HJ, Tkachuk K, Thompson CA, Tilly H, Tinker LF, Travis RC, Turner J, Vachon CM, Vajdic CM, Van Den Berg A, Van Den Berg DJ, Vermeulen RCH, Vineis P, Wang SS, Weiderpass E, Weiner GJ, Weinstein S, Doo NW, Ye Y, Yeager M, Yu K, Zeleniuch-Jacquotte A, Zhang Y, Zheng T, Ziv E, Sampson J, Chatterjee N, Offit K, Cozen W, Wu X, Cerhan JR, Chanock SJ, Slager SL, Rothman N. Correction: Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes. Leukemia 2023; 37:2142. [PMID: 37666943 DOI: 10.1038/s41375-023-01978-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Affiliation(s)
- Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA.
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yolanda Benavente
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Nicola J Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Alexandra Nieters
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Karin E Smedby
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Hematology Center, Karolinska University Hospital, Stockholm, Sweden
| | | | - Henrik Hjalgrim
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Haematology, Rigshospitalet, Copenhagen, Denmark
- Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark
| | - Caroline Besson
- Centre Hospitalier de Versailles, Le Chesnay, France
- Université Paris-Saclay, UVSQ, Inserm, Équipe "Exposome et Hérédité", CESP, Villejuif, France
| | - Christine F Skibola
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Angela R Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Charles Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Joshua Arias
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Institute of Health and Society, Clinical Effectiveness Research Group, University of Oslo, Oslo, Norway
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Kenneth C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Stephen M Ansell
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Bryan Bassig
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Nikolaus Becker
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany
| | - Parveen Bhatti
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Paolo Boffetta
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, New York, 11794, NY, USA
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, 41026, Italy
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Elizabeth E Brown
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Laurie Burdett
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MA, USA
| | - Lisa A Cannon-Albright
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Ellen T Chang
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Center for Health Sciences, Exponent, Inc., Menlo Park, CA, USA
| | - Brian C H Chiu
- Department of Public Health Sciences University of Chicago, Chicago, IL, USA
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Jacqueline Clavel
- CRESS, UMR1153, INSERM, Villejuif, France
- Université de Paris-Cité, Villejuif, France
| | - Pierluigi Cocco
- Centre for Occupational and Environmental Health, Division of Population Science, Health Services Research & Primary Care, University of Manchester, Manchester, UK
| | - Graham Colditz
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, UK
| | - David V Conti
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David G Cox
- INSERM U1052, Cancer Research Center of Lyon, Centre Léon Bérard, Lyon, France
| | - Karen Curtin
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Delphine Casabonne
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - W Ryan Diver
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Ahmet Dogan
- Departments of Laboratory Medicine and Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher K Edlund
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Attilio Gabbas
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, Monserrato, Cagliari, Italy
| | - Hervé Ghesquières
- Department of Hematology, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre Benite, France
- CIRI, Centre International de Recherche en Infectiologie, Team Lymphoma Immuno-Biology, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VC, Australia
| | - Sally Glaser
- Cancer Prevention Institute of California, Fremont, CA, USA
- Stanford Cancer Institute, Stanford, CA, USA
| | - Martha Glenn
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jian Gu
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | | | - Christopher A Haiman
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Corinne Haioun
- Lymphoid Malignancies Unit, Henri Mondor Hospital and University Paris Est, Créteil, France
| | - Jonathan N Hofmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Theodore R Holford
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MA, USA
| | - Aalin Izhar
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, OH, USA
| | - Ruth F Jarrett
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Rudolph Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany
| | - Eleanor Kane
- Department of Health Sciences, University of York, York, UK
| | - Laurence N Kolonel
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Yinfei Kong
- Information Systems and Decision Sciences, California State University, Fullerton, Fullerton, CA, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anne Kricker
- Sydney School of Public Health, The University of Sydney, Sydney, NSW, Australia
| | - Annette Lake
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | | | - Dalin Li
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mark Liebow
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Brian K Link
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Corrado Magnani
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Marc Maynadie
- INSERM U1231, EA 4184, Registre des Hémopathies Malignes de Côte d'Or, University of Burgundy and Dijon University Hospital, Dijon, France
| | - James McKay
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Mads Melbye
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Jebsen Center for Genetic epidemiology, NTNU, Trondheim, Norway
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Genetics, Stanford University Medical School, Stanford, CA, USA
| | - Lucia Miligi
- Environmental and Occupational Epidemiology Unit, Cancer Prevention and Research Institute (ISPO), Florence, Italy
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VC, Australia
| | - Thierry J Molina
- Department of Pathology, APHP, Necker and Robert Debré, Université Paris Cité, Institut Imagine, INSERM U1163, Paris, France
| | - Alain Monnereau
- CRESS, UMR1153, INSERM, Villejuif, France
- Registre des hémopathies malignes de la Gironde, Institut Bergonié, Bordeaux, Cedex, France
| | | | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anne J Novak
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Kenan Onel
- Donald and Barbara Zucker School of Medicine, Hofstra/Northwell, Hempstead, New York, NY, USA
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Kristin A Rand
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London, United Kingdom
| | - Jacques Riby
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, CA, USA
| | - Eve Roman
- Department of Health Sciences, University of York, York, UK
| | - Gilles Salles
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Douglas W Sborov
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Richard K Severson
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, MI, USA
| | - Tait D Shanafelt
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Martyn T Smith
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, CA, USA
| | | | - Kevin W Song
- Leukemia/Bone Marrow Transplantation Program, BC Cancer Agency, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Lei Song
- Center for Cancer Research, National Cancer Institute, Frederick, MA, USA
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VC, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - John J Spinelli
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Anthony Staines
- School of Nursing, Psychotherapy and Community Health, Dublin City University, Dublin, Ireland
| | - Deborah Stephens
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Heather J Sutherland
- Leukemia/Bone Marrow Transplantation Program, BC Cancer Agency, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Hervé Tilly
- Centre Henri Becquerel, Université de Rouen, Rouen, France
| | - Lesley F Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford, UK
| | - Jenny Turner
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
- Department of Histopathology, Douglass Hanly Moir Pathology, Sydney, NSW, Australia
| | - Celine M Vachon
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Claire M Vajdic
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Anke Van Den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - David J Van Den Berg
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Roel C H Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Human Genetics Foundation, Turin, Italy
| | - Sophia S Wang
- Division of Health Analytics, City of Hope Beckman Research Institute, Duarte, CA, USA
| | | | - George J Weiner
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Nicole Wong Doo
- Concord Clinical School, University of Sydney, Concord, NSW, Australia
| | - Yuanqing Ye
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MA, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University School of Medicine, New York, NY, USA
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY, USA
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Tongzhang Zheng
- Department of Epidemiology, Brown University, Providence, RI, USA
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, Institute of Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MA, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wendy Cozen
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Xifeng Wu
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
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Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, 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K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short 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Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, 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KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, 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Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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Berndt SI, Vijai J, Benavente Y, Camp NJ, Nieters A, Wang Z, Smedby KE, Kleinstern G, Hjalgrim H, Besson C, Skibola CF, Morton LM, Brooks-Wilson AR, Teras LR, Breeze C, Arias J, Adami HO, Albanes D, Anderson KC, Ansell SM, Bassig B, Becker N, Bhatti P, Birmann BM, Boffetta P, Bracci PM, Brennan P, Brown EE, Burdett L, Cannon-Albright LA, Chang ET, Chiu BCH, Chung CC, Clavel J, Cocco P, Colditz G, Conde L, Conti DV, Cox DG, Curtin K, Casabonne D, De Vivo I, Diepstra A, Diver WR, Dogan A, Edlund CK, Foretova L, Fraumeni JF, Gabbas A, Ghesquières H, Giles GG, Glaser S, Glenn M, Glimelius B, Gu J, Habermann TM, Haiman CA, Haioun C, Hofmann JN, Holford TR, Holly EA, Hutchinson A, Izhar A, Jackson RD, Jarrett RF, Kaaks R, Kane E, Kolonel LN, Kong Y, Kraft P, Kricker A, Lake A, Lan Q, Lawrence C, Li D, Liebow M, Link BK, Magnani C, Maynadie M, McKay J, Melbye M, Miligi L, Milne RL, Molina TJ, Monnereau A, Montalvan R, North KE, Novak AJ, Onel K, Purdue MP, Rand KA, Riboli E, Riby J, Roman E, Salles G, Sborov DW, Severson RK, Shanafelt TD, Smith MT, Smith A, Song KW, Song L, Southey MC, Spinelli JJ, Staines A, Stephens D, Sutherland HJ, Tkachuk K, Thompson CA, Tilly H, Tinker LF, Travis RC, Turner J, Vachon CM, Vajdic CM, Van Den Berg A, Van Den Berg DJ, Vermeulen RCH, Vineis P, Wang SS, Weiderpass E, Weiner GJ, Weinstein S, Doo NW, Ye Y, Yeager M, Yu K, Zeleniuch-Jacquotte A, Zhang Y, Zheng T, Ziv E, Sampson J, Chatterjee N, Offit K, Cozen W, Wu X, Cerhan JR, Chanock SJ, Slager SL, Rothman N. Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes. Leukemia 2022; 36:2835-2844. [PMID: 36273105 PMCID: PMC10337695 DOI: 10.1038/s41375-022-01711-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 03/21/2022] [Revised: 05/22/2022] [Accepted: 09/15/2022] [Indexed: 11/08/2022]
Abstract
Lymphoma risk is elevated for relatives with common non-Hodgkin lymphoma (NHL) subtypes, suggesting shared genetic susceptibility across subtypes. To evaluate the extent of mutual heritability among NHL subtypes and discover novel loci shared among subtypes, we analyzed data from eight genome-wide association studies within the InterLymph Consortium, including 10,629 cases and 9505 controls. We utilized Association analysis based on SubSETs (ASSET) to discover loci for subsets of NHL subtypes and evaluated shared heritability across the genome using Genome-wide Complex Trait Analysis (GCTA) and polygenic risk scores. We discovered 17 genome-wide significant loci (P < 5 × 10-8) for subsets of NHL subtypes, including a novel locus at 10q23.33 (HHEX) (P = 3.27 × 10-9). Most subset associations were driven primarily by only one subtype. Genome-wide genetic correlations between pairs of subtypes varied broadly from 0.20 to 0.86, suggesting substantial heterogeneity in the extent of shared heritability among subtypes. Polygenic risk score analyses of established loci for different lymphoid malignancies identified strong associations with some NHL subtypes (P < 5 × 10-8), but weak or null associations with others. Although our analyses suggest partially shared heritability and biological pathways, they reveal substantial heterogeneity among NHL subtypes with each having its own distinct germline genetic architecture.
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Affiliation(s)
- Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA.
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yolanda Benavente
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Nicola J Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Alexandra Nieters
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Karin E Smedby
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Hematology Center, Karolinska University Hospital, Stockholm, Sweden
| | | | - Henrik Hjalgrim
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Haematology, Rigshospitalet, Copenhagen, Denmark
- Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark
| | - Caroline Besson
- Centre Hospitalier de Versailles, Le Chesnay, France
- Université Paris-Saclay, UVSQ, Inserm, Équipe "Exposome et Hérédité", CESP, Villejuif, France
| | - Christine F Skibola
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Angela R Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Charles Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Joshua Arias
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Institute of Health and Society, Clinical Effectiveness Research Group, University of Oslo, Oslo, Norway
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Kenneth C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Stephen M Ansell
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Bryan Bassig
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Nikolaus Becker
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany
| | - Parveen Bhatti
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Paolo Boffetta
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, New York, 11794, NY, USA
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, 41026, Italy
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Elizabeth E Brown
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Laurie Burdett
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MA, USA
| | - Lisa A Cannon-Albright
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Ellen T Chang
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Center for Health Sciences, Exponent, Inc., Menlo Park, CA, USA
| | - Brian C H Chiu
- Department of Public Health Sciences University of Chicago, Chicago, IL, USA
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Jacqueline Clavel
- CRESS, UMR1153, INSERM, Villejuif, France
- Université de Paris-Cité, Villejuif, France
| | - Pierluigi Cocco
- Centre for Occupational and Environmental Health, Division of Population Science, Health Services Research & Primary Care, University of Manchester, Manchester, United Kingdom
| | - Graham Colditz
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, United Kingdom
| | - David V Conti
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David G Cox
- INSERM U1052, Cancer Research Center of Lyon, Centre Léon Bérard, Lyon, France
| | - Karen Curtin
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Delphine Casabonne
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - W Ryan Diver
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Ahmet Dogan
- Departments of Laboratory Medicine and Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher K Edlund
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Attilio Gabbas
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, Monserrato, Cagliari, Italy
| | - Hervé Ghesquières
- Department of Hematology, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre Benite, France
- CIRI, Centre International de Recherche en Infectiologie, Team Lymphoma Immuno-Biology, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VC, Australia
| | - Sally Glaser
- Cancer Prevention Institute of California, Fremont, CA, USA
- Stanford Cancer Institute, Stanford, CA, USA
| | - Martha Glenn
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jian Gu
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | | | - Christopher A Haiman
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Corinne Haioun
- Lymphoid Malignancies Unit, Henri Mondor Hospital and University Paris Est, Créteil, France
| | - Jonathan N Hofmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Theodore R Holford
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MA, USA
| | - Aalin Izhar
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, OH, USA
| | - Ruth F Jarrett
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Rudolph Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany
| | - Eleanor Kane
- Department of Health Sciences, University of York, York, United Kingdom
| | - Laurence N Kolonel
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Yinfei Kong
- Information Systems and Decision Sciences, California State University, Fullerton, Fullerton, CA, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anne Kricker
- Sydney School of Public Health, The University of Sydney, Sydney, NSW, Australia
| | - Annette Lake
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | | | - Dalin Li
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mark Liebow
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Brian K Link
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Corrado Magnani
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Marc Maynadie
- INSERM U1231, EA 4184, Registre des Hémopathies Malignes de Côte d'Or, University of Burgundy and Dijon University Hospital, Dijon, France
| | - James McKay
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Mads Melbye
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Jebsen Center for Genetic epidemiology, NTNU, Trondheim, Norway
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Genetics, Stanford University Medical School, Stanford, CA, USA
| | - Lucia Miligi
- Environmental and Occupational Epidemiology Unit, Cancer Prevention and Research Institute (ISPO), Florence, Italy
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VC, Australia
| | - Thierry J Molina
- Department of Pathology, APHP, Necker and Robert Debré, Université Paris Cité, Institut Imagine, INSERM U1163, Paris, France
| | - Alain Monnereau
- CRESS, UMR1153, INSERM, Villejuif, France
- Registre des hémopathies malignes de la Gironde, Institut Bergonié, Bordeaux, Cedex, France
| | | | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anne J Novak
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Kenan Onel
- Donald and Barbara Zucker School of Medicine, Hofstra/Northwell, Hempstead, New York, NY, USA
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Kristin A Rand
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London, United Kingdom
| | - Jacques Riby
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, CA, USA
| | - Eve Roman
- Department of Health Sciences, University of York, York, United Kingdom
| | - Gilles Salles
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Douglas W Sborov
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Richard K Severson
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, MI, USA
| | - Tait D Shanafelt
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Martyn T Smith
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, CA, USA
| | - Alexandra Smith
- Department of Health Sciences, University of York, York, United Kingdom
| | - Kevin W Song
- Leukemia/Bone Marrow Transplantation Program, BC Cancer Agency, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Lei Song
- Center for Cancer Research, National Cancer Institute, Frederick, MA, USA
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VC, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, VC, 3010, Australia
| | - John J Spinelli
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Anthony Staines
- School of Nursing, Psychotherapy and Community Health, Dublin City University, Dublin, Ireland
| | - Deborah Stephens
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Heather J Sutherland
- Leukemia/Bone Marrow Transplantation Program, BC Cancer Agency, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Hervé Tilly
- Centre Henri Becquerel, Université de Rouen, Rouen, France
| | - Lesley F Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford, United Kingdom
| | - Jenny Turner
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
- Department of Histopathology, Douglass Hanly Moir Pathology, Sydney, NSW, Australia
| | - Celine M Vachon
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Claire M Vajdic
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Anke Van Den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - David J Van Den Berg
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Roel C H Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
- Human Genetics Foundation, Turin, Italy
| | - Sophia S Wang
- Division of Health Analytics, City of Hope Beckman Research Institute, Duarte, CA, USA
| | | | - George J Weiner
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Nicole Wong Doo
- Concord Clinical School, University of Sydney, Concord, NSW, Australia
| | - Yuanqing Ye
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MA, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University School of Medicine, New York, NY, USA
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY, USA
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Tongzhang Zheng
- Department of Epidemiology, Brown University, Providence, RI, USA
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, Institute of Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MA, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wendy Cozen
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Xifeng Wu
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
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6
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Lee M, Huan T, McCartney DL, Chittoor G, de Vries M, Lahousse L, Nguyen JN, Brody JA, Castillo-Fernandez J, Terzikhan N, Qi C, Joehanes R, Min JL, Smilnak GJ, Shaw JR, Yang CX, Colicino E, Hoang TT, Bermingham ML, Xu H, Justice AE, Xu CJ, Rich SS, Cox SR, Vonk JM, Prokić I, Sotoodehnia N, Tsai PC, Schwartz JD, Leung JM, Sikdar S, Walker RM, Harris SE, van der Plaat DA, Van Den Berg DJ, Bartz TM, Spector TD, Vokonas PS, Marioni RE, Taylor AM, Liu Y, Barr RG, Lange LA, Baccarelli AA, Obeidat M, Fornage M, Wang T, Ward JM, Motsinger-Reif AA, Hemani G, Koppelman GH, Bell JT, Gharib SA, Brusselle G, Boezen HM, North KE, Levy D, Evans KL, Dupuis J, Breeze CE, Manichaikul A, London SJ. Pulmonary Function and Blood DNA Methylation: A Multiancestry Epigenome-Wide Association Meta-analysis. Am J Respir Crit Care Med 2022; 206:321-336. [PMID: 35536696 PMCID: PMC9890261 DOI: 10.1164/rccm.202108-1907oc] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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] [Indexed: 02/04/2023] Open
Abstract
Rationale: Methylation integrates factors present at birth and modifiable across the lifespan that can influence pulmonary function. Studies are limited in scope and replication. Objectives: To conduct large-scale epigenome-wide meta-analyses of blood DNA methylation and pulmonary function. Methods: Twelve cohorts analyzed associations of methylation at cytosine-phosphate-guanine probes (CpGs), using Illumina 450K or EPIC/850K arrays, with FEV1, FVC, and FEV1/FVC. We performed multiancestry epigenome-wide meta-analyses (total of 17,503 individuals; 14,761 European, 2,549 African, and 193 Hispanic/Latino ancestries) and interpreted results using integrative epigenomics. Measurements and Main Results: We identified 1,267 CpGs (1,042 genes) differentially methylated (false discovery rate, <0.025) in relation to FEV1, FVC, or FEV1/FVC, including 1,240 novel and 73 also related to chronic obstructive pulmonary disease (1,787 cases). We found 294 CpGs unique to European or African ancestry and 395 CpGs unique to never or ever smokers. The majority of significant CpGs correlated with nearby gene expression in blood. Findings were enriched in key regulatory elements for gene function, including accessible chromatin elements, in both blood and lung. Sixty-nine implicated genes are targets of investigational or approved drugs. One example novel gene highlighted by integrative epigenomic and druggable target analysis is TNFRSF4. Mendelian randomization and colocalization analyses suggest that epigenome-wide association study signals capture causal regulatory genomic loci. Conclusions: We identified numerous novel loci differentially methylated in relation to pulmonary function; few were detected in large genome-wide association studies. Integrative analyses highlight functional relevance and potential therapeutic targets. This comprehensive discovery of potentially modifiable, novel lung function loci expands knowledge gained from genetic studies, providing insights into lung pathogenesis.
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Affiliation(s)
| | - Tianxiao Huan
- Department of Ophthalmology, University of Massachusetts Medical School, Worcester, Massachusetts.,Framingham Heart Study, National Heart, Lung, and Blood Institute, National Institutes of Health, U.S. Department of Health and Human Services, Framingham, Massachusetts
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer and
| | - Geetha Chittoor
- Department of Population Health Sciences, Geisinger, Danville, Pennsylvania.,Department of Epidemiology, School of Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Maaike de Vries
- Department of Epidemiology.,Groningen Research Institute for Asthma and COPD, and
| | - Lies Lahousse
- Department of Bioanalysis, Ghent University, Ghent, Belgium.,Department of Epidemiology and
| | - Jennifer N Nguyen
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Division of Cardiology, Department of Medicine
| | - Juan Castillo-Fernandez
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | | | - Cancan Qi
- Groningen Research Institute for Asthma and COPD, and.,Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Roby Joehanes
- Framingham Heart Study, National Heart, Lung, and Blood Institute, National Institutes of Health, U.S. Department of Health and Human Services, Framingham, Massachusetts
| | - Josine L Min
- Medical Research Council Integrative Epidemiology Unit and.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | | | - Jessica R Shaw
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, and
| | - Chen Xi Yang
- Centre for Heart Lung Innovation, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elena Colicino
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Mairead L Bermingham
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer and
| | - Hanfei Xu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Anne E Justice
- Department of Population Health Sciences, Geisinger, Danville, Pennsylvania.,Department of Epidemiology, School of Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine, a joint venture between Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,Research Group Bioinformatics and Computational Genomics, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany.,Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.,Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Simon R Cox
- Lothian Birth Cohorts Group, Department of Psychology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Judith M Vonk
- Department of Epidemiology.,Groningen Research Institute for Asthma and COPD, and
| | | | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, Department of Epidemiology
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom.,Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Joel D Schwartz
- Department of Environmental Health and.,Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts.,Channing Laboratory, Harvard Medical School, Boston, Massachusetts
| | - Janice M Leung
- Centre for Heart Lung Innovation, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sinjini Sikdar
- Epidemiology Branch.,Department of Mathematics and Statistics, Old Dominion University, Norfolk, Virginia
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer and
| | - Sarah E Harris
- Lothian Birth Cohorts Group, Department of Psychology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Diana A van der Plaat
- Department of Epidemiology.,National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - David J Van Den Berg
- Department of Preventive Medicine and.,Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Department of Biostatistics
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Pantel S Vokonas
- Veterans Affairs Boston Healthcare System, School of Medicine and School of Public Health, Boston University, Boston, Massachusetts
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer and
| | - Adele M Taylor
- Lothian Birth Cohorts Group, Department of Psychology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Yongmei Liu
- Division of Cardiology, Department of Medicine, Duke University, Durham, North Carolina
| | - R Graham Barr
- Department of Medicine and.,Department of Epidemiology, Columbia University Medical Center, New York, New York
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, and.,Department of Epidemiology, University of Colorado, Aurora, Colorado
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Ma'en Obeidat
- Centre for Heart Lung Innovation, The University of British Columbia, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, and.,Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, Texas
| | | | | | - Alison A Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, U.S. Department of Health and Human Services, Research Triangle Park, North Carolina
| | - Gibran Hemani
- Medical Research Council Integrative Epidemiology Unit and.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Gerard H Koppelman
- Groningen Research Institute for Asthma and COPD, and.,Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Sina A Gharib
- Cardiovascular Health Research Unit, Division of Cardiology, Department of Medicine.,Computational Medicine Core, Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, Washington
| | - Guy Brusselle
- Department of Epidemiology and.,Department of Respiratory Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium; and
| | - H Marike Boezen
- Department of Epidemiology.,Groningen Research Institute for Asthma and COPD, and
| | - Kari E North
- Department of Epidemiology, School of Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Daniel Levy
- Framingham Heart Study, National Heart, Lung, and Blood Institute, National Institutes of Health, U.S. Department of Health and Human Services, Framingham, Massachusetts
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer and
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | | | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
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7
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Wang P, Castellani CA, Yao J, Huan T, Bielak LF, Zhao W, Haessler J, Joehanes R, Sun X, Guo X, Longchamps RJ, Manson JE, Grove ML, Bressler J, Taylor KD, Lappalainen T, Kasela S, Van Den Berg DJ, Hou L, Reiner A, Liu Y, Boerwinkle E, Smith JA, Peyser PA, Fornage M, Rich SS, Rotter JI, Kooperberg C, Arking DE, Levy D, Liu C. Epigenome-wide association study of mitochondrial genome copy number. Hum Mol Genet 2021; 31:309-319. [PMID: 34415308 PMCID: PMC8742999 DOI: 10.1093/hmg/ddab240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 04/16/2021] [Revised: 07/27/2021] [Accepted: 08/11/2021] [Indexed: 01/03/2023] Open
Abstract
We conducted cohort- and race-specific epigenome-wide association analyses of mitochondrial deoxyribonucleic acid (mtDNA) copy number (mtDNA CN) measured in whole blood from participants of African and European origins in five cohorts (n = 6182, mean age = 57-67 years, 65% women). In the meta-analysis of all the participants, we discovered 21 mtDNA CN-associated DNA methylation sites (CpG) (P < 1 × 10-7), with a 0.7-3.0 standard deviation increase (3 CpGs) or decrease (18 CpGs) in mtDNA CN corresponding to a 1% increase in DNA methylation. Several significant CpGs have been reported to be associated with at least two risk factors (e.g. chronological age or smoking) for cardiovascular disease (CVD). Five genes [PR/SET domain 16, nuclear receptor subfamily 1 group H member 3 (NR1H3), DNA repair protein, DNA polymerase kappa and decaprenyl-diphosphate synthase subunit 2], which harbor nine significant CpGs, are known to be involved in mitochondrial biosynthesis and functions. For example, NR1H3 encodes a transcription factor that is differentially expressed during an adipose tissue transition. The methylation level of cg09548275 in NR1H3 was negatively associated with mtDNA CN (effect size = -1.71, P = 4 × 10-8) and was positively associated with the NR1H3 expression level (effect size = 0.43, P = 0.0003), which indicates that the methylation level in NR1H3 may underlie the relationship between mtDNA CN, the NR1H3 transcription factor and energy expenditure. In summary, the study results suggest that mtDNA CN variation in whole blood is associated with DNA methylation levels in genes that are involved in a wide range of mitochondrial activities. These findings will help reveal molecular mechanisms between mtDNA CN and CVD.
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Affiliation(s)
- Penglong Wang
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christina A Castellani
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario N6A 5C1, Canada
| | - Jie Yao
- 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
| | - Tianxiao Huan
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffrey Haessler
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Roby Joehanes
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xianbang Sun
- Department of Biostatistics, Boston University, Boston, MA 02118, 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 90502, USA
| | - Ryan J Longchamps
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - JoAnn E Manson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Megan L Grove
- 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
| | - Jan Bressler
- 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
| | - Kent D Taylor
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario N6A 5C1, Canada
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY 10013, USA
- Department of Systems Biology, Columbia University, New York, NY 10034, USA
| | - Silva Kasela
- New York Genome Center, New York, NY 10013, USA
- Department of Systems Biology, Columbia University, New York, NY 10034, USA
| | - David J Van Den Berg
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90033, USA
| | - Lifang Hou
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Alexander Reiner
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yongmei Liu
- Department of Medicine, Divisions of Cardiology and Neurology, Duke University Medical Center, Durham, NC 27704, 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
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Myriam Fornage
- 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
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, 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
| | - Charles Kooperberg
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Dan E Arking
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Framingham Heart Study, National Heart, Lung, and Blood Institute (NHLBI), Framingham, MA 01702, USA
| | - Chunyu Liu
- Department of Biostatistics, Boston University, Boston, MA 02118, USA
- Framingham Heart Study, National Heart, Lung, and Blood Institute (NHLBI), Framingham, MA 01702, USA
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8
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McCartney DL, Min JL, Richmond RC, Lu AT, Sobczyk MK, Davies G, Broer L, Guo X, Jeong A, Jung J, Kasela S, Katrinli S, Kuo PL, Matias-Garcia PR, Mishra PP, Nygaard M, Palviainen T, Patki A, Raffield LM, Ratliff SM, Richardson TG, Robinson O, Soerensen M, Sun D, Tsai PC, van der Zee MD, Walker RM, Wang X, Wang Y, Xia R, Xu Z, Yao J, Zhao W, Correa A, Boerwinkle E, Dugué PA, Durda P, Elliott HR, Gieger C, de Geus EJC, Harris SE, Hemani G, Imboden M, Kähönen M, Kardia SLR, Kresovich JK, Li S, Lunetta KL, Mangino M, Mason D, McIntosh AM, Mengel-From J, Moore AZ, Murabito JM, Ollikainen M, Pankow JS, Pedersen NL, Peters A, Polidoro S, Porteous DJ, Raitakari O, Rich SS, Sandler DP, Sillanpää E, Smith AK, Southey MC, Strauch K, Tiwari H, Tanaka T, Tillin T, Uitterlinden AG, Van Den Berg DJ, van Dongen J, Wilson JG, Wright J, Yet I, Arnett D, Bandinelli S, Bell JT, Binder AM, Boomsma DI, Chen W, Christensen K, Conneely KN, Elliott P, Ferrucci L, Fornage M, Hägg S, Hayward C, Irvin M, Kaprio J, Lawlor DA, Lehtimäki T, Lohoff FW, Milani L, Milne RL, Probst-Hensch N, Reiner AP, Ritz B, Rotter JI, Smith JA, Taylor JA, van Meurs JBJ, Vineis P, Waldenberger M, Deary IJ, Relton CL, Horvath S, Marioni RE. Genome-wide association studies identify 137 genetic loci for DNA methylation biomarkers of aging. Genome Biol 2021; 22:194. [PMID: 34187551 PMCID: PMC8243879 DOI: 10.1186/s13059-021-02398-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [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: 10/14/2020] [Accepted: 06/03/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Biological aging estimators derived from DNA methylation data are heritable and correlate with morbidity and mortality. Consequently, identification of genetic and environmental contributors to the variation in these measures in populations has become a major goal in the field. RESULTS Leveraging DNA methylation and SNP data from more than 40,000 individuals, we identify 137 genome-wide significant loci, of which 113 are novel, from genome-wide association study (GWAS) meta-analyses of four epigenetic clocks and epigenetic surrogate markers for granulocyte proportions and plasminogen activator inhibitor 1 levels, respectively. We find evidence for shared genetic loci associated with the Horvath clock and expression of transcripts encoding genes linked to lipid metabolism and immune function. Notably, these loci are independent of those reported to regulate DNA methylation levels at constituent clock CpGs. A polygenic score for GrimAge acceleration showed strong associations with adiposity-related traits, educational attainment, parental longevity, and C-reactive protein levels. CONCLUSION This study illuminates the genetic architecture underlying epigenetic aging and its shared genetic contributions with lifestyle factors and longevity.
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Affiliation(s)
- Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Josine L Min
- MRC Integrative Epidemiology Unit University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Maria K Sobczyk
- MRC Integrative Epidemiology Unit University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Gail Davies
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Linda Broer
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - 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
| | - Ayoung Jeong
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jeesun Jung
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, USA
| | - Silva Kasela
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Seyma Katrinli
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Pei-Lun Kuo
- Longitudinal Study Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Pamela R Matias-Garcia
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland
| | - Marianne Nygaard
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Amit Patki
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott M Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Oliver Robinson
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Mette Soerensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Dianjianyi Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Matthijs D van der Zee
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Xiaochuan Wang
- Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, Victoria, 3004, Australia
| | - Yunzhang Wang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden
| | - Rui Xia
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zongli Xu
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, 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
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Eric Boerwinkle
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Pierre-Antoine Dugué
- Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, Victoria, 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, 3168, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, 207 Bouverie Street, Melbourne, Victoria, 3010, Australia
| | - Peter Durda
- Department of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05446, USA
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
| | - Eco J C de Geus
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33521, Tampere, Finland
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Jacob K Kresovich
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Shengxu Li
- Children's Minnesota Research Institute, Children's Minnesota, Minneapolis, MN, 55404, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, USA
| | - 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, SE1 9RT, UK
| | - Dan Mason
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | | | - Jonas Mengel-From
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Ann Zenobia Moore
- Longitudinal Study Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Joanne M Murabito
- Section of General Internal Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - James S Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Silvia Polidoro
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Olli 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
| | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Dale P Sandler
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Elina Sillanpää
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Gerontology Research Center, Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, Victoria, 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, 3168, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, 207 Bouverie Street, Melbourne, Victoria, 3010, Australia
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, 55101, Mainz, Germany
- Chair of Genetic Epidemiology, Institute for Medical Information Processing, Biometry, and Epidemiology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hemant Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, USA
| | - Toshiko Tanaka
- Longitudinal Study Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Therese Tillin
- MRC Unit for Lifelong Health and Ageing at UCL, London, UK
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - David J Van Den Berg
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - James G Wilson
- Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - John Wright
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Idil Yet
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Bioinformatics, Institute of Health Sciences, Hacettepe University, 06100, Ankara, Turkey
| | - Donna Arnett
- Deans Office, College of Public Health, University of Kentucky, Lexington, UK
| | | | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Alexandra M Binder
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, USA
- Population Sciences in the Pacific Program (Cancer Epidemiology), University of Hawai'i Cancer Center, University of Hawai'i, Honolulu, HI, USA
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Wei Chen
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Kaare Christensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Paul Elliott
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Luigi Ferrucci
- Longitudinal Study Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd. South, Edinburgh, EH4 2XU, UK
| | - Marguerite Irvin
- Dept of Epidemiology, University of Alabama at Birmingham, Birmingham, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland
| | - Falk W Lohoff
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, USA
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, Victoria, 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, 3168, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, 207 Bouverie Street, Melbourne, Victoria, 3010, Australia
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Beate Ritz
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, 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, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Jack A Taylor
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Paolo Vineis
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Ian J Deary
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK.
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9
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Graff M, Justice AE, Young KL, Marouli E, Zhang X, Fine RS, Lim E, Buchanan V, Rand K, Feitosa MF, Wojczynski MK, Yanek LR, Shao Y, Rohde R, Adeyemo AA, Aldrich MC, Allison MA, Ambrosone CB, Ambs S, Amos C, Arnett DK, Atwood L, Bandera EV, Bartz T, Becker DM, Berndt SI, Bernstein L, Bielak LF, Blot WJ, Bottinger EP, Bowden DW, Bradfield JP, Brody JA, Broeckel U, Burke G, Cade BE, Cai Q, Caporaso N, Carlson C, Carpten J, Casey G, Chanock SJ, Chen G, Chen M, Chen YDI, Chen WM, Chesi A, Chiang CWK, Chu L, Coetzee GA, Conti DV, Cooper RS, Cushman M, Demerath E, Deming SL, Dimitrov L, Ding J, Diver WR, Duan Q, Evans MK, Falusi AG, Faul JD, Fornage M, Fox C, Freedman BI, Garcia M, Gillanders EM, Goodman P, Gottesman O, Grant SFA, Guo X, Hakonarson H, Haritunians T, Harris TB, Harris CC, Henderson BE, Hennis A, Hernandez DG, Hirschhorn JN, McNeill LH, Howard TD, Howard B, Hsing AW, Hsu YHH, Hu JJ, Huff CD, Huo D, Ingles SA, Irvin MR, John EM, Johnson KC, Jordan JM, Kabagambe EK, Kang SJ, Kardia SL, Keating BJ, Kittles RA, Klein EA, Kolb S, Kolonel LN, Kooperberg C, Kuller L, Kutlar A, Lange L, Langefeld CD, Le Marchand L, Leonard H, Lettre G, Levin AM, Li Y, Li J, Liu Y, Liu Y, Liu S, Lohman K, Lotay V, Lu Y, Maixner W, Manson JE, McKnight B, Meng Y, Monda KL, Monroe K, Moore JH, Mosley TH, Mudgal P, Murphy AB, Nadukuru R, Nalls MA, Nathanson KL, Nayak U, N'Diaye A, Nemesure B, Neslund-Dudas C, Neuhouser ML, Nyante S, Ochs-Balcom H, Ogundiran TO, Ogunniyi A, Ojengbede O, Okut H, Olopade OI, Olshan A, Padhukasahasram B, Palmer J, Palmer CD, Palmer ND, Papanicolaou G, Patel SR, Pettaway CA, Peyser PA, Press MF, Rao DC, Rasmussen-Torvik LJ, Redline S, Reiner AP, Rhie SK, Rodriguez-Gil JL, Rotimi CN, Rotter JI, Ruiz-Narvaez EA, Rybicki BA, Salako B, Sale MM, Sanderson M, Schadt E, Schreiner PJ, Schurmann C, Schwartz AG, Shriner DA, Signorello LB, Singleton AB, Siscovick DS, Smith JA, Smith S, Speliotes E, Spitz M, Stanford JL, Stevens VL, Stram A, Strom SS, Sucheston L, Sun YV, Tajuddin SM, Taylor H, Taylor K, Tayo BO, Thun MJ, Tucker MA, Vaidya D, Van Den Berg DJ, Vedantam S, Vitolins M, Wang Z, Ware EB, Wassertheil-Smoller S, Weir DR, Wiencke JK, Williams SM, Williams LK, Wilson JG, Witte JS, Wrensch M, Wu X, Yao J, Zakai N, Zanetti K, Zemel BS, Zhao W, Zhao JH, Zheng W, Zhi D, Zhou J, Zhu X, Ziegler RG, Zmuda J, Zonderman AB, Psaty BM, Borecki IB, Cupples LA, Liu CT, Haiman CA, Loos R, Ng MCY, North KE. Discovery and fine-mapping of height loci via high-density imputation of GWASs in individuals of African ancestry. Am J Hum Genet 2021; 108:564-582. [PMID: 33713608 PMCID: PMC8059339 DOI: 10.1016/j.ajhg.2021.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 06/05/2020] [Accepted: 02/09/2021] [Indexed: 01/21/2023] Open
Abstract
Although many loci have been associated with height in European ancestry populations, very few have been identified in African ancestry individuals. Furthermore, many of the known loci have yet to be generalized to and fine-mapped within a large-scale African ancestry sample. We performed sex-combined and sex-stratified meta-analyses in up to 52,764 individuals with height and genome-wide genotyping data from the African Ancestry Anthropometry Genetics Consortium (AAAGC). We additionally combined our African ancestry meta-analysis results with published European genome-wide association study (GWAS) data. In the African ancestry analyses, we identified three novel loci (SLC4A3, NCOA2, ECD/FAM149B1) in sex-combined results and two loci (CRB1, KLF6) in women only. In the African plus European sex-combined GWAS, we identified an additional three novel loci (RCCD1, G6PC3, CEP95) which were equally driven by AAAGC and European results. Among 39 genome-wide significant signals at known loci, conditioning index SNPs from European studies identified 20 secondary signals. Two of the 20 new secondary signals and none of the 8 novel loci had minor allele frequencies (MAF) < 5%. Of 802 known European height signals, 643 displayed directionally consistent associations with height, of which 205 were nominally significant (p < 0.05) in the African ancestry sex-combined sample. Furthermore, 148 of 241 loci contained ≤20 variants in the credible sets that jointly account for 99% of the posterior probability of driving the associations. In summary, trans-ethnic meta-analyses revealed novel signals and further improved fine-mapping of putative causal variants in loci shared between African and European ancestry populations.
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Affiliation(s)
- Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Anne E Justice
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Population Health Services, Geisinger Health, Danville, PA 17822, USA
| | - Kristin L Young
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - 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, Life Sciences, Queen Mary University of London, London EC1M 6BQ, UK
| | - Xinruo Zhang
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Elise Lim
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Victoria Buchanan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kristin Rand
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Mary K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yaming Shao
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rebecca Rohde
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Melinda C Aldrich
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Thoracic Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Matthew A Allison
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA 92093, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Christopher Amos
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Donna K Arnett
- School of Public Health, University of Kentucky, Lexington, KY 40563, USA
| | - Larry Atwood
- Framingham Heart Study, Boston University School of Medicine, Boston, MA 02118, USA
| | - Elisa V Bandera
- Department of Population Science, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Traci Bartz
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA; Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Diane M Becker
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Leslie Bernstein
- Division of Biomarkers of Early Detection and Prevention, Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; International Epidemiology Institute, Rockville, MD 20850, USA
| | - Erwin P Bottinger
- The Charles R. Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Donald W Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Diabetes Research, Wake Forest school of Medicine, Winston-Salem, NC 27157, USA
| | - Jonathan P Bradfield
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Ulrich Broeckel
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Gregory Burke
- Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Chris Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - John Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Minhui Chen
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yii-Der I Chen
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Wei-Min Chen
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Alessandra Chesi
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Lisa Chu
- Cancer Prevention Institute of California, Fremont, CA 94538, USA
| | - Gerry A Coetzee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA; Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, LA 90033, USA
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Richard S Cooper
- Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago Stritch School of Medicine, Maywood, IL 60153, USA
| | - Mary Cushman
- Department of Medicine, University of Vermont College of Medicine, Burlington, VT 05405, USA
| | - Ellen Demerath
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN 55455, USA
| | - Sandra L Deming
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Latchezar Dimitrov
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Jingzhong Ding
- Section on Gerontology and Geriatric Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, GA 30303, USA
| | - Qing Duan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michele K Evans
- Health Disparities Research Section, Clinical Research Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Adeyinka G Falusi
- Institute for Medical Research and Training, University of Ibadan, Ibadan, Nigeria
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| | - Myriam Fornage
- Center for Human Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Caroline Fox
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Framingham Heart Study, Framingham, MA 01702, USA; Division of Endocrinology and Metabolism, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Melissa Garcia
- National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Elizabeth M Gillanders
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD 20892, USA
| | - Phyllis Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Omri Gottesman
- The Charles R. Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Struan F A Grant
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia Research Institute, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Talin Haritunians
- Medical Genetics Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Tamara B Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Anselm Hennis
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Chronic Disease Research Centre and Faculty of Medical Sciences, University of West Indies, Bridgetown, Barbados; Ministry of Health, Bridgetown, Barbados
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Joel N Hirschhorn
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lorna Haughton McNeill
- Department of Health Disparities Research, Division of OVP, Cancer Prevention and Population Sciences, and Center for Community Implementation and Dissemination Research, Duncan Family Institute, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Timothy D Howard
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | | | - Ann W Hsing
- Cancer Prevention Institute of California, Fremont, CA 94538, USA; Department of Medicine, Stanford Prevention Research Center and Cancer Institute, Stanford, CA 94305, USA
| | - Yu-Han H Hsu
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jennifer J Hu
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Chad D Huff
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Esther M John
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Karen C Johnson
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Joanne M Jordan
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Edmond K Kabagambe
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Sun J Kang
- Genetic Epidemiology Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sharon L Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brendan J Keating
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rick A Kittles
- Division of Health Equities, Department of Population Sciences, City of Hope Medical Center, Duarte, CA 91010, USA
| | - Eric A Klein
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Laurence N Kolonel
- Epidemiology Program, Cancer Research Center, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Lewis Kuller
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Abdullah Kutlar
- Sickle Cell Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Leslie Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Loic Le Marchand
- Epidemiology Program, Cancer Research Center, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Hampton Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA; Data Tecnica Int'l, LLC, Glen Echo, MD 20812, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; Department of Medicine, Université de Montréal, Montréal, QC H1T 1C8, Canada
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI 48202, USA
| | - Yun Li
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jin Li
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Yongmei Liu
- Department of Medicine, Division of Cardiology, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
| | - Youfang Liu
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Simin Liu
- Department of Epidemiology, Brown University, Providence, RI 02912, USA
| | - Kurt Lohman
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Vaneet Lotay
- The Charles R. Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; The Charles R. Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - William Maixner
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University Medical Center, Durham, NC 27710, USA
| | - JoAnn E Manson
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Barbara McKnight
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA; Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Yan Meng
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Keri L Monda
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; The Center for Observational Research, Amgen, Inc., Thousand Oaks, CA 91320, USA
| | - Kris Monroe
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jason H Moore
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas H Mosley
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Poorva Mudgal
- Center for Diabetes Research, Wake Forest school of Medicine, Winston-Salem, NC 27157, USA
| | - Adam B Murphy
- Department of Urology, Northwestern University, Chicago, IL 60611, USA
| | - Rajiv Nadukuru
- The Charles R. Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA; Data Tecnica Int'l, LLC, Glen Echo, MD 20812, USA
| | | | - Uma Nayak
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | | | - Barbara Nemesure
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Marian L Neuhouser
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Sarah Nyante
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Heather Ochs-Balcom
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, The State University of New York, Buffalo, NY 14214, USA
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adesola Ogunniyi
- Department of Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oladosu Ojengbede
- Centre for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Hayrettin Okut
- Center for Diabetes Research, Wake Forest school of Medicine, Winston-Salem, NC 27157, USA
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Andrew Olshan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Badri Padhukasahasram
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, MI 48202, USA
| | - Julie Palmer
- Slone Epidemiology Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Cameron D Palmer
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Nicholette D Palmer
- Department of Biochemistry, School of Medicine, Wake Forest University, Winston-Salem, NC 27157, USA
| | - George Papanicolaou
- Division of Cardiovascular Sciences, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sanjay R Patel
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Curtis A Pettaway
- Department of Urology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael F Press
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - D C Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Suhn K Rhie
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Jorge L Rodriguez-Gil
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Edward A Ruiz-Narvaez
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI 48202, USA
| | - Babatunde Salako
- Centre for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Michele M Sale
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN 37208, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pamela J Schreiner
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN 55455, USA
| | - Claudia Schurmann
- The Charles R. Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ann G Schwartz
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA; Karmanos Cancer Institute, Detroit, MI 48201, USA
| | - Daniel A Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lisa B Signorello
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; International Epidemiology Institute, Rockville, MD 20850, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | | | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA; Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| | - Shad Smith
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Elizabeth Speliotes
- Division of Gastroenterology and Hepatology, University of Michigan Health System, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Margaret Spitz
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington School of Public Health, Seattle, WA 98195, USA
| | - Victoria L Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, GA 30303, USA
| | - Alex Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Sara S Strom
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lara Sucheston
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Yan V Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Salman M Tajuddin
- National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Herman Taylor
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Kira Taylor
- Department of Epidemiology and Population Health, School of Public Health and Information Sciences, University of Louisville, Louisville, KY 40202, USA
| | - Bamidele O Tayo
- Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago Stritch School of Medicine, Maywood, IL 60153, USA
| | - Michael J Thun
- Epidemiology Research Program, American Cancer Society, Atlanta, GA 30303, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Dhananjay Vaidya
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - David J Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Sailaja Vedantam
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Mara Vitolins
- Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Erin B Ware
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA; Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| | - Sylvia Wassertheil-Smoller
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| | - John K Wiencke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Scott M Williams
- Departments of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - L Keoki Williams
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, MI 48202, USA; Department of Internal Medicine, Henry Ford Health System, Detroit, MI 48202, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jie Yao
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Neil Zakai
- Department of Medicine, University of Vermont College of Medicine, Burlington, VT 05405, USA
| | - Krista Zanetti
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD 20892, USA
| | - Babette S Zemel
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Gastroenterology, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jing Hua Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Degui Zhi
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaofeng Zhu
- Departments of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Regina G Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Joe Zmuda
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Ingrid B Borecki
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA; BioData Catalyst Program, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA; Framingham Heart Study, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Ruth Loos
- The Charles R. Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maggie C Y Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Diabetes Research, Wake Forest school of Medicine, Winston-Salem, NC 27157, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Taliun D, Harris DN, Kessler MD, Carlson J, Szpiech ZA, Torres R, Taliun SAG, Corvelo A, Gogarten SM, Kang HM, Pitsillides AN, LeFaive J, Lee SB, Tian X, Browning BL, Das S, Emde AK, Clarke WE, Loesch DP, Shetty AC, Blackwell TW, Smith AV, Wong Q, Liu X, Conomos MP, Bobo DM, Aguet F, Albert C, Alonso A, Ardlie KG, Arking DE, Aslibekyan S, Auer PL, Barnard J, Barr RG, Barwick L, Becker LC, Beer RL, Benjamin EJ, Bielak LF, Blangero J, Boehnke M, Bowden DW, Brody JA, Burchard EG, Cade BE, Casella JF, Chalazan B, Chasman DI, Chen YDI, Cho MH, Choi SH, Chung MK, Clish CB, Correa A, Curran JE, Custer B, Darbar D, Daya M, de Andrade M, DeMeo DL, Dutcher SK, Ellinor PT, Emery LS, Eng C, Fatkin D, Fingerlin T, Forer L, Fornage M, Franceschini N, Fuchsberger C, Fullerton SM, Germer S, Gladwin MT, Gottlieb DJ, Guo X, Hall ME, He J, Heard-Costa NL, Heckbert SR, Irvin MR, Johnsen JM, Johnson AD, Kaplan R, Kardia SLR, Kelly T, Kelly S, Kenny EE, Kiel DP, Klemmer R, Konkle BA, Kooperberg C, Köttgen A, Lange LA, Lasky-Su J, Levy D, Lin X, Lin KH, Liu C, Loos RJF, Garman L, Gerszten R, Lubitz SA, Lunetta KL, Mak ACY, Manichaikul A, Manning AK, Mathias RA, McManus DD, McGarvey ST, Meigs JB, Meyers DA, Mikulla JL, Minear MA, Mitchell BD, Mohanty S, Montasser ME, Montgomery C, Morrison AC, Murabito JM, Natale A, Natarajan P, Nelson SC, North KE, O'Connell JR, Palmer ND, Pankratz N, Peloso GM, Peyser PA, Pleiness J, Post WS, Psaty BM, Rao DC, Redline S, Reiner AP, Roden D, Rotter JI, Ruczinski I, Sarnowski C, Schoenherr S, Schwartz DA, Seo JS, Seshadri S, Sheehan VA, Sheu WH, Shoemaker MB, Smith NL, Smith JA, Sotoodehnia N, Stilp AM, Tang W, Taylor KD, Telen M, Thornton TA, Tracy RP, Van Den Berg DJ, Vasan RS, Viaud-Martinez KA, Vrieze S, Weeks DE, Weir BS, Weiss ST, Weng LC, Willer CJ, Zhang Y, Zhao X, Arnett DK, Ashley-Koch AE, Barnes KC, Boerwinkle E, Gabriel S, Gibbs R, Rice KM, Rich SS, Silverman EK, Qasba P, Gan W, Papanicolaou GJ, Nickerson DA, Browning SR, Zody MC, Zöllner S, Wilson JG, Cupples LA, Laurie CC, Jaquish CE, Hernandez RD, O'Connor TD, Abecasis GR. Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature 2021; 590:290-299. [PMID: 33568819 PMCID: PMC7875770 DOI: 10.1038/s41586-021-03205-y] [Citation(s) in RCA: 801] [Impact Index Per Article: 267.0] [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: 03/06/2019] [Accepted: 01/07/2021] [Indexed: 02/08/2023]
Abstract
The Trans-Omics for Precision Medicine (TOPMed) programme seeks to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases. The initial phases of the programme focused on whole-genome sequencing of individuals with rich phenotypic data and diverse backgrounds. Here we describe the TOPMed goals and design as well as the available resources and early insights obtained from the sequence data. The resources include a variant browser, a genotype imputation server, and genomic and phenotypic data that are available through dbGaP (Database of Genotypes and Phenotypes)1. In the first 53,831 TOPMed samples, we detected more than 400 million single-nucleotide and insertion or deletion variants after alignment with the reference genome. Additional previously undescribed variants were detected through assembly of unmapped reads and customized analysis in highly variable loci. Among the more than 400 million detected variants, 97% have frequencies of less than 1% and 46% are singletons that are present in only one individual (53% among unrelated individuals). These rare variants provide insights into mutational processes and recent human evolutionary history. The extensive catalogue of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and noncoding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and reach of genome-wide association studies to include variants down to a frequency of approximately 0.01%.
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Affiliation(s)
- 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
| | - Daniel N Harris
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michael D Kessler
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jedidiah Carlson
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Zachary A Szpiech
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, USA
| | - Raul Torres
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, 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
| | | | | | - Hyun Min Kang
- 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
| | | | - Jonathon LeFaive
- 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
| | - Seung-Been Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Xiaowen Tian
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Brian L Browning
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Sayantan Das
- 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
| | | | | | - Douglas P Loesch
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Thomas W Blackwell
- 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
| | - Albert V Smith
- 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
| | - Quenna Wong
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Xiaoming Liu
- USF Genomics, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Dean M Bobo
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - François Aguet
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin Milwaukee, Milwaukee, WI, USA
| | | | - R Graham Barr
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
- Department of Epidemiology, Columbia University Medical Center, New York, NY, USA
| | | | | | - Rebecca L Beer
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emelia J Benjamin
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Lawrence F Bielak
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, 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
| | - 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
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A Brody
- Department of Medicine, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Esteban G Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Brian E Cade
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - James F Casella
- Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA
- Division of Pediatric Hematology, Johns Hopkins University, Baltimore, MD, USA
| | - Brandon Chalazan
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Mina K Chung
- Department of Cardiovascular Medicine, Heart & Vascular Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Clary B Clish
- Metabolomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Population Health Science, University of Mississippi Medical Center, Jackson, MS, 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
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Dawood Darbar
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Michelle Daya
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Susan K Dutcher
- McDonnell Genome Institute, Washington University, St Louis, MO, USA
- Department of Genetics, Washington University, St Louis, MO, USA
| | - Patrick T Ellinor
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Leslie S Emery
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Diane Fatkin
- Molecular Cardiology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Kensington, New South Wales, Australia
- Cardiology Department, St Vincent's Hospital, Darlinghurst, New South Wales, Australia
| | - Tasha Fingerlin
- National Jewish Health, Center for Genes, Environment and Health, Denver, CO, USA
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Myriam Fornage
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - 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 of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Stephanie M Fullerton
- Department of Bioethics & Humanities, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Mark T Gladwin
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel J Gottlieb
- VA Boston Healthcare System, Boston, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Michael E Hall
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jiang He
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
- Tulane University Translational Science Institute, Tulane University, New Orleans, LA, USA
| | - Nancy L Heard-Costa
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Susan R Heckbert
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jill M Johnsen
- Department of Medicine, University of Washington, Seattle, WA, USA
- Bloodworks Northwest Research Institute, Seattle, WA, USA
| | - Andrew D Johnson
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Framingham, MA, USA
| | - Robert Kaplan
- Albert Einstein College of Medicine, New York, NY, USA
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Tanika Kelly
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
| | - Shannon Kelly
- Department of Epidemiology, Vitalant Research Institute, San Francisco, CA, USA
- Department of Pediatrics, UCSF Benioff Children's Hospital, Oakland, CA, USA
- Division of Pediatric Hematology, UCSF Benioff Children's Hospital, Oakland, CA, USA
| | - Eimear E Kenny
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Douglas P Kiel
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Robert Klemmer
- 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
| | - Barbara A Konkle
- Department of Medicine, University of Washington, Seattle, WA, USA
- Bloodworks Northwest Research Institute, Seattle, WA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Leslie A Lange
- Department of Medicine, University of Colorado at Denver, Aurora, CO, USA
| | - Jessica Lasky-Su
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Daniel Levy
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Framingham, MA, USA
| | - Xihong Lin
- Biostatistics and Statistics, Harvard University, Boston, MA, USA
| | - Keng-Han Lin
- 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
| | - Chunyu Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, 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
| | - Lori Garman
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | | | | | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Angel C Y Mak
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Alisa K Manning
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, USA
- Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David D McManus
- Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Stephen T McGarvey
- International Health Institute, Brown University, Providence, RI, USA
- Department of Epidemiology, Brown University, Providence, RI, USA
- Department of Anthropology, Brown University, Providence, RI, USA
| | - James B Meigs
- Division of General Internal Medicine, Massachusetts General Hospital, Harvard Medical School, The Broad Institute of MIT and Harvard, Boston, MA, USA
| | | | - Julie L Mikulla
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mollie A Minear
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Braxton D Mitchell
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Sanghamitra Mohanty
- Texas Cardiac Arrhythmia Institute, St David's Medical Center, Austin, TX, USA
- Department of Internal Medicine, Dell Medical School, Austin, TX, USA
| | - May E Montasser
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Courtney Montgomery
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joanne M Murabito
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Andrea Natale
- Texas Cardiac Arrhythmia Institute, St David's Medical Center, Austin, TX, USA
| | - Pradeep Natarajan
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sarah C Nelson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Jeffrey R O'Connell
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jacob Pleiness
- 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
| | - Wendy S Post
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Bruce M Psaty
- Department of Medicine, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Services, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - D C Rao
- Division of Biostatistics, Washington University in St Louis, St Louis, MO, USA
| | - Susan Redline
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Dan Roden
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Chloé Sarnowski
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Sebastian Schoenherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Jeong-Sun Seo
- Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Macrogen Inc, Seoul, Republic of Korea
- Gong Wu Genomic Medicine Institute, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Sudha Seshadri
- Framingham Heart Study, Framingham, MA, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center at San Antonio, San Antonio, TX, USA
| | - Vivien A Sheehan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Wayne H Sheu
- Taichung Veterans General Hospital Taiwan, Taichung City, Taiwan
| | | | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
| | - 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
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Weihong Tang
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | | | - Russell P Tracy
- Department of Pathology & Laboratory Medicine, University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - David J Van Den Berg
- Center for Genetic Epidemiology, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ramachandran S Vasan
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | | | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Daniel E Weeks
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Scott T Weiss
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | | | - Cristen J Willer
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine-Cardiology, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Yingze Zhang
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xutong Zhao
- 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
| | - Donna K Arnett
- Department of Epidemiology, University of Kentucky, Lexington, KY, USA
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Eric Boerwinkle
- University of Texas Health Science Center at Houston, Houston, TX, USA
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Stacey Gabriel
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Pankaj Qasba
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Weiniu Gan
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - George J Papanicolaou
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Northwest Genomics Center, Seattle, WA, USA
- Brotman Baty Institute, Seattle, WA, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - Sebastian Zöllner
- 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
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
- Framingham Heart Study, Framingham, MA, USA.
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA.
| | - Cashell E Jaquish
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Gonçalo R Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA.
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Du Z, Weinhold N, Song GC, Rand KA, Van Den Berg DJ, Hwang AE, Sheng X, Hom V, Ailawadhi S, Nooka AK, Singhal S, Pawlish K, Peters E, Bock C, Mohrbacher A, Stram A, Berndt SI, Blot WJ, Casey G, Stevens VL, Kittles R, Goodman PJ, Diver WR, Hennis A, Nemesure B, Klein EA, Rybicki BA, Stanford JL, Witte JS, Signorello L, John EM, Bernstein L, Stroup A, Stephens OW, Zangari M, Van Rhee F, Olshan A, Zheng W, Hu JJ, Ziegler R, Nyante SJ, Ingles SA, Press M, Carpten JD, Chanock S, Mehta J, Colditz GA, Wolf J, Martin TG, Tomasson M, Fiala MA, Terebelo H, Janakiraman N, Kolonel L, Anderson KC, Le Marchand L, Auclair D, Chiu BCH, Ziv E, Stram D, Vij R, Bernal-Mizrachi L, Morgan GJ, Zonder JA, Huff CA, Lonial S, Orlowski RZ, Conti DV, Haiman CA, Cozen W. Abstract PR05: A meta-analysis of genome-wide association study and eQTL analysis of multiple myeloma among African Americans. Cancer Epidemiol Biomarkers Prev 2020. [DOI: 10.1158/1538-7755.disp19-pr05] [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] Open
Abstract
Abstract
Background: Persons of African ancestry (AA) experience a 1.5-2-fold risk of multiple myeloma (MM) compared to persons of European ancestry (EA). We assembled a set of MM patients with self-reported AA in order to evaluate the contribution of genetics to etiology in this high-risk group.
Methods: Here we present the results of a meta-analysis of two GWAS in 1,813 cases and 8,871 controls of AA. We also conducted an admixture mapping scan to identify risk alleles associated with local ancestry, fine-mapped the 23 known susceptibility loci to find markers that could better capture MM risk in individuals of AA, and constructed a polygenic risk score (PRS) to assess the aggregated effect of known MM risk alleles. Finally, we conducted an eQTL analysis measuring gene expression in those genes harboring a risk variant in malignant plasma cells from 292 of the patients from a single site.
Results: In GWAS analysis, we identified two suggestive novel loci located at 9p24.3 and 9p13.1 at P<1 × 10-6, but no genome-wide significant association was noted. In admixture mapping, we observed a genome-wide significant inverse association between local AA at 2p24.1-23.1 and MM risk in AA individuals. 20 of the 23 known EA risk variants showed directional consistency and 9 replicated at P<0.05 in AA individuals. In eight regions, we identified markers that better capture MM risk in persons of AA. AA individuals with a PRS in the top 10% had a 1.82-fold (95%CI: 1.56, 2.11) increased MM risk compared to those with average risk (25-75%). The strongest functional association was between the risk allele for variant rs56219066 at 5q15 and lower ELL2 expression (P= 5.1 × 10–12).
Conclusion: Our study shows that common genetic variation contributes to MM risk individuals of AA.
This abstract is also being presented as Poster C040.
Citation Format: Zhaohui Du, Niels Weinhold, Gregory Chi Song, Kristen A. Rand, David J. Van Den Berg, Amie E. Hwang, Xin Sheng, Victor Hom, Sikander Ailawadhi, Ajay K. Nooka, Seema Singhal, Karen Pawlish, Edward Peters, Cathryn Bock, Ann Mohrbacher, Alexander Stram, Sonja I. Berndt, William J. Blot, Graham Casey, Victoria L. Stevens, Rick Kittles, Phyllis J. Goodman, W. Ryan Diver, Anselm Hennis, Barbara Nemesure, Eric A. Klein, Benjamin A. Rybicki, Janet L. Stanford, John S. Witte, Lisa Signorello, Esther M. John, Leslie Bernstein, Antoinette Stroup, Owen W. Stephens, Maurizio Zangari, Frits Van Rhee, Andrew Olshan, Wei Zheng, Jennifer J. Hu, Regina Ziegler, Sarah J. Nyante, Sue Ann Ingles, Michael Press, John David Carpten, Stephen Chanock, Jayesh Mehta, Graham A Colditz, Jeffrey Wolf, Thomas G. Martin, Michael Tomasson, Mark A. Fiala, Howard Terebelo, Nalini Janakiraman, Laurence Kolonel, Kenneth C. Anderson, Loic Le Marchand, Daniel Auclair, Brian C.-H. Chiu, Elad Ziv, Daniel Stram, Ravi Vij, Leon Bernal-Mizrachi, Gareth J. Morgan, Jeffrey A. Zonder, Carol Ann Huff, Sagar Lonial, Robert Z. Orlowski, David V. Conti, Christopher A. Haiman, Wendy Cozen. A meta-analysis of genome-wide association study and eQTL analysis of multiple myeloma among African Americans [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr PR05.
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Affiliation(s)
- Zhaohui Du
- 1Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA,
| | - Niels Weinhold
- 2Myeloma Center, University of Arkansas For Medical Sciences, Little Rock, AR,
| | - Gregory Chi Song
- 2Myeloma Center, University of Arkansas For Medical Sciences, Little Rock, AR,
| | - Kristen A. Rand
- 3Millennium Pharmaceuticals Inc., Takeda Pharmaceutical Company Limited, Cambridge, MA,
| | - David J. Van Den Berg
- 1Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA,
| | - Amie E. Hwang
- 1Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA,
| | - Xin Sheng
- 1Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA,
| | - Victor Hom
- 1Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA,
| | | | - Ajay K. Nooka
- 5Winship Cancer Institute/Hematology and Medical Oncology, Emory University, Atlanta, GA,
| | - Seema Singhal
- 6Feinberg School of Medicine, Northwestern University, Chicago, IL,
| | | | - Edward Peters
- 8Louisiana State University School of Public Health, New Orleans, LA,
| | - Cathryn Bock
- 9Karmanos Cancer Center, Wayne State University, Detroit, MI,
| | - Ann Mohrbacher
- 10Department of Medicine, Division of Hematology, University of Southern California, Los Angeles, CA,
| | | | - Sonja I. Berndt
- 12National Cancer Institute, Division of Cancer Genetics and Epidemiology; NIH, DHHS, Bethesda, MD,
| | | | - Graham Casey
- 14University of Virginia, University of Virginia School of Medicine, Charlottesville, VA,
| | | | - Rick Kittles
- 16City of Hope National Medical Center, Duarte, CA,
| | | | - W. Ryan Diver
- 14University of Virginia, University of Virginia School of Medicine, Charlottesville, VA,
| | | | | | | | | | | | - John S. Witte
- 21University of California San Francisco, San Francisco, CA,
| | - Lisa Signorello
- 12National Cancer Institute, Division of Cancer Genetics and Epidemiology; NIH, DHHS, Bethesda, MD,
| | | | | | | | - Owen W. Stephens
- 2Myeloma Center, University of Arkansas For Medical Sciences, Little Rock, AR,
| | - Maurizio Zangari
- 2Myeloma Center, University of Arkansas For Medical Sciences, Little Rock, AR,
| | - Frits Van Rhee
- 2Myeloma Center, University of Arkansas For Medical Sciences, Little Rock, AR,
| | | | - Wei Zheng
- 13Vanderbilt University, Nashville, TN,
| | - Jennifer J. Hu
- 25University of Miami Miller School of Medicine, Miami, FL,
| | - Regina Ziegler
- 12National Cancer Institute, Division of Cancer Genetics and Epidemiology; NIH, DHHS, Bethesda, MD,
| | | | - Sue Ann Ingles
- 1Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA,
| | - Michael Press
- 26Department of Pathology, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA,
| | - John David Carpten
- 27Center for Translational Genomics, Department of Translational Genomics, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA,
| | - Stephen Chanock
- 12National Cancer Institute, Division of Cancer Genetics and Epidemiology; NIH, DHHS, Bethesda, MD,
| | - Jayesh Mehta
- 6Feinberg School of Medicine, Northwestern University, Chicago, IL,
| | - Graham A Colditz
- 28Division of Oncology, Washington University School of Medicine, St. Louis, MO,
| | - Jeffrey Wolf
- 21University of California San Francisco, San Francisco, CA,
| | | | | | - Mark A. Fiala
- 28Division of Oncology, Washington University School of Medicine, St. Louis, MO,
| | | | | | | | - Kenneth C. Anderson
- 33J. Lipper Cancer Center for Multiple Myeloma, Dana-Farber Cancer Institute, Harvard University, Boston, MA,
| | | | | | - Brian C.-H. Chiu
- 35Department of Public Health Sciences, University of Chicago, Chicago, IL,
| | - Elad Ziv
- 21University of California San Francisco, San Francisco, CA,
| | | | - Ravi Vij
- 28Division of Oncology, Washington University School of Medicine, St. Louis, MO,
| | | | | | | | - Carol Ann Huff
- 39Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD,
| | - Sagar Lonial
- 5Winship Cancer Institute/Hematology and Medical Oncology, Emory University, Atlanta, GA,
| | - Robert Z. Orlowski
- 40Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX
| | - David V. Conti
- 1Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA,
| | - Christopher A. Haiman
- 1Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA,
| | - Wendy Cozen
- 1Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA,
- 26Department of Pathology, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA,
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Yu Y, Brown Wade N, Hwang AE, Nooka AK, Fiala MA, Mohrbacher A, Peters ES, Pawlish K, Bock C, Van Den Berg DJ, Rand KA, Stram D, Conti DV, Auclair D, Colditz GA, Mehta J, Haiman CA, Terebelo H, Janakiraman N, Singhal S, Chiu B, Vij R, Bernal-Mizrachi L, Zonder JA, Huff CA, Lonial S, Orlowski RZ, Cozen W, Ailawadhi S. Variability in Cytogenetic Testing for Multiple Myeloma: A Comprehensive Analysis From Across the United States. JCO Oncol Pract 2020; 16:e1169-e1180. [PMID: 32469686 DOI: 10.1200/jop.19.00639] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
PURPOSE Multiple myeloma (MM) treatment has changed tremendously, with significant improvement in patient out-comes. One group with a suboptimal benefit is patients with high-risk cytogenetics, as tested by conventional karyotyping or fluorescence in situ hybridization (FISH). Methodology for these tests has been published, but not necessarily standardized. METHODS We address variability in the testing and reporting methodology for MM cytogenetics in the United States using the ongoing African American Multiple Myeloma Study (AAMMS). We evaluated clinical and cytogenetic data from 1,221 patients (1,161 with conventional karyotyping and 976 with FISH) tested between 1998 and 2016 across 58 laboratories nationwide. RESULTS Interlab and intralab variability was noted for the number of cells analyzed for karyotyping, with a significantly higher number of cells analyzed in patients in whom cytogenetics were normal (P 5.0025). For FISH testing, CD138-positive cell enrichment was used in 29.7% of patients and no enrichment in 50% of patients, whereas the remainder had unknown status. A significantly smaller number of cells was analyzed for patients in which CD138 cell enrichment was used compared with those without such enrichment (median, 50 v 200; P, .0001). A median of 7 loci probes (range, 1-16) were used for FISH testing across all laboratories, with variability in the loci probed even within a given laboratory. Chromosome 13-related abnormalities were the most frequently tested abnormality (n5956; 97.9%), and t(14;16) was the least frequently tested abnormality (n 5 119; 12.2%). CONCLUSIONS We report significant variability in cytogenetic testing across the United States for MM, potentially leading to variability in risk stratification, with possible clinical implications and personalized treatment approaches.
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Affiliation(s)
- Yang Yu
- Department of Preventive Medicine, Center for Genetic Epidemiology, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA
| | - Niquelle Brown Wade
- Department of Preventive Medicine, Center for Genetic Epidemiology, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA
| | - Amie E Hwang
- Department of Preventive Medicine, Center for Genetic Epidemiology, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA
| | - Ajay K Nooka
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA
| | - Mark A Fiala
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO
| | - Ann Mohrbacher
- Department of Medicine, Division of Hematology, University of Southern California, Los Angeles, CA
| | - Edward S Peters
- Louisiana State University School of Public Health, New Orleans, LA
| | | | - Cathryn Bock
- Karmanos Cancer Center, Wayne State University, Detroit, MI
| | - David J Van Den Berg
- Department of Preventive Medicine, Center for Genetic Epidemiology, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA
| | | | | | - David V Conti
- Department of Preventive Medicine, Center for Genetic Epidemiology, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA
| | | | - Graham A Colditz
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO
| | - Jayesh Mehta
- Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Christopher A Haiman
- Department of Preventive Medicine, Center for Genetic Epidemiology, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA
| | | | | | - Seema Singhal
- Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Brian Chiu
- Department of Public Health Sciences, University of Chicago, Chicago, IL
| | - Ravi Vij
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO
| | | | | | - Carol A Huff
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA
| | - Robert Z Orlowski
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wendy Cozen
- Department of Preventive Medicine, Center for Genetic Epidemiology, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA.,Department of Pathology, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA
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Stobbe MD, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, von Mering C. Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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Gong G, Wang W, Hsieh CL, Van Den Berg DJ, Haiman C, Oakley-Girvan I, Whittemore AS. Data-adaptive multi-locus association testing in subjects with arbitrary genealogical relationships. Stat Appl Genet Mol Biol 2019; 18:sagmb-2018-0030. [PMID: 30956231 DOI: 10.1515/sagmb-2018-0030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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
Genome-wide sequencing enables evaluation of associations between traits and combinations of variants in genes and pathways. But such evaluation requires multi-locus association tests with good power, regardless of the variant and trait characteristics. And since analyzing families may yield more power than analyzing unrelated individuals, we need multi-locus tests applicable to both related and unrelated individuals. Here we describe such tests, and we introduce SKAT-X, a new test statistic that uses genome-wide data obtained from related or unrelated subjects to optimize power for the specific data at hand. Simulations show that: a) SKAT-X performs well regardless of variant and trait characteristics; and b) for binary traits, analyzing affected relatives brings more power than analyzing unrelated individuals, consistent with previous findings for single-locus tests. We illustrate the methods by application to rare unclassified missense variants in the tumor suppressor gene BRCA2, as applied to combined data from prostate cancer families and unrelated prostate cancer cases and controls in the Multi-ethnic Cohort (MEC). The methods can be implemented using open-source code for public use as the R-package GATARS (Genetic Association Tests for Arbitrarily Related Subjects) <https://gailg.github.io/gatars/>.
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Affiliation(s)
- Gail Gong
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wei Wang
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chih-Lin Hsieh
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David J Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Alice S Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA 94305, USA
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15
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Schmit SL, Edlund CK, Schumacher FR, Gong J, Harrison TA, Huyghe JR, Qu C, Melas M, Van Den Berg DJ, Wang H, Tring S, Plummer SJ, Albanes D, Alonso MH, Amos CI, Anton K, Aragaki AK, Arndt V, Barry EL, Berndt SI, Bezieau S, Bien S, Bloomer A, Boehm J, Boutron-Ruault MC, Brenner H, Brezina S, Buchanan DD, Butterbach K, Caan BJ, Campbell PT, Carlson CS, Castelao JE, Chan AT, Chang-Claude J, Chanock SJ, Cheng I, Cheng YW, Chin LS, Church JM, Church T, Coetzee GA, Cotterchio M, Cruz Correa M, Curtis KR, Duggan D, Easton DF, English D, Feskens EJM, Fischer R, FitzGerald LM, Fortini BK, Fritsche LG, Fuchs CS, Gago-Dominguez M, Gala M, Gallinger SJ, Gauderman WJ, Giles GG, Giovannucci EL, Gogarten SM, Gonzalez-Villalpando C, Gonzalez-Villalpando EM, Grady WM, Greenson JK, Gsur A, Gunter M, Haiman CA, Hampe J, Harlid S, Harju JF, Hayes RB, Hofer P, Hoffmeister M, Hopper JL, Huang SC, Huerta JM, Hudson TJ, Hunter DJ, Idos GE, Iwasaki M, Jackson RD, Jacobs EJ, Jee SH, Jenkins MA, Jia WH, Jiao S, Joshi AD, Kolonel LN, Kono S, Kooperberg C, Krogh V, Kuehn T, Küry S, LaCroix A, Laurie CA, Lejbkowicz F, Lemire M, Lenz HJ, Levine D, Li CI, Li L, Lieb W, Lin Y, Lindor NM, Liu YR, Loupakis F, Lu Y, Luh F, Ma J, Mancao C, Manion FJ, Markowitz SD, Martin V, Matsuda K, Matsuo K, McDonnell KJ, McNeil CE, Milne R, Molina AJ, Mukherjee B, Murphy N, Newcomb PA, Offit K, Omichessan H, Palli D, Cotoré JPP, Pérez-Mayoral J, Pharoah PD, Potter JD, Qu C, Raskin L, Rennert G, Rennert HS, Riggs BM, Schafmayer C, Schoen RE, Sellers TA, Seminara D, Severi G, Shi W, Shibata D, Shu XO, Siegel EM, Slattery ML, Southey M, Stadler ZK, Stern MC, Stintzing S, Taverna D, Thibodeau SN, Thomas DC, Trichopoulou A, Tsugane S, Ulrich CM, van Duijnhoven FJB, van Guelpan B, Vijai J, Virtamo J, Weinstein SJ, White E, Win AK, Wolk A, Woods M, Wu AH, Wu K, Xiang YB, Yen Y, Zanke BW, Zeng YX, Zhang B, Zubair N, Kweon SS, Figueiredo JC, Zheng W, Marchand LL, Lindblom A, Moreno V, Peters U, Casey G, Hsu L, Conti DV, Gruber SB. Novel Common Genetic Susceptibility Loci for Colorectal Cancer. J Natl Cancer Inst 2019; 111:146-157. [PMID: 29917119 PMCID: PMC6555904 DOI: 10.1093/jnci/djy099] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [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: 12/27/2017] [Revised: 03/09/2018] [Accepted: 04/27/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10-8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk. METHODS We conducted a GWAS in European descent CRC cases and control subjects using a discovery-replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10-8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided. RESULTS The discovery GWAS identified 11 variants associated with CRC at P < 5 × 10-8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0. CONCLUSIONS This study provides insight into the architecture of common genetic variation contributing to CRC etiology and improves risk prediction for individualized screening.
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Affiliation(s)
- Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | | | | | | | | | | | - Chenxu Qu
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- Public Health Sciences Division
| | - Marilena Melas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | | | - Hansong Wang
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI
| | - Stephanie Tring
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- National Cancer Center, Tokyo, Japan
- Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Sarah J Plummer
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - M Henar Alonso
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- University of Barcelona, Barcelona, Spain
| | | | | | | | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research
| | - Elizabeth L Barry
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | | | - Stephanie Bien
- Centre Hospitalier Universitaire Hotel-Dieu, Nantes, France
| | - Amanda Bloomer
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Juergen Boehm
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT
| | - Marie-Christine Boutron-Ruault
- CESP (U1018 INSERM), Facultés de Médecine Université Paris-Sud, UVSQ, Université Paris-Saclay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research
- German Cancer Consortium
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Stefanie Brezina
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU), Nantes, France
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Colorectal Oncogenomics Group, Department of Pathology (DDB) and Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia
- Genetic Medicine and Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | | | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program of Northern California, Oakland, CA
| | - Peter T Campbell
- Epidemiology Research Program, American Cancer Society, Atlanta, GA
| | | | - Jose E Castelao
- Genetic Oncology Unit, Instituto de Investigación Sanitaria Galicia Sur (IISGS), Complejo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo (Pontevedra) Spain
| | - Andrew T Chan
- Division of Gastroenterology
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA
| | - Jenny Chang-Claude
- Unit of Genetic Epidemiology, Division of Cancer Epidemiology
- Harvard Medical School, Boston, MA
- University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, CA
| | - Ya-Wen Cheng
- Ph.D. Program of Cancer Research and Drug Discovery
| | - Lee Soo Chin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - James M Church
- Department of Colorectal Surgery, Cleveland Clinic, Cleveland, OH
| | - Timothy Church
- Division of Environmental Health Sciences, University of Minnesota, Minneapolis, MN
| | | | | | | | | | - David Duggan
- Genetic Basis of Human Disease Division, Translational Genomics Research Institute, Phoenix, AZ
| | | | - Dallas English
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Edith J M Feskens
- Division of Human Nutrition, Wageningen University and Research, Wageningen, the Netherlands
| | - Rocky Fischer
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI
| | - Liesel M FitzGerald
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Lars G Fritsche
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Sør-Trøndelag, Norway
| | - Charles S Fuchs
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brookline, MA
- Department of Medicine, Brigham and Women’s Institute, Brookline, MA
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Complejo Hospitalario Universitario de Santiago, Servicio Galego de Saude (SERGAS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago De Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | | | - Steven J Gallinger
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - W James Gauderman
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Edward L Giovannucci
- Harvard Medical School, Boston, MA
- Channing Division of Network Medicine, Brigham and Women’s Institute, Brookline, MA
| | | | - Clicerio Gonzalez-Villalpando
- Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Centro de Investigacion en Salud Poblacional, Instituto Nacional de Salud Publica, Cuernavaca, Morelos, Mexico
| | | | - William M Grady
- Department of Medicine, Division of Gastroenterology, School of Medicine
| | - Joel K Greenson
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Andrea Gsur
- Medical University of Vienna, Department of Medicine I, Institute of Cancer Research, Vienna, Austria
| | - Marc Gunter
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA
| | | | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, TU Dresden, Dresden, Germany
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology, Umea University, Umea, Sweden
| | - John F Harju
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY
| | - Philipp Hofer
- Medical University of Vienna, Department of Medicine I, Institute of Cancer Research, Vienna, Austria
| | | | - John L Hopper
- Centre for MEGA Epidemiology, The University of Melbourne, Carlton, Victoria, Australia
| | - Shu-Chen Huang
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Jose Maria Huerta
- Department of Epidemiology, Murcia Regional Health Council, IMIB-Arrixaca, Murcia, Spain
| | - Thomas J Hudson
- AbbVie, Redwood City, CA
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - David J Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Gregory E Idos
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences
| | | | - Eric J Jacobs
- Epidemiology Research Program, American Cancer Society, Atlanta, GA
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yatsen University, Guangzhou, China
| | | | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Laurence N Kolonel
- Office of Public Health Studies, University of Hawaii Manoa, Honolulu, HI
| | - Suminori Kono
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU), Nantes, France
| | | | - Vittorio Krogh
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Sébastien Küry
- Department of Preventive Medicine, Kyushu University, Fukuoka, Japan
| | | | | | - Flavio Lejbkowicz
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
- School of Medicine, Taipei Medical University, Taipei, Taiwan
- Sino-American Cancer Foundation, Temple City, CA
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Heinz-Josef Lenz
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- Department of Medicine, University of Southern California, Los Angeles, CA
| | | | - Christopher I Li
- Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Li Li
- Department of Family Medicine and Community Health, Mary Ann Swetland Center for Environmental Health, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
| | - Wolfgang Lieb
- Institute of Epidemiology, PopGen Biobank, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Yi Lin
- Public Health Sciences Division
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, AZ
- Unit of Oncology, Department of Clinical and Experimental Oncology, Instituto Oncologico Veneto, IRCCS Padua, Italy
| | | | | | - Yingchang Lu
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Frank Luh
- Clalit Health Services National Israeli Cancer Control Center, Haifa, Israel
| | - Jing Ma
- Harvard School of Public Health, Boston, MA
| | | | - Frank J Manion
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI
| | - Sanford D Markowitz
- Departments of Medicine and Genetics, Case Comprehensive Cancer Center, Case Western Reserve University, and University Hospitals of Cleveland, Cleveland, OH
| | - Vicente Martin
- Biomedicine Institute (IBIOMED), University of León, León, Spain
| | - Koichi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | - Keitaro Matsuo
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya, Japan
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Chikusa-Ku Nagoya, Japan
| | - Kevin J McDonnell
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Caroline E McNeil
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Roger Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Antonio J Molina
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Research Group on Gene-Environment Interactions and Health, University of León, León, Spain
| | | | - Neil Murphy
- Nutrition and Metabolism Section, IARC, Lyon, CEDEX 08, France
| | | | - Kenneth Offit
- Clinical Genetics Service (KO), Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hanane Omichessan
- CESP (U1018 INSERM), Facultés de Médecine Université Paris-Sud, UVSQ, Université Paris-Saclay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Domenico Palli
- Cancer Risk Factors and Life-Style Epidemiology Unit, Cancer Research and Prevention Institute-ISPO, Florence, Italy
| | - Jesus P Paredes Cotoré
- Department of Surgery, Complejo Hospitalario Universitario de Santiago (CHUS), Servicio Galego de Saúde (SERGAS), Santiago De Compostela, Spain
| | | | - Paul D Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Conghui Qu
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- Public Health Sciences Division
| | - Leon Raskin
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | - Gad Rennert
- Clalit Health Services National Israeli Cancer Control Center, Haifa, Israel
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
- Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hedy S Rennert
- Clalit Health Services National Israeli Cancer Control Center, Haifa, Israel
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
| | - Bridget M Riggs
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Clemens Schafmayer
- Department of Visceral and Thoracic Surgery, University Hospital Schleswig-Holstein, Kiel Campus, Kiel, Germany
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Thomas A Sellers
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Daniela Seminara
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Gianluca Severi
- CESP (U1018 INSERM), Facultés de Médecine Université Paris-Sud, UVSQ, Université Paris-Saclay, Villejuif, France
- Human Genetics Foundation (HuGeF), Torino, Italy
| | - Wei Shi
- Department of Surgery, Children’s Hospital Los Angeles, Los Angeles, CA
| | - David Shibata
- Department of Surgery, University of Tennessee Health Science Center, Memphis, TN
| | - Xiao-Ou Shu
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | - Erin M Siegel
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah Health Sciences Center, Salt Lake City, UT
| | - Melissa Southey
- Colorectal Oncogenomics Group, Department of Pathology (DDB) and Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Zsofia K Stadler
- Clinical Genetics Service (KO), Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical Center, New York, NY
| | - Mariana C Stern
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Sebastian Stintzing
- Department of Hematology and Oncology University of Munich (LMU), Munich, Germany
| | | | | | - Duncan C Thomas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | | | - Shoichiro Tsugane
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- National Cancer Center, Tokyo, Japan
- Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT
| | | | | | - Joseph Vijai
- Clinical Genetics Service (KO), Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | | | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Michael Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Anna H Wu
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Kana Wu
- Department of Nutrition, Harvard School of Public Health, Boston, MA
| | - Yong-Bing Xiang
- State Key Laboratory of Oncogene and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Yun Yen
- Ph.D. Program of Cancer Research and Drug Discovery
- Department of Medical Oncology and Therapeutic Research, City of Hope National Medical Center, Duarte, CA
| | - Brent W Zanke
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- The University of Ottawa, Ottawa, Ontario, Canada
| | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yatsen University, Guangzhou, China
| | - Ben Zhang
- Division of Noncommunicable Disease Epidemiology and Southwest Hospital Clinical Research Center, Third Military Medical University, Chongqing, China
| | | | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
- South Korea Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, South Korea
| | - Jane C Figueiredo
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet Solna, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Victor Moreno
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- University of Barcelona, Barcelona, Spain
| | - Ulrike Peters
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Li Hsu
- Public Health Sciences Division
| | - David V Conti
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
| | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center
- Department of Medicine, University of Southern California, Los Angeles, CA
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16
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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: 317] [Impact Index Per Article: 63.4] [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: 05/11/2018] [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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17
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Amos CI, Dennis J, Wang Z, Byun J, Schumacher FR, Gayther SA, Casey G, Hunter DJ, Sellers TA, Gruber SB, Dunning AM, Michailidou K, Fachal L, Doheny K, Spurdle AB, Li Y, Xiao X, Romm J, Pugh E, Coetzee GA, Hazelett DJ, Bojesen SE, Caga-Anan C, Haiman CA, Kamal A, Luccarini C, Tessier D, Vincent D, Bacot F, Van Den Berg DJ, Nelson S, Demetriades S, Goldgar DE, Couch FJ, Forman JL, Giles GG, Conti DV, Bickeböller H, Risch A, Waldenberger M, Brüske-Hohlfeld I, Hicks BD, Ling H, McGuffog L, Lee A, Kuchenbaecker K, Soucy P, Manz J, Cunningham JM, Butterbach K, Kote-Jarai Z, Kraft P, FitzGerald L, Lindström S, Adams M, McKay JD, Phelan CM, Benlloch S, Kelemen LE, Brennan P, Riggan M, O'Mara TA, Shen H, Shi Y, Thompson DJ, Goodman MT, Nielsen SF, Berchuck A, Laboissiere S, Schmit SL, Shelford T, Edlund CK, Taylor JA, Field JK, Park SK, Offit K, Thomassen M, Schmutzler R, Ottini L, Hung RJ, Marchini J, Amin Al Olama A, Peters U, Eeles RA, Seldin MF, Gillanders E, Seminara D, Antoniou AC, Pharoah PDP, Chenevix-Trench G, Chanock SJ, Simard J, Easton DF. The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers. Cancer Epidemiol Biomarkers Prev 2017; 26:126-135. [PMID: 27697780 PMCID: PMC5224974 DOI: 10.1158/1055-9965.epi-16-0106] [Citation(s) in RCA: 229] [Impact Index Per Article: 32.7] [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: 02/01/2016] [Revised: 06/30/2016] [Accepted: 07/29/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Common cancers develop through a multistep process often including inherited susceptibility. Collaboration among multiple institutions, and funding from multiple sources, has allowed the development of an inexpensive genotyping microarray, the OncoArray. The array includes a genome-wide backbone, comprising 230,000 SNPs tagging most common genetic variants, together with dense mapping of known susceptibility regions, rare variants from sequencing experiments, pharmacogenetic markers, and cancer-related traits. METHODS The OncoArray can be genotyped using a novel technology developed by Illumina to facilitate efficient genotyping. The consortium developed standard approaches for selecting SNPs for study, for quality control of markers, and for ancestry analysis. The array was genotyped at selected sites and with prespecified replicate samples to permit evaluation of genotyping accuracy among centers and by ethnic background. RESULTS The OncoArray consortium genotyped 447,705 samples. A total of 494,763 SNPs passed quality control steps with a sample success rate of 97% of the samples. Participating sites performed ancestry analysis using a common set of markers and a scoring algorithm based on principal components analysis. CONCLUSIONS Results from these analyses will enable researchers to identify new susceptibility loci, perform fine-mapping of new or known loci associated with either single or multiple cancers, assess the degree of overlap in cancer causation and pleiotropic effects of loci that have been identified for disease-specific risk, and jointly model genetic, environmental, and lifestyle-related exposures. IMPACT Ongoing analyses will shed light on etiology and risk assessment for many types of cancer. Cancer Epidemiol Biomarkers Prev; 26(1); 126-35. ©2016 AACR.
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Affiliation(s)
- Christopher I Amos
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinyoung Byun
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Fredrick R Schumacher
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Simon A Gayther
- The Center for Bioinformatics and Functional Genomics at Cedars Sinai Medical Center, Greater Los Angeles Area, Los Angeles, California
| | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - David J Hunter
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Thomas A Sellers
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Stephen B Gruber
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Laura Fachal
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Kimberly Doheny
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Amanda B Spurdle
- Molecular Cancer Epidemiology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Yafang Li
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Xiangjun Xiao
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Jane Romm
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | | | | | - Stig E Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Charlisse Caga-Anan
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Christopher A Haiman
- The Center for Bioinformatics and Functional Genomics at Cedars Sinai Medical Center, Greater Los Angeles Area, Los Angeles, California
| | - Ahsan Kamal
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Daniel Tessier
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - Daniel Vincent
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - François Bacot
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - David J Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Stefanie Nelson
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Stephen Demetriades
- University Health Network- The Princess Margaret Cancer Centre, Toronto, California
| | | | | | - Judith L Forman
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Cancer, Genetics and Immunology, Menzies Institute for Medical Research, Hobart, Australia
| | - David V Conti
- Division of Biostatistics, Department of Preventive Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Angela Risch
- University of Salzburg and Cancer Cluster Salzburg, Salzburg, Austria
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research, Heidelberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Irene Brüske-Hohlfeld
- Helmholtz Zentrum München, Institut für Epidemiologie I, Neuherberg, Oberschleissheim, Germany
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Hua Ling
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Lesley McGuffog
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Cancer, Genetics and Immunology, Menzies Institute for Medical Research, Hobart, Australia
| | - Andrew Lee
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Karoline Kuchenbaecker
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Penny Soucy
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Québec City, Canada
| | - Judith Manz
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Katja Butterbach
- Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | | | - Peter Kraft
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Liesel FitzGerald
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Cancer, Genetics and Immunology, Menzies Institute for Medical Research, Hobart, Australia
| | - Sara Lindström
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Marcia Adams
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - James D McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Catherine M Phelan
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Sara Benlloch
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Linda E Kelemen
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Marjorie Riggan
- Department of Gynecology, Duke University Medical Center, Durham, North Carolina
| | - Tracy A O'Mara
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, P.R. China
| | - Yongyong Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | | | - Sune F Nielsen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Andrew Berchuck
- Department of Gynecology, Duke University Medical Center, Durham, North Carolina
| | - Sylvie Laboissiere
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida
| | - Tameka Shelford
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Christopher K Edlund
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Jack A Taylor
- Molecular and Genetic Epidemiology Group, National Institute for Environmental Health Sciences, Research Triangle Park, North Carolina
| | - John K Field
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Sue K Park
- College of Medicine, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Kenneth Offit
- Clinical Genetics Service, Memorial Hospital, New York, New York
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Rita Schmutzler
- Zentrum Familiärer Brust- und Eierstockkrebs, Universitätsklinikum Köln, Köln, Germany
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza, University of Rome, Rome, Italy
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | | | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, California
- Department of Internal Medicine, University of California at Davis, Davis, California
| | - Elizabeth Gillanders
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Jacques Simard
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Québec City, Canada
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
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18
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Rand KA, Song C, Dean E, Serie DJ, Curtin K, Sheng X, Hu D, Huff CA, Bernal-Mizrachi L, Tomasson MH, Ailawadhi S, Singhal S, Pawlish K, Peters ES, Bock CH, Stram A, Van Den Berg DJ, Edlund CK, Conti DV, Zimmerman T, Hwang AE, Huntsman S, Graff J, Nooka A, Kong Y, Pregja SL, Berndt SI, Blot WJ, Carpten J, Casey G, Chu L, Diver WR, Stevens VL, Lieber MR, Goodman PJ, Hennis AJM, Hsing AW, Mehta J, Kittles RA, Kolb S, Klein EA, Leske C, Murphy AB, Nemesure B, Neslund-Dudas C, Strom SS, Vij R, Rybicki BA, Stanford JL, Signorello LB, Witte JS, Ambrosone CB, Bhatti P, John EM, Bernstein L, Zheng W, Olshan AF, Hu JJ, Ziegler RG, Nyante SJ, Bandera EV, Birmann BM, Ingles SA, Press MF, Atanackovic D, Glenn MJ, Cannon-Albright LA, Jones B, Tricot G, Martin TG, Kumar SK, Wolf JL, Deming Halverson SL, Rothman N, Brooks-Wilson AR, Rajkumar SV, Kolonel LN, Chanock SJ, Slager SL, Severson RK, Janakiraman N, Terebelo HR, Brown EE, De Roos AJ, Mohrbacher AF, Colditz GA, Giles GG, Spinelli JJ, Chiu BC, Munshi NC, Anderson KC, Levy J, Zonder JA, Orlowski RZ, Lonial S, Camp NJ, Vachon CM, Ziv E, Stram DO, Hazelett DJ, Haiman CA, Cozen W. A Meta-analysis of Multiple Myeloma Risk Regions in African and European Ancestry Populations Identifies Putatively Functional Loci. Cancer Epidemiol Biomarkers Prev 2016; 25:1609-1618. [PMID: 27587788 PMCID: PMC5524541 DOI: 10.1158/1055-9965.epi-15-1193] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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: 11/21/2015] [Revised: 06/20/2016] [Accepted: 07/05/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) in European populations have identified genetic risk variants associated with multiple myeloma. METHODS We performed association testing of common variation in eight regions in 1,318 patients with multiple myeloma and 1,480 controls of European ancestry and 1,305 patients with multiple myeloma and 7,078 controls of African ancestry and conducted a meta-analysis to localize the signals, with epigenetic annotation used to predict functionality. RESULTS We found that variants in 7p15.3, 17p11.2, 22q13.1 were statistically significantly (P < 0.05) associated with multiple myeloma risk in persons of African ancestry and persons of European ancestry, and the variant in 3p22.1 was associated in European ancestry only. In a combined African ancestry-European ancestry meta-analysis, variation in five regions (2p23.3, 3p22.1, 7p15.3, 17p11.2, 22q13.1) was statistically significantly associated with multiple myeloma risk. In 3p22.1, the correlated variants clustered within the gene body of ULK4 Correlated variants in 7p15.3 clustered around an enhancer at the 3' end of the CDCA7L transcription termination site. A missense variant at 17p11.2 (rs34562254, Pro251Leu, OR, 1.32; P = 2.93 × 10-7) in TNFRSF13B encodes a lymphocyte-specific protein in the TNF receptor family that interacts with the NF-κB pathway. SNPs correlated with the index signal in 22q13.1 cluster around the promoter and enhancer regions of CBX7 CONCLUSIONS: We found that reported multiple myeloma susceptibility regions contain risk variants important across populations, supporting the use of multiple racial/ethnic groups with different underlying genetic architecture to enhance the localization and identification of putatively functional alleles. IMPACT A subset of reported risk loci for multiple myeloma has consistent effects across populations and is likely to be functional. Cancer Epidemiol Biomarkers Prev; 25(12); 1609-18. ©2016 AACR.
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Affiliation(s)
- Kristin A Rand
- Keck School of Medicine of USC and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Chi Song
- Keck School of Medicine of USC and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | | | | | - Karen Curtin
- University of Utah School of Medicine, Salt Lake City, Utah
| | - Xin Sheng
- Keck School of Medicine of USC and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Donglei Hu
- University of California at San Francisco, San Francisco, California
| | - Carol Ann Huff
- Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | | | - Michael H Tomasson
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, Washington University, St. Louis, Missouri
| | | | - Seema Singhal
- Robert H. Lurie Cancer Center, Northwestern University, Chicago, Illinois
| | - Karen Pawlish
- New Jersey State Cancer Registry, New Jersey Department of Health, Trenton, New Jersey
| | - Edward S Peters
- Louisiana State University School of Public Health, Louisiana State University, New Orleans, Louisiana
| | - Cathryn H Bock
- Karmanos Cancer Institute and Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
| | - Alex Stram
- Genomic Health, Inc., Redwood City, California
| | - David J Van Den Berg
- Keck School of Medicine of USC and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Christopher K Edlund
- Keck School of Medicine of USC and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - David V Conti
- Keck School of Medicine of USC and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | | | - Amie E Hwang
- Keck School of Medicine of USC and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Scott Huntsman
- University of California at San Francisco, San Francisco, California
| | - John Graff
- Rutgers-Robert Wood Johnson Medical School, Rutgers State University of New Jersey, New Brunswick, New Jersey
| | - Ajay Nooka
- Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Yinfei Kong
- Keck School of Medicine of USC and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Silvana L Pregja
- Karmanos Cancer Institute and Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, U.S. NIH, Bethesda, Maryland
| | - William J Blot
- International Epidemiology Institute, Rockville, Maryland
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - John Carpten
- The Translational Genomics Research Institute, Phoenix, Arizona
| | - Graham Casey
- Keck School of Medicine of USC and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Lisa Chu
- Cancer Prevention Institute of California, Fremont, California
- Stanford University School of Medicine and Stanford Cancer Institute, Palo Alto, California
| | | | | | - Michael R Lieber
- Keck School of Medicine of USC and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | | | - Anselm J M Hennis
- Stony Brook University, Stony Brook, New York
- Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies, Bridgetown, Barbados
| | - Ann W Hsing
- Stanford University School of Medicine and Stanford Cancer Institute, Palo Alto, California
| | - Jayesh Mehta
- Robert H. Lurie Cancer Center, Northwestern University, Chicago, Illinois
| | - Rick A Kittles
- Department of Surgery, University of Arizona, Tucson, Arizona
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Eric A Klein
- Glickman Urologic and Kidney Institute, Cleveland Clinic, Cleveland, Ohio
| | | | - Adam B Murphy
- Robert H. Lurie Cancer Center, Northwestern University, Chicago, Illinois
| | | | | | - Sara S Strom
- The University of Texas MD Anderson Cancer Center, University of Texas, Houston, Texas
| | - Ravi Vij
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, Washington University, St. Louis, Missouri
| | | | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Lisa B Signorello
- Harvard School of Public Health, Harvard University, Boston, Massachusetts
| | - John S Witte
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California
| | | | - Parveen Bhatti
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Esther M John
- Cancer Prevention Institute of California, Fremont, California
- Stanford University School of Medicine and Stanford Cancer Institute, Palo Alto, California
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, California
| | - Wei Zheng
- International Epidemiology Institute, Rockville, Maryland
| | - Andrew F Olshan
- Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Jennifer J Hu
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida
| | - Regina G Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, U.S. NIH, Bethesda, Maryland
| | - Sarah J Nyante
- Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Elisa V Bandera
- Rutgers-Robert Wood Johnson Medical School, Rutgers State University of New Jersey, New Brunswick, New Jersey
| | - Brenda M Birmann
- Harvard School of Public Health, Harvard University, Boston, Massachusetts
| | - Sue A Ingles
- Keck School of Medicine of USC and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Michael F Press
- Keck School of Medicine of USC and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | | | - Martha J Glenn
- University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Brandt Jones
- University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Thomas G Martin
- University of California at San Francisco, San Francisco, California
| | | | - Jeffrey L Wolf
- University of California at San Francisco, San Francisco, California
| | | | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, U.S. NIH, Bethesda, Maryland
| | | | | | - Laurence N Kolonel
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, Hawaii
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, U.S. NIH, Bethesda, Maryland
| | | | - Richard K Severson
- Karmanos Cancer Institute and Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
| | | | | | | | | | - Ann F Mohrbacher
- Keck School of Medicine of USC and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Graham A Colditz
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, Washington University, St. Louis, Missouri
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council of Victoria, Melbourne, Victoria, Australia
- School of Population and Global Health, Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, Victoria, Australia
- Monash University, Melbourne, Melbourne, Victoria, Australia
| | - John J Spinelli
- BC Cancer Agency, Vancouver, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | | | - Nikhil C Munshi
- Dana Farber Cancer Institute, Harvard School of Medicine, Harvard University, Boston, Massachusetts
| | - Kenneth C Anderson
- Dana Farber Cancer Institute, Harvard School of Medicine, Harvard University, Boston, Massachusetts
| | - Joan Levy
- Multiple Myeloma Research Foundation, Norwalk, Connecticut
| | - Jeffrey A Zonder
- Karmanos Cancer Institute and Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
| | - Robert Z Orlowski
- The University of Texas MD Anderson Cancer Center, University of Texas, Houston, Texas
| | - Sagar Lonial
- Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Nicola J Camp
- University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Elad Ziv
- University of California at San Francisco, San Francisco, California
| | - Daniel O Stram
- Keck School of Medicine of USC and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Dennis J Hazelett
- Center for Bioinformatics and Computational Biology, Cedars Sinai Medical Center, Los Angeles, California.
| | - Christopher A Haiman
- Keck School of Medicine of USC and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California.
| | - Wendy Cozen
- Keck School of Medicine of USC and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California.
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Bolton KL, Tyrer J, Song H, Ramus SJ, Notaridou M, Jones C, Sher T, Gentry-Maharaj A, Wozniak E, Tsai YY, Weidhaas J, Paik D, Van Den Berg DJ, Stram DO, Pearce CL, Wu AH, Brewster W, Anton-Culver H, Ziogas A, Narod SA, Levine DA, Kaye SB, Brown R, Paul J, Flanagan J, Sieh W, McGuire V, Whittemore AS, Campbell I, Gore ME, Lissowska J, Yang HP, Medrek K, Gronwald J, Lubinski J, Jakubowska A, Le ND, Cook LS, Kelemen LE, Brooks-Wilson A, Massuger LFAG, Kiemeney LA, Aben KKH, van Altena AM, Houlston R, Tomlinson I, Palmieri RT, Moorman PG, Schildkraut J, Iversen ES, Phelan C, Vierkant RA, Cunningham JM, Goode EL, Fridley BL, Kruger-Kjaer S, Blaeker J, Hogdall E, Hogdall C, Gross J, Karlan BY, Ness RB, Edwards RP, Odunsi K, Moyisch KB, Baker JA, Modugno F, Heikkinenen T, Butzow R, Nevanlinna H, Leminen A, Bogdanova N, Antonenkova N, Doerk T, Hillemanns P, Dürst M, Runnebaum I, Thompson PJ, Carney ME, Goodman MT, Lurie G, Wang-Gohrke S, Hein R, Chang-Claude J, Rossing MA, Cushing-Haugen KL, Doherty J, Chen C, Rafnar T, Besenbacher S, Sulem P, Stefansson K, Birrer MJ, Terry KL, Hernandez D, Cramer DW, Vergote I, Amant F, Lambrechts D, Despierre E, Fasching PA, Beckmann MW, Thiel FC, Ekici AB, Chen X, Johnatty SE, Webb PM, Beesley J, Chanock S, Garcia-Closas M, Sellers T, Easton DF, Berchuck A, Chenevix-Trench G, Pharoah PDP, Gayther SA. Corrigendum: Common variants at 19p13 are associated with susceptibility to ovarian cancer. Nat Genet 2016; 48:101. [PMID: 26711112 DOI: 10.1038/ng0116-101b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Rand KA, Song C, Dean E, Serie D, Curtin K, Hazelett D, Hwang AE, Sheng X, Stram A, Van Den Berg DJ, Huff CA, Bernal-Mizrachi L, Tomasson MH, Ailawadhi S, De Roos A, Singhal S, Pawlish K, Peters E, Bock C, Conti DV, Colditz G, Zimmerman T, Huntsman S, Graff J, Chanock SJ, Lieber M, Mehta J, Klein EA, Janakiraman N, Severson RK, Brooks-Wilson AR, Rajkumar V, Brown EE, Kolonel L, Slager S, Henderson BE, Giles GG, Spinelli JJ, Chiu B, Anderson KC, Zonder J, Orlowski RZ, Lonial S, Camp N, Vachon C, Ziv E, Stram DO, Haiman CA, Cozen W. Abstract 4629: Multiple myeloma susceptibility loci examined in African and European ancestry populations. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-4629] [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
Genome-wide association studies (GWAS) of multiple myeloma (MM) in Northern Europeans have identified seven novel risk loci (2p23.3, 3p22.1, 3q26.2, 6p21.33, 7p15.3, 17p11.2, 22q13.1). We performed a multiethnic meta-analysis of these regions in 1,274 MM patients and 1,486 controls of European ancestry (EA) and 1,049 MM patients and 7,080 controls of African ancestry (AA), leveraging the differential linkage-disequilibrium of these populations in order to better localize the putative functional variants. We observed directionally consistent effects for all seven index SNPs in both populations, with four significantly associated (p<0.05) with risk in EAs (3p22.1, 7p15.3, 17p11.2, 22q13.1), and two significantly associated with risk in AAs (7p15.3 and 22q13.1). In a fixed effects meta-analysis of six regions (excluding the HLA region on chromosome 6), variation in five of the regions (2p33.3, 3p22.1, 7p15.3, 17p11.2, 22q13.1) had statistically significant associations with risk (Table 1). In one region, the index variant had the strongest association [rs4487645 at 7p15.3, (OR = 1.30, p = 8.7×10−8)]. Five of the six most significantly associated variants identified in the multiethnic analyses overlapped with biologically relevant features indicating regulatory activity based on CD20+ (B lymphocyte) cells, showing evidence of potential function; those included a missense variant in (17p11.2, rs34562254, Pro251Leu) in TNFRSF13B, which encodes a lymphocyte-specific protein in the tumor necrosis factor receptor family that interacts with the NF-kb pathway. Our study shows that these regions are important in MM risk across ethnicities and further supports the use of multiple ethnic groups in genetic studies to enhance identification of risk variants.
Table 1.Most significant associations for each region in the multiethnic meta-analysis.Individuals of European AncestryIndividuals of African AncestryMulitethnic Metar2 with IndexcCHRSNPRAaFreqbORP-valueFreqbORP-valueORP-valueP-het2rs732075G0.591.222.0×10−30.621.122.0×10−21.162.6×10−40.280.09/0.283rs73069394A0.191.243.0×10−30.621.181.5×10−21.201.3×10−50.550.77/0.963rs12637184G0.761.136.0×10−20.921.192.7×10−11.151.0×10−20.640.94/1.007rs4487645C0.671.237.0×10−40.891.485.5×10−51.308.7×10−80.07-d17rs34562254A0.121.452.4×10−50.131.212.2×10−31.312.5×10−60.120.33/0.9022rs139400T0.491.224.0×10−40.531.172.1×10−31.191.2×10−60.630.63/0.96aRisk allelebFrequency of the risk allele in European and African ancestry studiescr2 metrics based on 1000 Genomes Project AFR/EUR populationsdIndex SNP
Citation Format: Kristin A. Rand, Chi Song, Eric Dean, Daniel Serie, Karen Curtin, Dennis Hazelett, Amie E. Hwang, Xin Sheng, Alex Stram, David J. Van Den Berg, Carol Ann Huff, Leon Bernal-Mizrachi, Michael H. Tomasson, Sikander Ailawadhi, Anneclaire De Roos, Seema Singhal, Karen Pawlish, Edward Peters, Catherine Bock, David V. Conti, Graham Colditz, Todd Zimmerman, Scott Huntsman, John Graff, African Ancestry Prostate Cancer GWAS Consortium,African Ancestry Breast Cancer GWAS Consortium, Stephen J. Chanock, Michael Lieber, Jayesh Mehta, Eric A. Klein, Nalini Janakiraman, Richard K. Severson, Angela R. Brooks-Wilson, Vincent Rajkumar, Elizabeth E. Brown, Laurence Kolonel, Susan Slager, Brian E. Henderson, Graham G. Giles, John J. Spinelli, Brian Chiu, Kenneth C. Anderson, Jeffrey Zonder, Robert Z. Orlowski, Sagar Lonial, Nicola Camp, Celine Vachon, Elad Ziv, Dan O. Stram, Christopher A. Haiman, Wendy Cozen. Multiple myeloma susceptibility loci examined in African and European ancestry populations. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4629. doi:10.1158/1538-7445.AM2015-4629
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Affiliation(s)
- Kristin A. Rand
- 1Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Chi Song
- 1Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Eric Dean
- 2University of California San Francisco, San Francisco, CA
| | | | - Karen Curtin
- 4University of Utah School of Medicine, Salt Lake City, UT
| | - Dennis Hazelett
- 1Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Amie E. Hwang
- 1Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Xin Sheng
- 1Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Alex Stram
- 1Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - David J. Van Den Berg
- 1Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | | | - Michael H. Tomasson
- 7Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | | | | | - Seema Singhal
- 9Robert H. Lurie Cancer Center, Northwestern University, Chicago, IL
| | - Karen Pawlish
- 10New Jersey State Cancer Registry, New Jersey Department of Health, Trenton, NJ
| | - Edward Peters
- 11Louisiana State University School of Public Health, New Orleans, LA
| | - Catherine Bock
- 12Karmanos Cancer Institute, Wayne State University of Medicine, Detroit, MI
| | - David V. Conti
- 1Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Graham Colditz
- 7Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | | | - Scott Huntsman
- 2University of California San Francisco, San Francisco, CA
| | - John Graff
- 14Rutgers-Robert Wood Johnson Medical School, Rutgers State University of New Jersey, New Brunswick, NJ
| | - Stephen J. Chanock
- 15Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Michael Lieber
- 1Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Jayesh Mehta
- 9Robert H. Lurie Cancer Center, Northwestern University, Chicago, IL
| | | | | | - Richard K. Severson
- 12Karmanos Cancer Institute, Wayne State University of Medicine, Detroit, MI
| | | | | | | | | | | | - Brian E. Henderson
- 1Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Graham G. Giles
- 22Cancer Council of Victoria, University of Melbourne, and Monash University, Melbourne, Australia
| | - John J. Spinelli
- 23Cancer Control Research and School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Jeffrey Zonder
- 12Karmanos Cancer Institute, Wayne State University of Medicine, Detroit, MI
| | - Robert Z. Orlowski
- 25The University of Texas MD Anderson Cancer Center, The University of Texas, Houston, TX
| | - Sagar Lonial
- 6Emory University School of Medicine, Atlanta, GA
| | - Nicola Camp
- 4University of Utah School of Medicine, Salt Lake City, UT
| | | | - Elad Ziv
- 2University of California San Francisco, San Francisco, CA
| | - Dan O. Stram
- 1Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Christopher A. Haiman
- 1Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Wendy Cozen
- 1Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA
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Brat DJ, Verhaak RGW, Aldape KD, Yung WKA, Salama SR, Cooper LAD, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DPC, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang J. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med 2015; 372:2481-98. [PMID: 26061751 PMCID: PMC4530011 DOI: 10.1056/nejmoa1402121] [Citation(s) in RCA: 2125] [Impact Index Per Article: 236.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Diffuse low-grade and intermediate-grade gliomas (which together make up the lower-grade gliomas, World Health Organization grades II and III) have highly variable clinical behavior that is not adequately predicted on the basis of histologic class. Some are indolent; others quickly progress to glioblastoma. The uncertainty is compounded by interobserver variability in histologic diagnosis. Mutations in IDH, TP53, and ATRX and codeletion of chromosome arms 1p and 19q (1p/19q codeletion) have been implicated as clinically relevant markers of lower-grade gliomas. METHODS We performed genomewide analyses of 293 lower-grade gliomas from adults, incorporating exome sequence, DNA copy number, DNA methylation, messenger RNA expression, microRNA expression, and targeted protein expression. These data were integrated and tested for correlation with clinical outcomes. RESULTS Unsupervised clustering of mutations and data from RNA, DNA-copy-number, and DNA-methylation platforms uncovered concordant classification of three robust, nonoverlapping, prognostically significant subtypes of lower-grade glioma that were captured more accurately by IDH, 1p/19q, and TP53 status than by histologic class. Patients who had lower-grade gliomas with an IDH mutation and 1p/19q codeletion had the most favorable clinical outcomes. Their gliomas harbored mutations in CIC, FUBP1, NOTCH1, and the TERT promoter. Nearly all lower-grade gliomas with IDH mutations and no 1p/19q codeletion had mutations in TP53 (94%) and ATRX inactivation (86%). The large majority of lower-grade gliomas without an IDH mutation had genomic aberrations and clinical behavior strikingly similar to those found in primary glioblastoma. CONCLUSIONS The integration of genomewide data from multiple platforms delineated three molecular classes of lower-grade gliomas that were more concordant with IDH, 1p/19q, and TP53 status than with histologic class. Lower-grade gliomas with an IDH mutation either had 1p/19q codeletion or carried a TP53 mutation. Most lower-grade gliomas without an IDH mutation were molecularly and clinically similar to glioblastoma. (Funded by the National Institutes of Health.).
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Hwang AE, Ailwadhi S, Huff CA, Bernal-Mizrachi L, Haiman CA, Peters E, Singhal S, Pawlish K, Bock C, Zimmerman T, Berg DJVD, Conti DV, Birmann BB, Mehta J, Graff JJ, Stram DO, Brown N, Yu Y, Azadian M, Kolonel L, Henderson BE, Mohrbacher A, Colditz G, Chiu BC, Tomasson M, Zonder J, Orlowski RZ, Lonial S, Cozen W. Abstract 3852: Obesity is associated with clinical characteristics in African American multiple myeloma patients. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-3852] [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
African-American ethnicity, male sex, older age and obesity are accepted risk factors for multiple myeloma (MM). Obesity early in life is a risk factor for many cancers, including MM; most studies have focused on populations of European origin. African-Americans have a higher prevalence of obesity than other populations, and may have a distinct genetic contribution to this condition. We established a multi-center study to investigate possible explanations for the excess risk of MM among African-Americans. The aim of the present case-case analysis was to determine whether body mass index (BMI) was associated with clinical characteristics at presentation in African-American MM patients.
1,065 patients diagnosed with active MM from January 1, 2009 through September 30, 2013 were recruited through nine outpatient centers at academic medical centers and 3 SEER population-based cancer registries. Information on weight and height at 20 years of age and at 5 years prior to diagnosis was obtained from questionnaires. Clinical information collected from the medical records and interviews included age at diagnosis, stage, percent plasmacytosis on bone marrow biopsy,
B2 microglobulin level, immunoglobulin class and presence of lytic bone lesions. Molecular profiling abstracted from pathology reports included chromosomal gain/deletions (1P-, 1Q+, +3, +5, +7, +9, +11, 12P-, Del(13), +15, Del(17P), Del(17P13)), translocations (4;14), (11;14), and (14;16 ). Analysis of Variance (ANOVA) was used to test the null hypothesis that age at diagnosis was similar across BMI categories. A T-test was used to test the null hypothesis that the mean age at diagnosis in underweight/normal patients was not different than that for overweight and obese patients. The Mantel-Haenszel Chi square test for trend was used to test the null hypothesis that the proportion of cytogenetic and molecular abnormalities was similar across BMI categories.
The study population consists of 306 African American male and 396 African American female MM patients. In both, obesity at 20 years of age was associated with younger age at diagnosis, compared to a normal/underweight (p=0.0015). Among males only, obesity at 5 years prior to diagnosis was also associated with younger age at diagnosis (p=0.03). A trend between increasing BMI and molecular characteristics associated with a poor prognosis was suggested.
We observed a strong association between obesity at age 20 and younger age at diagnosis among males and females, and in males only at 5 years prior to diagnosis. Obesity is one of the few known potentially modifiable risk factors for MM. Younger age at diagnosis reflects an earlier accumulation of either or both genetic and environmental risk factors. We also observed a link between obesity at each of the two time points and specific molecular markers of poor prognosis. Additional studies are needed to determine biological significance of the results.
Citation Format: Amie E. Hwang, Sikander Ailwadhi, Carol Ann Huff, Leon Bernal-Mizrachi, Christopher A. Haiman, Edward Peters, Seema Singhal, Karen Pawlish, Cathryn Bock, Todd Zimmerman, David J. Van Den Berg, David V. Conti, Brenda B. Birmann, Jayesh Mehta, John J. Graff, Daniel O. Stram, Niquelle Brown, Yang Yu, Moosa Azadian, Laurence Kolonel, Brian E. Henderson, Ann Mohrbacher, Graham Colditz, Brian-C Chiu, Michael Tomasson, Jeffrey Zonder, Robert Z. Orlowski, Sagar Lonial, Wendy Cozen. Obesity is associated with clinical characteristics in African American multiple myeloma patients. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3852. doi:10.1158/1538-7445.AM2014-3852
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Affiliation(s)
- Amie E. Hwang
- 1USC/Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | | | | | | | | | | | - Karen Pawlish
- 6Cancer Epidemiology Services New Jersey Department of Health, Trenton, NJ
| | - Cathryn Bock
- 7Wayne State University School of Medicine, Detroit, MI
| | | | | | - David V. Conti
- 1USC/Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | | | | | | | - Niquelle Brown
- 1USC/Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Yang Yu
- 1USC/Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Moosa Azadian
- 1USC/Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | | | - Ann Mohrbacher
- 1USC/Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | | | | | | | | | | | - Wendy Cozen
- 1USC/Norris Comprehensive Cancer Center, Los Angeles, CA
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Ellingjord-Dale M, Grotmol T, Lee E, Van Den Berg DJ, Hofvind S, Couto E, Sovio U, Dos-Santos-Silva I, Ursin G. Breast cancer susceptibility variants and mammographic density phenotypes in norwegian postmenopausal women. Cancer Epidemiol Biomarkers Prev 2014; 23:1752-63. [PMID: 25002657 DOI: 10.1158/1055-9965.epi-13-1212] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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] Open
Abstract
BACKGROUND Mammographic density (MD) is one of the strongest known breast cancer risk factors. Twin studies have suggested that a large part of the variation in MD is genetically determined. We hypothesized that breast cancer susceptibility variants may affect MD, and that their effects may be modified by nongenetic factors. METHODS We assessed MD, using a computer-assisted method, on 2,348 postmenopausal Caucasian women (50-69 years) who participated in the Norwegian Breast Cancer Screening Program (NBCSP) in 2004 or 2006-07. We used linear regression (additive models) to determine the association between each SNP and MD, adjusting for age, body mass index (BMI), and study. We evaluated MD associations with 17 established breast cancer SNPs, overall, and by strata defined by non-genetic factors. RESULTS Two variants, 6q25.1-rs9383938 and TXNRD2-rs8141691, were statistically significantly associated with percent MD (P = 0.019 and 0.03, respectively), with the 6q25.1-rs9383938 association being consistent with the SNP effect on breast cancer risk. The effect of 6q25.1-rs3734805 on percent MD varied between parous and nulliparous women (Pinteraction = 0.02), whereas the effects of 9q31.2-rs865686 and MRPS30:FGF10-rs4415084 differed across strata of BMI (Pinteraction = 0.01 and 0.005, respectively). There was no evidence of effect modification by estrogen and progestin therapy use or alcohol consumption. CONCLUSION This study provides novel evidence of shared genetic risk factors between MD and breast cancer and of possible MD genetic-environmental interactions. IMPACT Although the results may be chance findings, they nevertheless highlight the need to investigate interactions with nongenetic factors in studies on the genetics of MD.
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Affiliation(s)
| | | | - Eunjung Lee
- University of Southern California, Los Angeles, California
| | | | | | - Elisabeth Couto
- Norwegian Knowledge Centre for the Health Services, Health Economic and Drug Unit, Oslo, Norway
| | - Ulla Sovio
- University of Cambridge, Cambridge, United Kingdom
| | | | - Giske Ursin
- University of Oslo, Oslo, Norway. Cancer Registry of Norway, Oslo, Norway.
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Okitsu CY, Van Den Berg DJ, Lieber MR, Hsieh CL. Reproducibility and reliability of SNP analysis using human cellular DNA at or near nanogram levels. BMC Res Notes 2013; 6:515. [PMID: 24314330 PMCID: PMC4029319 DOI: 10.1186/1756-0500-6-515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 09/20/2013] [Accepted: 12/02/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Illumina SNP arrays have been routinely used for genome-wide association studies to identify potential biomarkers for various diseases. The recommended 200 ng of DNA for high-quality results is a roadblock to utilizing this assay when such quantities of DNA are not available. The goal of this study is to determine the reproducibility and reliability of the assay when reduced amounts of DNA are used for the SNP arrays. FINDINGS A serial 3-fold reduction of DNA from 200 ng to 0.8 ng was used for an Illumina SNP array in duplicates (200 ng, 66.7 ng, 22,2 ng, and 7.4 ng) or triplicates (2.47 ng and 0.8 ng). The reproducibility of the assay was determined by comparing allele calls (genotypes) at each locus within the duplicates or triplicates. The reliability of samples of reduced quantity was determined by comparing allele calls from samples of different quantities. As expected, the reproducibility and reliability both decrease with decreasing amounts of DNA used for the arrays. However, results of comparable quality to the 200 ng DNA recommended by Illumina can be obtained with much reduced amounts of DNA. CONCLUSION Reasonably reproducible and reliable results can be obtained with quantities of DNA, as low as 0.8 ng (equivalent to 133 human cells), well below the manufacturer's recommendation. Results of nearly equal quality to that of using 200 ng DNA can be obtained with 22.2 ng of DNA reliably, and clearly acceptable data can be obtained using 7.4 ng of DNA for Illumina SNP arrays.
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Affiliation(s)
| | | | | | - Chih-Lin Hsieh
- Department of Urology, University of Southern California, 1441 Eastlake Ave,,Rm 5420, Los Angeles, CA 90033, USA.
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Schumacher FR, Wang Z, Skotheim RI, Koster R, Chung CC, Hildebrandt MAT, Kratz CP, Bakken AC, Bishop DT, Cook MB, Erickson RL, Fosså SD, Greene MH, Jacobs KB, Kanetsky PA, Kolonel LN, Loud JT, Korde LA, Le Marchand L, Lewinger JP, Lothe RA, Pike MC, Rahman N, Rubertone MV, Schwartz SM, Siegmund KD, Skinner EC, Turnbull C, Van Den Berg DJ, Wu X, Yeager M, Nathanson KL, Chanock SJ, Cortessis VK, McGlynn KA. Testicular germ cell tumor susceptibility associated with the UCK2 locus on chromosome 1q23. Hum Mol Genet 2013; 22:2748-53. [PMID: 23462292 DOI: 10.1093/hmg/ddt109] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified multiple common genetic variants associated with an increased risk of testicular germ cell tumors (TGCTs). A previous GWAS reported a possible TGCT susceptibility locus on chromosome 1q23 in the UCK2 gene, but failed to reach genome-wide significance following replication. We interrogated this region by conducting a meta-analysis of two independent GWASs including a total of 940 TGCT cases and 1559 controls for 122 single-nucleotide polymorphisms (SNPs) on chromosome 1q23 and followed up the most significant SNPs in an additional 2202 TGCT cases and 2386 controls from four case-control studies. We observed genome-wide significant associations for several UCK2 markers, the most significant of which was for rs3790665 (PCombined = 6.0 × 10(-9)). Additional support is provided from an independent familial study of TGCT where a significant over-transmission for rs3790665 with TGCT risk was observed (PFBAT = 2.3 × 10(-3)). Here, we provide substantial evidence for the association between UCK2 genetic variation and TGCT risk.
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Affiliation(s)
- Fredrick R Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
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26
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Song C, Chen GK, Millikan RC, Ambrosone CB, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming SL, Rodriguez-Gil JL, Chanock SJ, Wan P, Sheng X, Pooler LC, Van Den Berg DJ, Le Marchand L, Kolonel LN, Henderson BE, Haiman CA, Stram DO. A genome-wide scan for breast cancer risk haplotypes among African American women. PLoS One 2013; 8:e57298. [PMID: 23468962 PMCID: PMC3585353 DOI: 10.1371/journal.pone.0057298] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [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: 07/31/2012] [Accepted: 01/23/2013] [Indexed: 12/03/2022] Open
Abstract
Genome-wide association studies (GWAS) simultaneously investigating hundreds of thousands of single nucleotide polymorphisms (SNP) have become a powerful tool in the investigation of new disease susceptibility loci. Haplotypes are sometimes thought to be superior to SNPs and are promising in genetic association analyses. The application of genome-wide haplotype analysis, however, is hindered by the complexity of haplotypes themselves and sophistication in computation. We systematically analyzed the haplotype effects for breast cancer risk among 5,761 African American women (3,016 cases and 2,745 controls) using a sliding window approach on the genome-wide scale. Three regions on chromosomes 1, 4 and 18 exhibited moderate haplotype effects. Furthermore, among 21 breast cancer susceptibility loci previously established in European populations, 10p15 and 14q24 are likely to harbor novel haplotype effects. We also proposed a heuristic of determining the significance level and the effective number of independent tests by the permutation analysis on chromosome 22 data. It suggests that the effective number was approximately half of the total (7,794 out of 15,645), thus the half number could serve as a quick reference to evaluating genome-wide significance if a similar sliding window approach of haplotype analysis is adopted in similar populations using similar genotype density.
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Affiliation(s)
- Chi Song
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Gary K. Chen
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Robert C. Millikan
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Esther M. John
- Cancer Prevention Institute of California, Fremont, California, United States of America
- Stanford University School of Medicine and Stanford Cancer Institute, Stanford, California, United States of America
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Science, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jennifer J. Hu
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Regina G. Ziegler
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Sarah Nyante
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Elisa V. Bandera
- The Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
| | - Sue A. Ingles
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Michael F. Press
- Department of Pathology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Sandra L. Deming
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jorge L. Rodriguez-Gil
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Stephen J. Chanock
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Peggy Wan
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Xin Sheng
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Loreall C. Pooler
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - David J. Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
- Epigenome Center, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Laurence N. Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Chris A. Haiman
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Daniel O. Stram
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
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Ellingjord-Dale M, Lee E, Couto E, Ozhand A, Qureshi S, Hofvind S, Van Den Berg DJ, Akslen LA, Grotmol T, Ursin G. Polymorphisms in hormone metabolism and growth factor genes and mammographic density in Norwegian postmenopausal hormone therapy users and non-users. Breast Cancer Res 2012; 14:R135. [PMID: 23095343 PMCID: PMC4053113 DOI: 10.1186/bcr3337] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 08/30/2012] [Indexed: 01/10/2023] Open
Abstract
INTRODUCTION Mammographic density (MD) is one of the strongest known breast cancer risk factors. Estrogen and progestin therapy (EPT) has been associated with increases in MD. Dense breast tissue is characterized by increased stromal tissue and (to a lesser degree) increased numbers of breast epithelial cells. It is possible that genetic factors modify the association between EPT and MD, and that certain genetic variants are particularly important in determining MD in hormone users. We evaluated the association between MD and 340 tagging single nucleotide polymorphisms (SNPs) from about 30 candidate genes in hormone metabolism/growth factor pathways among women who participated in the Norwegian Breast Cancer Screening Program (NBCSP) in 2004. METHODS We assessed MD on 2,036 postmenopausal women aged 50 to 69 years using a computer-assisted method (Madena, University of Southern California) in a cross-sectional study. We used linear regression to determine the association between each SNP and MD, adjusting for potential confounders. The postmenopausal women were stratified into HT users (EPT and estrogen-only) and non-users (never HT). RESULTS For current EPT users, there was an association between a variant in the prolactin gene (PRL; rs10946545) and MD (dominant model, Bonferroni-adjusted P (Pb) = 0.0144). This association remained statistically significant among current users of norethisterone acetate (NETA)-based EPT, a regimen common in Nordic countries. Among current estrogen-only users (ET), there was an association between rs4670813 in the cytochrome P450 gene (CYP1B1) and MD (dominant model, Pb = 0.0396). In never HT users, rs769177 in the tumor necrosis factor (TNF) gene and rs1968752 in the region of the sulfotransferase gene (SULT1A1/SULT1A2), were significantly associated with MD (Pb = 0.0202; Pb = 0.0349). CONCLUSIONS We found some evidence that variants in the PRL gene were associated with MD in current EPT and NETA users. In never HT users, variants in the TNF and SULT1A1/SULT1A2 genes were significantly associated with MD. These findings may suggest that several genes in the hormone metabolism and growth factor pathways are implicated in determining MD.
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Rand KA, Conti DV, Haiman CA, Van Den Berg DJ, Birmann BM, De Roos AJ, Severson RK, Gebregziabher M, Ailawadhi S, Morbacher A, Lieber MR, Wang SS, Bernstein L, Edlund CK, Rothman N, Chanock SJ, Kolonel LN, Colditz GA, Munshi N, Anderson KC, Cozen W. Abstract 2634: Polymorphisms in DNA repair genes and risk of multiple myeloma. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-2634] [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
Background and Objective: DNA repair is an essential process for development and differentiation of all cells, including plasma cells. Associations between single nucleotide polymorphisms (SNPs) in DNA repair genes and multiple myeloma risk have been reported but generally not replicated. In a pilot study, we observed suggestive evidence of an association between multiple myeloma risk and five nonsynonymous SNPs in DNA repair genes (rs25489 in XRCC1, rs1801516 in ATM, rs2227999 in XPC, rs2228528 in CSB and rs2228615 in ICAM5). The objective of this study was to examine the effect of these five SNPs on multiple myeloma risk in a large multi-center analysis. Methods: We conducted a pooled analysis in a multi-ethnic sample of 489 multiple myeloma cases and 939 controls. Studies contributing samples included two population-based case-control studies conducted in Los Angeles and Seattle/Detroit that used the Surveillance, Epidemiology and End Results (SEER) cancer registries to identify cases, and three nested case-control studies using subjects from the Multiethnic Cohort (MEC), the Health Professionals Follow Up Study (HPFS), and the Nurses’ Health Study (NHS). The SNPs coded for an amino acid substitution, and were assumed to have the same effect across ethnic groups, and thus subjects from all racial/ethnic groups were included in the analysis. Assuming a log-additive inheritance model, odds ratios (OR) and 95% confidence intervals (95% CIs) were calculated for allele-specific risk comparing cases to controls using unconditional logistic regression, adjusting for age, race/ethnicity, sex, and study site. Results: We observed a 40% decreased risk per variant T allele in the XRCC1 SNP rs25489 (OR=0.60, 95% CI=0.40, 0.91, p-value=0.02). The minor allele frequency in cases and controls was 3.4% and 5.6%, respectively. Non-significant OR's < 1.0 were observed when whites (OR=0.67, 95% CI=0.38, 1.17) and African Americans (OR=0.33, 95% CI= 0.09, 1.20) were considered separately. The SNPs in other DNA repair genes, ATM (rs1801516), XPC (rs2227999), CSB (rs2228528) and ICAM5 (rs2228615), showed no association with multiple myeloma risk. Conclusion: We observed an association between multiple myeloma and XRCC1, a gene that encodes a protein involved in the repair of single-stranded DNA breaks caused by ionizing radiation and alkylating agents. The variant allele of rs25489 results in a missense mutation substituting an amino acid (Arg > His). Several studies have shown diminished DNA repair capacity associated with the variant allele of this SNP, an effect which may be relevant to multiple myeloma etiology. Replication in additional studies is needed to validate this finding.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2634. doi:1538-7445.AM2012-2634
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Affiliation(s)
- Kristin A. Rand
- 1USC/Norris Comprehensive Cancer Center, Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - David V. Conti
- 1USC/Norris Comprehensive Cancer Center, Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Christopher A. Haiman
- 1USC/Norris Comprehensive Cancer Center, Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - David J. Van Den Berg
- 2USC/Norris Comprehensive Cancer Center, Depts of Preventive Medicine and Pathology, Los Angeles, CA
| | - Brenda M. Birmann
- 3Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | | | - Richard K. Severson
- 5Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, MI
| | - Mulugeta Gebregziabher
- 6Division of Biostatistics and Epidemiology, Medical University of South Carolina, Charleston, SC
| | - Sikander Ailawadhi
- 7USC/Norris Comprehensive Cancer Center, Division of Hematology, Department of Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Ann Morbacher
- 7USC/Norris Comprehensive Cancer Center, Division of Hematology, Department of Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Michael R. Lieber
- 1USC/Norris Comprehensive Cancer Center, Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Sophia S. Wang
- 8Division of Cancer Etiology, Department of Population Sciences, City of Hope Medical Center, Duarte, CA
| | - Leslie Bernstein
- 8Division of Cancer Etiology, Department of Population Sciences, City of Hope Medical Center, Duarte, CA
| | - Christopher K. Edlund
- 9Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Nathaniel Rothman
- 10Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Stephen J. Chanock
- 10Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | | | - Graham A. Colditz
- 12Department of Surgery and Alvin J. Siteman Cancer Center, Washington University School of Medicine and Barnes Jewish Hospital, St. Louis, MO
| | - Nikhil Munshi
- 13Jeroma Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Kenneth C. Anderson
- 13Jeroma Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Wendy Cozen
- 2USC/Norris Comprehensive Cancer Center, Depts of Preventive Medicine and Pathology, Los Angeles, CA
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Torgerson DG, Ampleford EJ, Chiu GY, Gauderman WJ, Gignoux CR, Graves PE, Himes BE, Levin AM, Mathias RA, Hancock DB, Baurley JW, Eng C, Stern DA, Celedón JC, Rafaels N, Capurso D, Conti DV, Roth LA, Soto-Quiros M, Togias A, Li X, Myers RA, Romieu I, Van Den Berg DJ, Hu D, Hansel NN, Hernandez RD, Israel E, Salam MT, Galanter J, Avila PC, Avila L, Rodriquez-Santana JR, Chapela R, Rodriguez-Cintron W, Diette GB, Adkinson NF, Abel RA, Ross KD, Shi M, Faruque MU, Dunston GM, Watson HR, Mantese VJ, Ezurum SC, Liang L, Ruczinski I, Ford JG, Huntsman S, Chung KF, Vora H, Li X, Calhoun WJ, Castro M, Sienra-Monge JJ, del Rio-Navarro B, Deichmann KA, Heinzmann A, Wenzel SE, Busse WW, Gern JE, Lemanske RF, Beaty TH, Bleecker ER, Raby BA, Meyers DA, London SJ, Gilliland FD, Burchard EG, Martinez FD, Weiss ST, Williams LK, Barnes KC, Ober C, Nicolae DL. Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations. Nat Genet 2011; 43:887-92. [PMID: 21804549 PMCID: PMC3445408 DOI: 10.1038/ng.888] [Citation(s) in RCA: 637] [Impact Index Per Article: 49.0] [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: 12/14/2010] [Accepted: 06/16/2011] [Indexed: 11/09/2022]
Abstract
Asthma is a common disease with a complex risk architecture including both genetic and environmental factors. We performed a meta-analysis of North American genome-wide association studies of asthma in 5,416 individuals with asthma (cases) including individuals of European American, African American or African Caribbean, and Latino ancestry, with replication in an additional 12,649 individuals from the same ethnic groups. We identified five susceptibility loci. Four were at previously reported loci on 17q21, near IL1RL1, TSLP and IL33, but we report for the first time, to our knowledge, that these loci are associated with asthma risk in three ethnic groups. In addition, we identified a new asthma susceptibility locus at PYHIN1, with the association being specific to individuals of African descent (P = 3.9 × 10(-9)). These results suggest that some asthma susceptibility loci are robust to differences in ancestry when sufficiently large samples sizes are investigated, and that ancestry-specific associations also contribute to the complex genetic architecture of asthma.
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Affiliation(s)
- Dara G Torgerson
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
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Pearce CL, Doherty JA, Van Den Berg DJ, Moysich K, Hsu C, Cushing-Haugen KL, Conti DV, Ramus SJ, Gentry-Maharaj A, Menon U, Gayther SA, Pharoah PDP, Song H, Kjaer SK, Hogdall E, Hogdall C, Whittemore AS, McGuire V, Sieh W, Gronwald J, Medrek K, Jakubowska A, Lubinski J, Chenevix-Trench G, Beesley J, Webb PM, Berchuck A, Schildkraut JM, Iversen ES, Moorman PG, Edlund CK, Stram DO, Pike MC, Ness RB, Rossing MA, Wu AH. Genetic variation in insulin-like growth factor 2 may play a role in ovarian cancer risk. Hum Mol Genet 2011; 20:2263-72. [PMID: 21422097 PMCID: PMC3090188 DOI: 10.1093/hmg/ddr087] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [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: 10/26/2010] [Revised: 02/17/2011] [Accepted: 02/23/2011] [Indexed: 01/20/2023] Open
Abstract
The insulin-like growth factor (IGF) signaling axis plays an important role in cancer biology. We hypothesized that genetic variation in this pathway may influence risk of ovarian cancer. A three-center study of non-Hispanic whites including 1880 control women, 1135 women with invasive epithelial ovarian cancer and 321 women with borderline epithelial ovarian tumors was carried out to test the association between tag single-nucleotide polymorphisms (tSNPs) (n=58) in this pathway and risk of ovarian cancer. We found no association between variation in IGF1, IGFBP1 or IGFBP3 and risk of invasive disease, whereas five tSNPs in IGF2 were associated with risk of invasive epithelial ovarian cancer at P<0.05 and followed-up one of the associated SNPs. We conducted genotyping in 3216 additional non-Hispanic white cases and 5382 additional controls and were able to independently replicate our initial findings. In the combined set of studies, rs4320932 was associated with a 13% decreased risk of ovarian cancer per copy of the minor allele carried (95% confidence interval 0.81-0.93, P-trend=7.4 × 10(-5)). No heterogeneity of effect across study centers was observed (p(het)=0.25). IGF2 is emerging as an important gene for ovarian cancer; additional genotyping is warranted to further confirm these associations with IGF2 and to narrow down the region harboring the causal SNP.
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Affiliation(s)
- Celeste Leigh Pearce
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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Notaridou M, Quaye L, Dafou D, Jones C, Song H, Høgdall E, Kjaer SK, Christensen L, Høgdall C, Blaakaer J, McGuire V, Wu AH, Van Den Berg DJ, Pike MC, Gentry-Maharaj A, Wozniak E, Sher T, Jacobs IJ, Tyrer J, Schildkraut JM, Moorman PG, Iversen ES, Jakubowska A, Mędrek K, Lubiński J, Ness RB, Moysich KB, Lurie G, Wilkens LR, Carney ME, Wang-Gohrke S, Doherty JA, Rossing MA, Beckmann MW, Thiel FC, Ekici AB, Chen X, Beesley J, Gronwald J, Fasching PA, Chang-Claude J, Goodman MT, Chenevix-Trench G, Berchuck A, Pearce CL, Whittemore AS, Menon U, Pharoah PD, Gayther SA, Ramus SJ. Common alleles in candidate susceptibility genes associated with risk and development of epithelial ovarian cancer. Int J Cancer 2011; 128:2063-74. [PMID: 20635389 PMCID: PMC3098608 DOI: 10.1002/ijc.25554] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [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: 03/26/2010] [Revised: 05/26/2010] [Accepted: 06/24/2010] [Indexed: 12/26/2022]
Abstract
Common germline genetic variation in the population is associated with susceptibility to epithelial ovarian cancer. Microcell-mediated chromosome transfer and expression microarray analysis identified nine genes associated with functional suppression of tumorogenicity in ovarian cancer cell lines; AIFM2, AKTIP, AXIN2, CASP5, FILIP1L, RBBP8, RGC32, RUVBL1 and STAG3. Sixty-three tagging single nucleotide polymorphisms (tSNPs) in these genes were genotyped in 1,799 invasive ovarian cancer cases and 3,045 controls to look for associations with disease risk. Two SNPs in RUVBL1, rs13063604 and rs7650365, were associated with increased risk of serous ovarian cancer [HetOR = 1.42 (1.15-1.74) and the HomOR = 1.63 (1.10-1.42), p-trend = 0.0002] and [HetOR = 0.97 (0.80-1.17), HomOR = 0.74 (0.58-0.93), p-trend = 0.009], respectively. We genotyped rs13063604 and rs7650365 in an additional 4,590 cases and 6,031 controls from ten sites from the United States, Europe and Australia; however, neither SNP was significant in Stage 2. We also evaluated the potential role of tSNPs in these nine genes in ovarian cancer development by testing for allele-specific loss of heterozygosity (LOH) in 286 primary ovarian tumours. We found frequent LOH for tSNPs in AXIN2, AKTIP and RGC32 (64, 46 and 34%, respectively) and one SNP, rs1637001, in STAG3 showed significant allele-specific LOH with loss of the common allele in 94% of informative tumours (p = 0.015). Array comparative genomic hybridisation indicated that this nonrandom allelic imbalance was due to amplification of the rare allele. In conclusion, we show evidence for the involvement of a common allele of STAG3 in the development of epithelial ovarian cancer.
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Affiliation(s)
- Maria Notaridou
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Lydia Quaye
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Dimitra Dafou
- Department of Medical and Molecular Genetics, King’s College London School of Medicine, Guy’s Hospital, London, United Kingdom
| | - Chris Jones
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Honglin Song
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Estrid Høgdall
- Department of Viruses, Hormones and Cancer, Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Susanne K. Kjaer
- Department of Viruses, Hormones and Cancer, Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Lise Christensen
- Department of Pathology, Bispebjerg Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Claus Høgdall
- The Gynaecologic Clinic, The Juliane Marie Centre, Rigshospitalet, University of Copenhagen, Denmark
| | - Jan Blaakaer
- Department of Gynaecology and Obstetrics, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | - Valerie McGuire
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA
| | - Anna H. Wu
- University of Southern California, Keck School of Medicine, Department of Preventive Medicine, Los Angeles, CA
| | - David J. Van Den Berg
- University of Southern California, Keck School of Medicine, Department of Preventive Medicine, Los Angeles, CA
| | - Malcolm C. Pike
- University of Southern California, Keck School of Medicine, Department of Preventive Medicine, Los Angeles, CA
| | - Aleksandra Gentry-Maharaj
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Eva Wozniak
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Tanya Sher
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Ian J. Jacobs
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Jonathan Tyrer
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | | | - Patricia G. Moorman
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC
| | - Edwin S. Iversen
- Department of Statistical Science, Duke University, Medical Center, Durham, NC
| | - Anna Jakubowska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Krzysztof Mędrek
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | | | - Kirsten B. Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY
| | - Galina Lurie
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, HI
| | - Lynne R. Wilkens
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, HI
| | - Michael E. Carney
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, HI
| | - Shan Wang-Gohrke
- Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - Jennifer A. Doherty
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mary Anne Rossing
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Matthias W. Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Falk C. Thiel
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Xiaoqing Chen
- Genetics and Population Health, The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Jonathan Beesley
- Genetics and Population Health, The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | | | - Jacek Gronwald
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Peter A. Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
- Division of Hematology and Oncology, University of California at Los Angeles, David Geffen School of Medicine, Los Angeles, CA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Marc T. Goodman
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, HI
| | - Georgia Chenevix-Trench
- Genetics and Population Health, The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology/Division of Gynecologic Oncology, Duke University Medical Center, Durham, NC, 27710
| | - C. Leigh Pearce
- University of Southern California, Keck School of Medicine, Department of Preventive Medicine, Los Angeles, CA
| | - Alice S. Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA
| | - Usha Menon
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Paul D.P. Pharoah
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Simon A. Gayther
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Susan J. Ramus
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
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Hinoue T, Weisenberger DJ, Lange CP, Noushmehr H, Byun HM, van Dijk CM, Pan F, Malik S, Van Den Berg DJ, Shen H, Tollenaar RA, Laird PW. Abstract LB-173: Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-lb-173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [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
Colorectal cancer (CRC) is a heterogeneous disease in which unique subtypes are characterized by distinct genetic and epigenetic alterations. Here we performed comprehensive genome-scale DNA methylation profiling of 125 colorectal tumors and 29 adjacent normal tissues. We identified four DNA methylation-based subgroups of CRC using model-based cluster analyses. Each subtype shows characteristic genetic and clinical features, indicating that they represent biologically distinct subgroups. A CIMP-high (CIMP-H) subgroup includes all CIMP-positive tumors characterized by the MethyLight five-marker panel, and is strongly associated with MLH1 DNA hypermethylation and the BRAFV600E mutation. A CIMP-low subgroup is enriched for KRAS mutations and characterized by DNA hypermethylation of a subset of CIMP-associated markers rather than a unique group of CpG islands. Non-CIMP tumors are separated into two distinct clusters. One non-CIMP subgroup is distinguished by a significantly higher frequency of TP53 mutations and frequent occurrence in the distal colon, while the tumors that belong to the fourth group exhibit a low frequency of both cancer-specific DNA hypermethylation and gene mutations and are significantly enriched for rectal tumors. Furthermore, we identified 114 genes that were downregulated more than 2-fold in CIMP-H tumors together with promoter DNA hypermethylation. These represent approximately 7% of genes that acquired promoter DNA methylation in CIMP-H tumors. Intriguingly, 48/114 genes were also transcriptionally silent in non-CIMP subgroups, but this was not attributable to promoter DNA hypermethylation. Together, we identified four distinct DNA methylation subgroups of CRC and provided novel insight regarding the role of CIMP-specific DNA hypermethylation in gene silencing.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-173. doi:10.1158/1538-7445.AM2011-LB-173
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Affiliation(s)
| | | | | | | | - Hyang-Min Byun
- 3USC/Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | - Fei Pan
- 1USC Epigenome Center, Los Angeles, CA
| | | | | | - Hui Shen
- 1USC Epigenome Center, Los Angeles, CA
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33
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Gago-Dominguez M, Jiang X, Conti DV, Castelao JE, Stern MC, Cortessis VK, Pike MC, Xiang YB, Gao YT, Yuan JM, Van Den Berg DJ. Genetic variations on chromosomes 5p15 and 15q25 and bladder cancer risk: findings from the Los Angeles-Shanghai bladder case-control study. Carcinogenesis 2010; 32:197-202. [PMID: 21081471 DOI: 10.1093/carcin/bgq233] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies have associated common variations at chromosomes 5p15 and 15q25 with lung cancer risk. The 5p15 locus has also been associated with increased bladder cancer risk in a recent report. The 15q25 locus has been associated with nicotine dependence and self-reported number of cigarettes smoked per day in some studies and it was proposed that its association with lung cancer may be mediated through differences in smoking behavior. Here, we investigated the roles of variations at 5p15 (rs401681, rs402710, rs2736098 and rs2736100) and 15q25 (rs1051730 and rs8034191) in bladder cancer etiology in two case-control studies conducted separately in Los Angeles County, CA, USA (498 cases and 588 controls) and in Shanghai, China (506 cases and 530 controls). We replicated the association between the 5p15 locus and bladder cancer among non-Hispanic whites (NHW) in Los Angeles [for rs2736100, per C allele odds ratio (OR) = 1.23; 95% confidence interval (CI), 1.02-1.48; P = 0.029] and among Chinese in Shanghai (OR = 1.22; 95% CI, 1.02-1.47; P = 0.033). Both rs1051730 and rs8034191 at 15q25 were rare among Chinese. Among NHW, a significant association was found between rs8034191 and bladder cancer which persisted after adjustment for cigarette smoking status, number of cigarettes smoked per day and number of years of smoking (per C allele OR = 1.26; 95% CI, 1.04-1.54; P = 0.017). Our results support 5p15 and 15q25 as susceptibility regions for bladder cancer risk.
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Affiliation(s)
- Manuela Gago-Dominguez
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089-9175, USA.
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34
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Bolton KL, Tyrer J, Song H, Ramus SJ, Notaridou M, Jones C, Sher T, Gentry-Maharaj A, Wozniak E, Tsai YY, Weidhaas J, Paik D, Van Den Berg DJ, Stram DO, Pearce CL, Wu AH, Brewster W, Anton-Culver H, Ziogas A, Narod SA, Levine DA, Kaye SB, Brown R, Paul J, Flanagan J, Sieh W, McGuire V, Whittemore AS, Campbell I, Gore ME, Lissowska J, Yang H, Medrek K, Gronwald J, Lubinski J, Jakubowska A, Le ND, Cook LS, Kelemen LE, Brooks-Wilson A, Massuger LF, Kiemeney LA, Aben KK, van Altena AM, Houlston R, Tomlinson I, Palmieri RT, Moorman PG, Schildkraut J, Iversen ES, Phelan C, Vierkant RA, Cunningham JM, Goode EL, Fridley BL, Kruger-Kjaer S, Blaeker J, Hogdall E, Hogdall C, Gross J, Karlan BY, Ness RB, Edwards RP, Odunsi K, Moyisch KB, Baker JA, Modugno F, Heikkinenen T, Butzow R, Nevanlinna H, Leminen A, Bogdanova N, Antonenkova N, Doerk T, Hillemanns P, Dürst M, Runnebaum I, Thompson PJ, Carney ME, Goodman MT, Lurie G, Wang-Gohrke S, Hein R, Chang-Claude J, Rossing MA, Cushing-Haugen KL, Doherty J, Chen C, Rafnar T, Besenbacher S, Sulem P, Stefansson K, Birrer MJ, Terry KL, Hernandez D, Cramer DW, Vergote I, Amant F, Lambrechts D, Despierre E, Fasching PA, Beckmann MW, Thiel FC, Ekici AB, Chen X, Johnatty SE, Webb PM, Beesley J, Chanock S, Garcia-Closas M, Sellers T, Easton DF, Berchuck A, Chenevix-Trench G, Pharoah PD, Gayther SA, Gayther SA. Common variants at 19p13 are associated with susceptibility to ovarian cancer. Nat Genet 2010; 42:880-4. [PMID: 20852633 PMCID: PMC3125495 DOI: 10.1038/ng.666] [Citation(s) in RCA: 217] [Impact Index Per Article: 15.5] [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: 04/05/2010] [Accepted: 07/30/2010] [Indexed: 02/02/2023]
Abstract
Epithelial ovarian cancer (EOC) is the leading cause of death from gynecological malignancy in the developed world, accounting for 4% of the deaths from cancer in women. We performed a three-phase genome-wide association study of EOC survival in 8,951 individuals with EOC (cases) with available survival time data and a parallel association analysis of EOC susceptibility. Two SNPs at 19p13.11, rs8170 and rs2363956, showed evidence of association with survival (overall P = 5 × 10⁻⁴ and P = 6 × 10⁻⁴, respectively), but they did not replicate in phase 3. However, the same two SNPs demonstrated genome-wide significance for risk of serous EOC (P = 3 × 10⁻⁹ and P = 4 × 10⁻¹¹, respectively). Expression analysis of candidate genes at this locus in ovarian tumors supported a role for the BRCA1-interacting gene C19orf62, also known as MERIT40, which contains rs8170, in EOC development.
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Affiliation(s)
- Kelly L. Bolton
- Department of Oncology, University of Cambridge, Cambridge, UK,Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Jonathan Tyrer
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Honglin Song
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Susan J. Ramus
- Department of Gynaecological Oncology, University College London, EGA Institute for Women’s Health, London, UK
| | - Maria Notaridou
- Department of Gynaecological Oncology, University College London, EGA Institute for Women’s Health, London, UK
| | - Chris Jones
- Department of Gynaecological Oncology, University College London, EGA Institute for Women’s Health, London, UK
| | - Tanya Sher
- Department of Gynaecological Oncology, University College London, EGA Institute for Women’s Health, London, UK
| | - Aleksandra Gentry-Maharaj
- Department of Gynaecological Oncology, University College London, EGA Institute for Women’s Health, London, UK
| | - Eva Wozniak
- Department of Gynaecological Oncology, University College London, EGA Institute for Women’s Health, London, UK
| | - Ya-Yu Tsai
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Joanne Weidhaas
- Department of Therapeutic Radiology, Yale University, New Haven, Connecticut, USA
| | - Daniel Paik
- Department of Obstetrics and Gynecology, Yale University, New Haven, Connecticut, USA
| | - David J. Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Daniel O. Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Celeste Leigh Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Anna H. Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Wendy Brewster
- Department of Epidemiology, School of Medicine, University of California, Irvine, California, USA
| | - Hoda Anton-Culver
- Department of Epidemiology, School of Medicine, University of California, Irvine, California, USA
| | - Argyrios Ziogas
- Department of Epidemiology, School of Medicine, University of California, Irvine, California, USA
| | | | - Douglas A. Levine
- Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Stanley B. Kaye
- Section of Medicine, Institute of Cancer Research, Sutton, UK
| | - Robert Brown
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Jim Paul
- Cancer Research UK Clinical Trials Unit, Glasgow University, Glasgow, UK
| | - James Flanagan
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Weiva Sieh
- Department of Health Research and Policy, Stanford University School of Medicine, Standford, California, USA
| | - Valerie McGuire
- Department of Health Research and Policy, Stanford University School of Medicine, Standford, California, USA
| | - Alice S. Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, Standford, California, USA
| | - Ian Campbell
- Peter MacCallum Cancer Institute, Melbourne, Australia
| | - Martin E. Gore
- The Royal Marsden Hospital, Gynecological Oncology Unit, London, UK
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M Sklodowska-Curie Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Hannah Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Krzysztof Medrek
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jacek Gronwald
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Anna Jakubowska
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Nhu D. Le
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Linda S. Cook
- Division of Epidemiology and Biostatistics, University of New Mexico, Albuquerque, New Mexico, USA,Alberta Health Services-Cancer Care, Calgary, AB, Canada
| | | | - Angela Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada,Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Leon F.A.G. Massuger
- Department of Gynaecology, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Lambertus A. Kiemeney
- Department of Gynaecology, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | | | - Anne M. van Altena
- Department of Gynaecology, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Richard Houlston
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, UK
| | - Ian Tomlinson
- Population and Functional Genetics Lab, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Rachel T. Palmieri
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Patricia G. Moorman
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Joellen Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Edwin S. Iversen
- Department of Statistics, Duke University, Durham, North Carolina, USA
| | - Catherine Phelan
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Robert A. Vierkant
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Julie M. Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Ellen L. Goode
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Brooke L. Fridley
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Susan Kruger-Kjaer
- Department of Virus, Hormones and Cancer Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Jan Blaeker
- Aarhus University Hospital, Skejby, Aarhus, Denmark
| | - Estrid Hogdall
- Department of Virus, Hormones and Cancer Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Claus Hogdall
- The Gynaecologic Clinic, The Juliane Marie Centre, Rigshospitalet, Copenhagen, Denmark
| | - Jenny Gross
- Women's Cancer Research Institute at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Beth Y. Karlan
- Women's Cancer Research Institute at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Roberta B. Ness
- University of Texas School of Public Health, Houston, Texas, USA
| | | | - Kunle Odunsi
- Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Kirsten B. Moyisch
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Julie A. Baker
- Department of Obstetrics and Gynecology, Brown University, Providence, Rhode Island, USA
| | - Francesmary Modugno
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Tuomas Heikkinenen
- Department of Obstetrics and Gynaecology, Helsinki University Central Hospital, Helsinki, Finland
| | - Ralf Butzow
- Department of Obstetrics and Gynaecology, Helsinki University Central Hospital, Helsinki, Finland
| | - Heli Nevanlinna
- Department of Obstetrics and Gynaecology, Helsinki University Central Hospital, Helsinki, Finland
| | - Arto Leminen
- Department of Obstetrics and Gynaecology, Helsinki University Central Hospital, Helsinki, Finland
| | - Natalia Bogdanova
- Byelorussian Institute for Oncology and Medical Radiology Aleksandrov N.N., Minsk, Belarus
| | - Natalia Antonenkova
- Byelorussian Institute for Oncology and Medical Radiology Aleksandrov N.N., Minsk, Belarus
| | - Thilo Doerk
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Peter Hillemanns
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Matthias Dürst
- Clinics of Obstetrics and Gynaecology, Friedrich Schiller University, Jena, Germany
| | - Ingo Runnebaum
- Clinics of Obstetrics and Gynaecology, Friedrich Schiller University, Jena, Germany
| | - Pamela J. Thompson
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, Hawaii, USA
| | - Michael E. Carney
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, Hawaii, USA
| | - Marc T. Goodman
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, Hawaii, USA
| | - Galina Lurie
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, Hawaii, USA
| | - Shan Wang-Gohrke
- Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - Rebecca Hein
- Unit of Genetic Epidemiology, Division of Cancer Epidemiology, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Jenny Chang-Claude
- Unit of Genetic Epidemiology, Division of Cancer Epidemiology, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Mary Anne Rossing
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Kara L. Cushing-Haugen
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jennifer Doherty
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Chu Chen
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | | | - Michael J. Birrer
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kathryn L. Terry
- Obstetrics and Gynecology Epidemology Center, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Dena Hernandez
- National Institute of Aging, National Institutues of Health, Bethesda, Maryland, USA
| | - Daniel W. Cramer
- Obstetrics and Gynecology Epidemology Center, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ignace Vergote
- Department of Gynaecologic Oncology, University Hospitals Leuven, Belgium
| | - Frederic Amant
- Department of Gynaecologic Oncology, University Hospitals Leuven, Belgium
| | | | - Evelyn Despierre
- Department of Gynaecologic Oncology, University Hospitals Leuven, Belgium
| | - Peter A. Fasching
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, Los Angeles, California, USA
| | - Matthias W. Beckmann
- Department of Cancer Epidemiology and Prevention, The M.Sklodowska-Curie Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Falk C. Thiel
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Xiaoqing Chen
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | | | | | | | - Sharon E. Johnatty
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Penelope M. Webb
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Jonathan Beesley
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Tom Sellers
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | | | - Andrew Berchuck
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Georgia Chenevix-Trench
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | | | - Simon A. Gayther
- Department of Gynaecological Oncology, University College London, EGA Institute for Women’s Health, London, UK
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Near AM, Wu AH, Templeman C, Van Den Berg DJ, Doherty JA, Rossing MA, Goode EL, Cunningham JM, Vierkant RA, Fridley BL, Chenevix-Trench G, Webb PM, Kjær SK, Hogdall E, Gayther SA, Ramus SJ, Menon U, Gentry-Maharaj A, Schildkraut JM, Moorman PG, Palmieri RT, Ness RB, Moysich K, Cramer DW, Terry KL, Vitonis AF, Pike MC, Berchuck A, Pearce CL. Progesterone receptor gene polymorphisms and risk of endometriosis: results from an international collaborative effort. Fertil Steril 2010; 95:40-5. [PMID: 20719308 DOI: 10.1016/j.fertnstert.2010.06.059] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 06/11/2010] [Accepted: 06/16/2010] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To investigate the association between self-reported endometriosis and the putative functional promoter +331C/T single nucleotide polymorphism and the PROGINS allele. DESIGN Control subjects from ovarian cancer case-control studies participating in the international Ovarian Cancer Association Consortium. The majority of controls are drawn from population-based studies. SETTING An international ovarian cancer consortium including studies from Australia, Europe, and the United States. PATIENT(S) Five thousand eight hundred twelve white female controls, of whom 348 had endometriosis, from eight ovarian cancer case-control studies. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Genotypes for the +331C/T single nucleotide polymorphism and PROGINS allele and a history of endometriosis. RESULT(S) The occurrence of endometriosis was reduced in women carrying one or more copies of the +331 T allele (odds ratio=0.65; 95% confidence interval: 0.43-0.98), whereas there was no association between the PROGINS allele and endometriosis (odds ratio=0.94, 95% confidence interval 0.76-1.16). CONCLUSION(S) Additional studies of the +331C/T variant are warranted given the current finding and the equivocal results of previous studies. The +331 T allele has been shown to result in a reduced progesterone (P) receptor A to P receptor B ratio, and if the observed association with endometriosis is confirmed it would suggest that this ratio is important for this disease.
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Affiliation(s)
- Aimee M Near
- Cancer Control Program, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
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Doherty JA, Rossing MA, Cushing-Haugen KL, Chen C, Van Den Berg DJ, Wu AH, Pike MC, Ness RB, Moysich K, Chenevix-Trench G, Beesley J, Webb PM, Chang-Claude J, Wang-Gohrke S, Goodman MT, Lurie G, Thompson PJ, Carney ME, Hogdall E, Kjaer SK, Hogdall C, Goode EL, Cunningham JM, Fridley BL, Vierkant RA, Berchuck A, Moorman PG, Schildkraut JM, Palmieri RT, Cramer DW, Terry KL, Yang HP, Garcia-Closas M, Chanock S, Lissowska J, Song H, Pharoah PDP, Shah M, Perkins B, McGuire V, Whittemore AS, Di Cioccio RA, Gentry-Maharaj A, Menon U, Gayther SA, Ramus SJ, Ziogas A, Brewster W, Anton-Culver H, Pearce CL. ESR1/SYNE1 polymorphism and invasive epithelial ovarian cancer risk: an Ovarian Cancer Association Consortium study. Cancer Epidemiol Biomarkers Prev 2010; 19:245-50. [PMID: 20056644 DOI: 10.1158/1055-9965.epi-09-0729] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [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] Open
Abstract
We genotyped 13 single nucleotide polymorphisms (SNPs) in the estrogen receptor alpha gene (ESR1) region in three population-based case-control studies of epithelial ovarian cancer conducted in the United States, comprising a total of 1,128 and 1,866 non-Hispanic white invasive cases and controls, respectively. A SNP 19 kb downstream of ESR1 (rs2295190, G-to-T change) was associated with invasive ovarian cancer risk, with a per-T-allele odds ratio (OR) of 1.24 [95% confidence interval (CI), 1.06-1.44, P = 0.006]. rs2295190 is a nonsynonymous coding SNP in a neighboring gene called spectrin repeat containing, nuclear envelope 1 (SYNE1), which is involved in nuclear organization and structural integrity, function of the Golgi apparatus, and cytokinesis. An isoform encoded by SYNE1 has been reported to be downregulated in ovarian and other cancers. rs2295190 was genotyped in an additional 12 studies through the Ovarian Cancer Association Consortium, with 5,279 invasive epithelial cases and 7,450 controls. The per-T-allele OR for this 12-study set was 1.09 (95% CI, 1.02-1.17; P = 0.017). Results for the serous subtype in the 15 combined studies were similar to those overall (n = 3,545; OR, 1.09; 95% CI, 1.01-1.18; P = 0.025), and our findings were strongest for the mucinous subtype (n = 447; OR, 1.32; 95% CI, 1.11-1.58; P = 0.002). No association was observed for the endometrioid subtype. In an additional analysis of 1,459 borderline ovarian cancer cases and 7,370 controls, rs2295190 was not associated with risk. These data provide suggestive evidence that the rs2295190 T allele, or another allele in linkage disequilibrium with it, may be associated with increased risk of invasive ovarian cancer.
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Affiliation(s)
- Jennifer A Doherty
- Program in Epidemiology (M4-C308), Fred Hutchinson Cancer Research Center, PO Box 19024, Seattle, WA 98109-1024, USA.
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37
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Phelan CM, Tsai YY, Goode EL, Vierkant RA, Fridley BL, Beesley J, Chen XQ, Webb PM, Chanock S, Cramer DW, Moysich K, Edwards RP, Chang-Claude J, Garcia-Closas M, Yang H, Wang-Gohrke S, Hein R, Green AC, Lissowska J, Carney ME, Lurie G, Wilkens LR, Ness RB, Pearce CL, Wu AH, Van Den Berg DJ, Stram DO, Terry KL, Whiteman DC, Whittemore AS, DiCioccio RA, McGuire V, Doherty JA, Rossing MA, Anton-Culver H, Ziogas A, Hogdall C, Hogdall E, Krüger Kjaer S, Blaakaer J, Quaye L, Ramus SJ, Jacobs I, Song H, Pharoah PDP, Iversen ES, Marks JR, Pike MC, Gayther SA, Cunningham JM, Goodman MT, Schildkraut JM, Chenevix-Trench G, Berchuck A, Sellers TA. Polymorphism in the GALNT1 gene and epithelial ovarian cancer in non-Hispanic white women: the Ovarian Cancer Association Consortium. Cancer Epidemiol Biomarkers Prev 2010; 19:600-4. [PMID: 20142253 PMCID: PMC2880167 DOI: 10.1158/1055-9965.epi-09-0861] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [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] [Indexed: 12/13/2022] Open
Abstract
Aberrant glycosylation is a well-described hallmark of cancer. In a previous ovarian cancer case control study that examined polymorphisms in 26 glycosylation-associated genes, we found strong statistical evidence (P = 0.00017) that women who inherited two copies of a single-nucleotide polymorphism in the UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferase, GALNT1, had decreased ovarian cancer risk. The current study attempted to replicate this observation. The GALNT1 single-nucleotide polymorphism rs17647532 was genotyped in 6,965 cases and 8,377 controls from 14 studies forming the Ovarian Cancer Association Consortium. The fixed effects estimate per rs17647532 allele was null (odds ratio, 0.99; 95% confidence interval, 0.92-1.07). When a recessive model was fit, the results were unchanged. Test for heterogeneity of the odds ratios revealed consistency across the 14 replication sites but significant differences compared with the original study population (P = 0.03). This study underscores the need for replication of putative findings in genetic association studies.
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Affiliation(s)
- Catherine M Phelan
- Department of Epidemiology and Genetics, Division of Cancer Prevention and Control, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
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38
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Inoue-Choi M, Yuan JM, Yang CS, Van Den Berg DJ, Lee MJ, Gao YT, Yu MC. Genetic Association Between the COMT Genotype and Urinary Levels of Tea Polyphenols and Their Metabolites among Daily Green Tea Drinkers. Int J Mol Epidemiol Genet 2010; 1:114-123. [PMID: 21191472 PMCID: PMC3010377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Accepted: 02/20/2010] [Indexed: 05/30/2023]
Abstract
Available in vitro and animal studies have shown cancer protective effects of tea polyphenols. Recent study suggests a greater protective effect of green tea intake on breast cancer risk among women possessing the low-activity associated genotype of the catechol-O-methyltransferase (COMT), which may modulate the metabolism and excretion of tea polyphenols through urine. To determine the effect of COMT genotype on urinary excretion of tea polyphenol metabolites of daily green tea drinkers, a cross-sectional analysis was performed within the Shanghai Cohort Study, a population-based, prospective investigation of diet and cancer in 18,244men. In addition to an in-person interview, each participant provided a blood and urine sample at baseline. In the present study, COMT genotype (rs4680) and five urinary metabolites of tea polyphenols were determined in 660 cohort subjects who self-identified as daily drinkers of green tea. All urinary tea polyphenol measurements were expressed in units of urinary creatinine. Men possessing the homozygous low-activity associated COMT genotype (LL) exhibited statistically significantly lower urinary levels of individual as well as all of the five tea polyphenol metabolites under study relative to individuals possessing the wild type high-activity associated COMT genotype (HH)or the heterozygous variant genotype (HL). Levels of urinary tea polyphenol metabolites were comparable between men possessing the HH and HL genotypes. The present study demonstrated that men carrying low-activity associated COMT genotype excreted less tea polyphenols from urine, which suggests that they may retain more tea polyphenols in their bodies and derive greater health benefits from green tea intake.
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Affiliation(s)
- Maki Inoue-Choi
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota1300 S. Second St., WBOB Suite 300, Minneapolis, MN 55454, USA
| | - Jian-Min Yuan
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota1300 S. Second St., WBOB Suite 300, Minneapolis, MN 55454, USA
- The Masonic Cancer Center, University of MinnesotaMinneapolis, Minnesota, USA
| | - Chung S Yang
- Department of Chemical Biology, Rutgers UniversityPiscataway, New Jersey, USA
| | - David J Van Den Berg
- USC/Norris Comprehensive Cancer Center, University of Southern CaliforniaLos Angeles, California, USA
| | - Mao-Jung Lee
- Department of Chemical Biology, Rutgers UniversityPiscataway, New Jersey, USA
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer InstituteShanghai, People's Republic of China
| | - Mimi C Yu
- The Masonic Cancer Center, University of MinnesotaMinneapolis, Minnesota, USA
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39
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Song H, Ramus SJ, Tyrer J, Bolton KL, Gentry-Maharaj A, Wozniak E, Anton-Culver H, Chang-Claude J, Cramer DW, DiCioccio R, Dörk T, Goode EL, Goodman MT, Schildkraut JM, Sellers T, Baglietto L, Beckmann MW, Beesley J, Blaakaer J, Carney ME, Chanock S, Chen Z, Cunningham JM, Dicks E, Doherty JA, Dürst M, Ekici AB, Fenstermacher D, Fridley BL, Giles G, Gore ME, De Vivo I, Hillemanns P, Hogdall C, Hogdall E, Iversen ES, Jacobs IJ, Jakubowska A, Li D, Lissowska J, Lubiński J, Lurie G, McGuire V, McLaughlin J, Mędrek K, Moorman PG, Moysich K, Narod S, Phelan C, Pye C, Risch H, Runnebaum IB, Severi G, Southey M, Stram DO, Thiel FC, Terry KL, Tsai YY, Tworoger SS, Van Den Berg DJ, Vierkant RA, Wang-Gohrke S, Webb PM, Wilkens LR, Wu AH, Yang H, Brewster W, Ziogas A, Houlston R, Tomlinson I, Whittemore AS, Rossing MA, Ponder BA, Pearce CL, Ness RB, Menon U, Kjaer SK, Gronwald J, Garcia-Closas M, Fasching PA, Easton DF, Chenevix-Trench G, Berchuck A, Pharoah PD, Gayther SA. A genome-wide association study identifies a new ovarian cancer susceptibility locus on 9p22.2. Nat Genet 2009; 41:996-1000. [PMID: 19648919 PMCID: PMC2844110 DOI: 10.1038/ng.424] [Citation(s) in RCA: 255] [Impact Index Per Article: 17.0] [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: 05/06/2009] [Accepted: 07/02/2009] [Indexed: 12/11/2022]
Abstract
Epithelial ovarian cancer has a major heritable component, but the known susceptibility genes explain less than half the excess familial risk. We performed a genome-wide association study (GWAS) to identify common ovarian cancer susceptibility alleles. We evaluated 507,094 SNPs genotyped in 1,817 cases and 2,353 controls from the UK and approximately 2 million imputed SNPs. We genotyped the 22,790 top ranked SNPs in 4,274 cases and 4,809 controls of European ancestry from Europe, USA and Australia. We identified 12 SNPs at 9p22 associated with disease risk (P < 10(-8)). The most significant SNP (rs3814113; P = 2.5 x 10(-17)) was genotyped in a further 2,670 ovarian cancer cases and 4,668 controls, confirming its association (combined data odds ratio (OR) = 0.82, 95% confidence interval (CI) 0.79-0.86, P(trend) = 5.1 x 10(-19)). The association differs by histological subtype, being strongest for serous ovarian cancers (OR 0.77, 95% CI 0.73-0.81, P(trend) = 4.1 x 10(-21)).
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Affiliation(s)
- Honglin Song
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Susan J. Ramus
- Department of Gynaecological Oncology, UCL EGA Institute for Women’s Health, University College London, UK
| | - Jonathan Tyrer
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Kelly L. Bolton
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Aleksandra Gentry-Maharaj
- Department of Gynaecological Oncology, UCL EGA Institute for Women’s Health, University College London, UK
| | - Eva Wozniak
- Department of Gynaecological Oncology, UCL EGA Institute for Women’s Health, University College London, UK
| | | | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Daniel W. Cramer
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women’s Hospital, Boston, MA
| | - Richard DiCioccio
- Department of Cancer Genetics and the Gilda Radner Familial Ovarian Cancer Registry Buffalo, NY, USA
| | - Thilo Dörk
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | | | - Marc T Goodman
- Epidemiology Program, Cancer Research Center of Hawaii, University of Hawaii, USA
| | | | - Thomas Sellers
- Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, USA
| | - Laura Baglietto
- Cancer Epidemiology Centre, The Cancer Council Victoria, Rathdowne Street, Carlton VIC 3053, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne, Swanston Street, Carlton VIC 3053, Australia
| | | | - Jonathan Beesley
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Jan Blaakaer
- Department of Gynaecological and Obstetrics, Skejby University Hospital, Arhus
| | - Michael E Carney
- Epidemiology Program, Cancer Research Center of Hawaii, University of Hawaii, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Zhihua Chen
- Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, USA
| | | | - Ed Dicks
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Jennifer A. Doherty
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Matthias Dürst
- Department of Gynaecology and Obstetrics, University Hospital of Jena, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | | | | | - Graham Giles
- Cancer Epidemiology Centre, The Cancer Council Victoria, Rathdowne Street, Carlton VIC 3053, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne, Swanston Street, Carlton VIC 3053, Australia
| | - Martin E. Gore
- The Royal Marsden Hospital, Gynecological Oncology Unit, London, UK
| | - Immaculata De Vivo
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital & Harvard Medical School, Boston, MA
| | - Peter Hillemanns
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Claus Hogdall
- The Gyneacologic Clinic, The Juliane Marie Centre, Rigshospitalet, Copenhagen, Denmark
| | - Estrid Hogdall
- Department of Viruses, Hormones and Cancer, Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | | | - Ian J Jacobs
- Department of Gynaecological Oncology, UCL EGA Institute for Women’s Health, University College London, UK
| | - Anna Jakubowska
- International Hereditary Cancer Center, Department Of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Dong Li
- Department of Epidemiology, University of California Irvine, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Cancer Centre and Institute of Oncology, Warsaw, Poland
| | - Jan Lubiński
- International Hereditary Cancer Center, Department Of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Galina Lurie
- Epidemiology Program, Cancer Research Center of Hawaii, University of Hawaii, USA
| | - Valerie McGuire
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, USA
| | - John McLaughlin
- Samuel Lunenfeld Research Institute, 60 Murray Street, Toronto, ON, Canada
| | - Krzysztof Mędrek
- International Hereditary Cancer Center, Department Of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Patricia G. Moorman
- The Comprehensive Cancer Center, Duke University Medical Center, Durham, NC, USA
| | | | - Steven Narod
- Center for Research in Women’s Health, 790 Bay St., Toronto, ON, Canada
| | | | - Carole Pye
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Harvey Risch
- Yale University, 60 College Street, New Haven, CT, USA
| | - Ingo B Runnebaum
- Department of Gynaecology and Obstetrics, University Hospital of Jena, Germany
| | - Gianluca Severi
- Cancer Epidemiology Centre, The Cancer Council Victoria, Rathdowne Street, Carlton VIC 3053, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne, Swanston Street, Carlton VIC 3053, Australia
| | - Melissa Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, VIC 3010, Australia
| | - Daniel O. Stram
- University of Southern California, Keck School of Medicine, Los Angeles, California, USA
| | - Falk C. Thiel
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Germany
| | - Kathryn L. Terry
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women’s Hospital, Boston, MA
| | - Ya-Yu Tsai
- Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, USA
| | - Shelley S. Tworoger
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital & Harvard Medical School, Boston, MA
| | - David J. Van Den Berg
- University of Southern California, Keck School of Medicine, Los Angeles, California, USA
| | | | - Shan Wang-Gohrke
- Department of Obstetrics and Gynaecology, University of Ulm, Ulm, Germany
| | - Penelope M. Webb
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Lynne R. Wilkens
- Epidemiology Program, Cancer Research Center of Hawaii, University of Hawaii, USA
| | - Anna H Wu
- University of Southern California, Keck School of Medicine, Los Angeles, California, USA
| | - Hannah Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Wendy Brewster
- Department of Obstetrics and Gynecology, University North Carolina, Chapel Hill, North Carolina, USA
| | - Argyrios Ziogas
- Department of Epidemiology, University of California Irvine, USA
| | | | | | | | - Richard Houlston
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, UK
| | - Ian Tomlinson
- Population and Functional Genetics Lab, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Alice S Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, USA
| | - Mary Anne Rossing
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bruce A.J. Ponder
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Celeste Leigh Pearce
- University of Southern California, Keck School of Medicine, Los Angeles, California, USA
| | - Roberta B. Ness
- The University of Texas, School of Public Health, Houston, TX, USA
| | - Usha Menon
- Department of Gynaecological Oncology, UCL EGA Institute for Women’s Health, University College London, UK
| | - Susanne Krüger Kjaer
- Department of Viruses, Hormones and Cancer, Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Jacek Gronwald
- International Hereditary Cancer Center, Department Of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Peter A. Fasching
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Germany
- University of California at Los Angeles, David Geffen School of Medicine, Division of Hematology and Oncology
| | - Douglas F Easton
- CR-UK Genetic Epidemiology Unit, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Georgia Chenevix-Trench
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Andrew Berchuck
- The Comprehensive Cancer Center, Duke University Medical Center, Durham, NC, USA
| | - Paul D.P. Pharoah
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Simon A. Gayther
- Department of Gynaecological Oncology, UCL EGA Institute for Women’s Health, University College London, UK
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40
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Song H, Ramus SJ, Kjaer SK, DiCioccio RA, Chenevix-Trench G, Pearce CL, Hogdall E, Whittemore AS, McGuire V, Hogdall C, Blaakaer J, Wu AH, Van Den Berg DJ, Stram DO, Menon U, Gentry-Maharaj A, Jacobs IJ, Webb PM, Beesley J, Chen X, Rossing MA, Doherty JA, Chang-Claude J, Wang-Gohrke S, Goodman MT, Lurie G, Thompson PJ, Carney ME, Ness RB, Moysich K, Goode EL, Vierkant RA, Cunningham JM, Anderson S, Schildkraut JM, Berchuck A, Iversen ES, Moorman PG, Garcia-Closas M, Chanock S, Lissowska J, Brinton L, Anton-Culver H, Ziogas A, Brewster WR, Ponder BAJ, Easton DF, Gayther SA, Pharoah PDP. Association between invasive ovarian cancer susceptibility and 11 best candidate SNPs from breast cancer genome-wide association study. Hum Mol Genet 2009; 18:2297-304. [PMID: 19304784 PMCID: PMC2685754 DOI: 10.1093/hmg/ddp138] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [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: 01/13/2009] [Revised: 03/11/2009] [Accepted: 03/18/2009] [Indexed: 11/13/2022] Open
Abstract
Because both ovarian and breast cancer are hormone-related and are known to have some predisposition genes in common, we evaluated 11 of the most significant hits (six with confirmed associations with breast cancer) from the breast cancer genome-wide association study for association with invasive ovarian cancer. Eleven SNPs were initially genotyped in 2927 invasive ovarian cancer cases and 4143 controls from six ovarian cancer case-control studies. Genotype frequencies in cases and controls were compared using a likelihood ratio test in a logistic regression model stratified by study. Initially, three SNPs (rs2107425 in MRPL23, rs7313833 in PTHLH, rs3803662 in TNRC9) were weakly associated with ovarian cancer risk and one SNP (rs4954956 in NXPH2) was associated with serous ovarian cancer in non-Hispanic white subjects (P-trend < 0.1). These four SNPs were then genotyped in an additional 4060 cases and 6308 controls from eight independent studies. Only rs4954956 was significantly associated with ovarian cancer risk both in the replication study and in combined analyses. This association was stronger for the serous histological subtype [per minor allele odds ratio (OR) 1.07 95% CI 1.01-1.13, P-trend = 0.02 for all types of ovarian cancer and OR 1.14 95% CI 1.07-1.22, P-trend = 0.00017 for serous ovarian cancer]. In conclusion, we found that rs4954956 was associated with increased ovarian cancer risk, particularly for serous ovarian cancer. However, none of the six confirmed breast cancer susceptibility variants we tested was associated with ovarian cancer risk. Further work will be needed to identify the causal variant associated with rs4954956 or elucidate its function.
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Affiliation(s)
- Honglin Song
- CR-UK Department of Oncology, Strangeways Research Laboratory, University of Cambridge, Cambridge, UK.
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Inoue M, Robien K, Wang R, Van Den Berg DJ, Koh WP, Yu MC. Green tea intake, MTHFR/TYMS genotype and breast cancer risk: the Singapore Chinese Health Study. Carcinogenesis 2008; 29:1967-72. [PMID: 18669903 DOI: 10.1093/carcin/bgn177] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The tea polyphenol (-)-epigallocatechin-3-gallate (EGCG) has been reported to act as a cancer preventive agent through folate pathway inhibition in experimental studies. We hypothesized that if folate pathway inhibition is the mechanism of cancer preventive activities of EGCG, then the protective effect against breast cancer would be stronger among women with low dietary folate intake and the high-activity methylenetetrahydrofolate reductase (MTHFR) and thymidylate synthase (TYMS) genotypes. In a nested case-control study of 380 women with incident breast cancer and 662 controls within the Singapore Chinese Health Study, we found no association between either green tea intake or gene polymorphisms of MTHFR (C677T and A1298C) and TYMS (1494 ins/del) and breast cancer risk. However, among women with low folate intake (<133.4 microg/day), weekly/daily green tea intake was inversely associated with breast cancer risk compared with less green tea intake [odds ratio (OR) = 0.45, 95% confidence interval (CI) = 0.26-0.79, P for interaction = 0.02]. Among women with high folate intake (>or=133.4 microg/day), green tea intake was not associated with breast cancer. Similarly, among women possessing the high-activity MTHFR/TYMS genotypes (0-1 variant allele), weekly/daily versus less frequent green tea intake was associated with lower breast cancer risk (OR = 0.66, 95% CI = 0.45-0.98), which was observed even more strongly among those who also had low folate intake (OR = 0.44, 95% CI = 0.22-0.89) than high folate intake (OR = 0.92, 95% CI = 0.55-1.54). This association was not observed among women possessing the low-activity genotypes (2-4 variant alleles). Our findings suggest that folate pathway inhibition may be one mechanism through which green tea protects against breast cancer in humans.
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Affiliation(s)
- Maki Inoue
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
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Ramus SJ, Vierkant RA, Johnatty SE, Pike MC, Van Den Berg DJ, Wu AH, Pearce CL, Menon U, Gentry-Maharaj A, Gayther SA, DiCioccio RA, McGuire V, Whittemore AS, Song H, Easton DF, Pharoah PDP, Garcia-Closas M, Chanock S, Lissowska J, Brinton L, Terry KL, Cramer DW, Tworoger SS, Hankinson SE, Berchuck A, Moorman PG, Schildkraut JM, Cunningham JM, Liebow M, Kjaer SK, Hogdall E, Hogdall C, Blaakaer J, Ness RB, Moysich KB, Edwards RP, Carney ME, Lurie G, Goodman MT, Wang-Gohrke S, Kropp S, Chang-Claude J, Webb PM, Chen X, Beesley J, Chenevix-Trench G, Goode EL. Consortium analysis of 7 candidate SNPs for ovarian cancer. Int J Cancer 2008; 123:380-388. [PMID: 18431743 DOI: 10.1002/ijc.23448] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Ovarian Cancer Association Consortium selected 7 candidate single nucleotide polymorphisms (SNPs), for which there is evidence from previous studies of an association with variation in ovarian cancer or breast cancer risks. The SNPs selected for analysis were F31I (rs2273535) in AURKA, N372H (rs144848) in BRCA2, rs2854344 in intron 17 of RB1, rs2811712 5' flanking CDKN2A, rs523349 in the 3' UTR of SRD5A2, D302H (rs1045485) in CASP8 and L10P (rs1982073) in TGFB1. Fourteen studies genotyped 4,624 invasive epithelial ovarian cancer cases and 8,113 controls of white non-Hispanic origin. A marginally significant association was found for RB1 when all studies were included [ordinal odds ratio (OR) 0.88 (95% confidence interval (CI) 0.79-1.00) p = 0.041 and dominant OR 0.87 (95% CI 0.76-0.98) p = 0.025]; when the studies that originally suggested an association were excluded, the result was suggestive although no longer statistically significant (ordinal OR 0.92, 95% CI 0.79-1.06). This SNP has also been shown to have an association with decreased risk in breast cancer. There was a suggestion of an association for AURKA, when one study that caused significant study heterogeneity was excluded [ordinal OR 1.10 (95% CI 1.01-1.20) p = 0.027; dominant OR 1.12 (95% CI 1.01-1.24) p = 0.03]. The other 5 SNPs in BRCA2, CDKN2A, SRD5A2, CASP8 and TGFB1 showed no association with ovarian cancer risk; given the large sample size, these results can also be considered to be informative. These null results for SNPs identified from relatively large initial studies shows the importance of replicating associations by a consortium approach.
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Affiliation(s)
- Susan J Ramus
- Translational Research Laboratory, University College London EGA Institute for Women's Health, London, United Kingdom
| | | | - Sharon E Johnatty
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Malcolm C Pike
- University of Southern California, Keck School of Medicine, Los Angeles, CA
| | | | - Anna H Wu
- University of Southern California, Keck School of Medicine, Los Angeles, CA
| | | | - Usha Menon
- Gynaecological Cancer Research Centre, University College London, EGA Institute for Women's Health, London, United Kingdom
| | - Aleksandra Gentry-Maharaj
- Gynaecological Cancer Research Centre, University College London, EGA Institute for Women's Health, London, United Kingdom
| | - Simon A Gayther
- Translational Research Laboratory, University College London EGA Institute for Women's Health, London, United Kingdom
| | | | | | | | - Honglin Song
- Cancer Research United Kingdom Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Douglas F Easton
- Cancer Research United Kingdom Genetic Epidemiology Unit, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Paul D P Pharoah
- Cancer Research United Kingdom Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | | | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, Cancer Center and M. Sklodowska-Curie Institute of Oncology, Warsaw, Poland
| | - Louise Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Kathryn L Terry
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, MA
| | - Daniel W Cramer
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, MA
| | - Shelley S Tworoger
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Susan E Hankinson
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC
| | - Patricia G Moorman
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC
| | - Joellen M Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC
| | | | - Mark Liebow
- College of Medicine, Mayo Clinic, Rochester, MN
| | | | | | - Claus Hogdall
- Rigshospitalet, The Juliane Marie Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Roberta B Ness
- Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | | | | | | | - Galina Lurie
- Cancer Research Center, University of Hawaii, Honolulu, Hawaii
| | - Marc T Goodman
- Cancer Research Center, University of Hawaii, Honolulu, Hawaii
| | | | - Silke Kropp
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Penelope M Webb
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Xiaoqing Chen
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Jonathan Beesley
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Georgia Chenevix-Trench
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
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Pearce CL, Van Den Berg DJ, Makridakis N, Reichardt JKV, Ross RK, Pike MC, Kolonel LN, Henderson BE. No association between the SRD5A2 gene A49T missense variant and prostate cancer risk: lessons learned. Hum Mol Genet 2008; 17:2456-61. [PMID: 18469342 DOI: 10.1093/hmg/ddn145] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The steroid 5-alpha reductase type II gene (SRD5A2) encodes the enzyme which converts testosterone (T) to the more active androgen dihydrotestosterone. A non-synonymous single-nucleotide polymorphism, A49T (rs9282858), in SRD5A2 has been implicated in prostate cancer risk; however, results have been inconsistent. In 1999, we reported a strong association between the A49T variant and prostate cancer risk among African-Americans and Latinos in the Hawaii-Los Angeles Multiethnic Cohort (MEC). We report here an updated analysis of MEC data including the five major ethnic groups of the MEC, an increased sample size, improved genotyping technology and a comprehensive meta-analysis of the published literature. We found a non-statistically significant positive association between prostate cancer risk and carrying either the AT or TT genotype [odds ratio (OR) = 1.16, 95% confidence interval (CI) 0.79-1.69] in the MEC. This finding is in contrast to our previous results of ORs of 3.28 and 2.50 for the association between prostate cancer risk and the variant in African-American and Latino men, respectively; this can be accounted for by genotyping error in our earlier study. Meta-analysis of the published literature, including the current MEC data, shows a summary OR of 1.13 (95% CI 0.95-1.34) for the A49T variant with prostate cancer risk among sporadic, unselected cases. After evaluating more than 6000 cases and 6000 controls, there is little evidence of a role for the SRD5A2 A49T variant in prostate cancer risk. Overall, this report highlights the importance of rigorous genotyping quality control measures and replication efforts in genetic association studies.
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Affiliation(s)
- C Leigh Pearce
- 1Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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Cozen W, Gebregziabher M, Conti DV, Van Den Berg DJ, Coetzee GA, Wang SS, Rothman N, Bernstein L, Hartge P, Morhbacher A, Coetzee SG, Salam MT, Wang W, Zadnick J, Ingles SA. Interleukin-6-Related Genotypes, Body Mass Index, and Risk of Multiple Myeloma and Plasmacytoma. Cancer Epidemiol Biomarkers Prev 2006; 15:2285-91. [PMID: 17119059 DOI: 10.1158/1055-9965.epi-06-0446] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [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] [Indexed: 11/16/2022] Open
Abstract
Interleukin-6 (IL-6) promotes normal plasma cell development and proliferation of myeloma cells in culture. We evaluated IL-6 genotypes and body mass index (BMI) in a case-control study of multiple myeloma and plasmacytoma. DNA samples and questionnaires were obtained from incident cases of multiple myeloma (n = 134) and plasmacytoma (n = 16; plasma cell neoplasms) ascertained from the Los Angeles County population-based cancer registry and from siblings or cousins of cases (family controls, n = 112) and population controls (n = 126). Genotypes evaluated included IL-6 promoter gene single nucleotide polymorphisms (SNP) at positions -174, -572, and -597; one variable number of tandem repeats (-373 A(n)T(n)); and one SNP in the IL-6 receptor (IL-6ralpha) gene at position -358. The variant allele of the IL-6 promoter SNP -572 was associated with a roughly 2-fold increased risk of plasma cell neoplasms when cases were compared with family [odds ratio (OR), 1.8; 95% confidence interval (95% CI), 0.7-4.7] or population controls (OR, 2.4; 95% CI, 1.2-4.7). The -373 9A/9A genotype was associated with a decreased risk compared with the most common genotype (OR for cases versus family controls, 0.4; 95% CI, 0.1-1.7; OR for cases versus population controls, 0.3; 95% CI, 0.1-0.9). No other SNPs were associated with risk. Obesity (BMI >or= 30 kg/m(2)) increased risk nonsignificantly by 40% and 80% when cases were compared with family controls or population controls, respectively, relative to persons with a BMI of <25 kg/m(2). These results suggest that IL-6 promoter genotypes may be associated with increased risk of plasma cell neoplasms.
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Affiliation(s)
- Wendy Cozen
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, MC 9175, Los Angeles, CA 90089-9175, USA.
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