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Matoy EJ, Plowman JN, Watson CJ, Belshan MA, Blue EE, Huff CD, Stessman HAF. In vitro data suggest a role for PMS2 Kozak sequence mutations in Lynch Syndrome risk. HGG Adv 2024:100298. [PMID: 38654521 DOI: 10.1016/j.xhgg.2024.100298] [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] [Received: 04/10/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024] Open
Abstract
Lynch Syndrome (LS) is the most common hereditary cancer syndrome. Heterozygous loss-of-function variants in PMS2 are linked to LS. While these variants are not directly cancer causing, reduced PMS2 function results in the accumulation of somatic variants and increased cancer risk over time due to DNA mismatch repair dysfunction. It is reasonable that other types of genetic variation that impact the expression of PMS2 may also contribute to cancer risk. The Kozak sequence is a highly conserved translation initiation motif among higher eukaryotes and is defined as the nine basepairs upstream of the translation start codon through the first four bases of the translated sequence (5'-[GTT]GCATCCATGG-3'; human PMS2 NM_000535.7). While Kozak sequence variants in PMS2 have been reported in ClinVar in suspected hereditary cancer patients, all variants upstream of the translation start site are currently classified as variants of undetermined significance (VUSs). We hypothesized that variants significantly disrupting the Kozak sequence of PMS2 would decrease PMS2 protein expression, contributing to increased cancer risk over time. Using a dual luciferase reporter plasmid and site-directed mutagenesis, we generated the wild-type human PMS2 and the ClinVar VUSs within the PMS2 Kozak sequence. Besides the c.1A>C variant, which is already known to be pathogenic, we implicate six additional variants as ACMG/AMP pathogenic supporting (PP) variants and classify ten as benign supporting (BP). In summary, we present a method developed for the classification of human PMS2 Kozak sequence variants that can contribute to the re-classification of VUSs identified in patients.
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Affiliation(s)
| | | | | | - Michael A Belshan
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE 68178, USA
| | - Elizabeth E Blue
- Department of Medicine, Division of Medical Genetics and; Institute for Public Health Genetics, University of Washington, Seattle, WA 98195, USA,; Brotman Baty Institute, Seattle, WA 98195, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Holly A F Stessman
- Department of Pharmacology and Neuroscience,; Creighton University Core Facilities,.
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Barnes DR, Tyrer JP, Dennis J, Leslie G, Bolla MK, Lush M, Aeilts AM, Aittomäki K, Andrieu N, Andrulis IL, Anton-Culver H, Arason A, Arun BK, Balmaña J, Bandera EV, Barkardottir RB, Berger LP, de Gonzalez AB, Berthet P, Białkowska K, Bjørge L, Blanco AM, Blok MJ, Bobolis KA, Bogdanova NV, Brenton JD, Butz H, Buys SS, Caligo MA, Campbell I, Castillo C, Claes KB, Colonna SV, Cook LS, Daly MB, Dansonka-Mieszkowska A, de la Hoya M, deFazio A, DePersia A, Ding YC, Domchek SM, Dörk T, Einbeigi Z, Engel C, Evans DG, Foretova L, Fortner RT, Fostira F, Foti MC, Friedman E, Frone MN, Ganz PA, Gentry-Maharaj A, Glendon G, Godwin AK, González-Neira A, Greene MH, Gronwald J, Guerrieri-Gonzaga A, Hamann U, Hansen TV, Harris HR, Hauke J, Heitz F, Hogervorst FB, Hooning MJ, Hopper JL, Huff CD, Huntsman DG, Imyanitov EN, Izatt L, Jakubowska A, James PA, Janavicius R, John EM, Kar S, Karlan BY, Kennedy CJ, Kiemeney LA, Konstantopoulou I, Kupryjanczyk J, Laitman Y, Lavie O, Lawrenson K, Lester J, Lesueur F, Lopez-Pleguezuelos C, Mai PL, Manoukian S, May T, McNeish IA, Menon U, Milne RL, Modugno F, Mongiovi JM, Montagna M, Moysich KB, Neuhausen SL, Nielsen FC, Noguès C, Oláh E, Olopade OI, Osorio A, Papi L, Pathak H, Pearce CL, Pedersen IS, Peixoto A, Pejovic T, Peng PC, Peshkin BN, Peterlongo P, Powell CB, Prokofyeva D, Pujana MA, Radice P, Rashid MU, Rennert G, Richenberg G, Sandler DP, Sasamoto N, Setiawan VW, Sharma P, Sieh W, Singer CF, Snape K, Sokolenko AP, Soucy P, Southey MC, Stoppa-Lyonnet D, Sutphen R, Sutter C, Teixeira MR, Terry KL, Thomsen LCV, Tischkowitz M, Toland AE, Van Gorp T, Vega A, Velez Edwards DR, Webb PM, Weitzel JN, Wentzensen N, Whittemore AS, Winham SJ, Wu AH, Yadav S, Yu Y, Ziogas A, Berchuck A, Couch FJ, Goode EL, Goodman MT, Monteiro AN, Offit K, Ramus SJ, Risch HA, Schildkraut JM, Thomassen M, Simard J, Easton DF, Jones MR, Chenevix-Trench G, Gayther SA, Antoniou AC, Pharoah PD. Large-scale genome-wide association study of 398,238 women unveils seven novel loci associated with high-grade serous epithelial ovarian cancer risk. medRxiv 2024:2024.02.29.24303243. [PMID: 38496424 PMCID: PMC10942532 DOI: 10.1101/2024.02.29.24303243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Background Nineteen genomic regions have been associated with high-grade serous ovarian cancer (HGSOC). We used data from the Ovarian Cancer Association Consortium (OCAC), Consortium of Investigators of Modifiers of BRCA1/BRCA2 (CIMBA), UK Biobank (UKBB), and FinnGen to identify novel HGSOC susceptibility loci and develop polygenic scores (PGS). Methods We analyzed >22 million variants for 398,238 women. Associations were assessed separately by consortium and meta-analysed. OCAC and CIMBA data were used to develop PGS which were trained on FinnGen data and validated in UKBB and BioBank Japan. Results Eight novel variants were associated with HGSOC risk. An interesting discovery biologically was finding that TP53 3'-UTR SNP rs78378222 was associated with HGSOC (per T allele relative risk (RR)=1.44, 95%CI:1.28-1.62, P=1.76×10-9). The optimal PGS included 64,518 variants and was associated with an odds ratio of 1.46 (95%CI:1.37-1.54) per standard deviation in the UKBB validation (AUROC curve=0.61, 95%CI:0.59-0.62). Conclusions This study represents the largest GWAS for HGSOC to date. The results highlight that improvements in imputation reference panels and increased sample sizes can identify HGSOC associated variants that previously went undetected, resulting in improved PGS. The use of updated PGS in cancer risk prediction algorithms will then improve personalized risk prediction for HGSOC.
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Affiliation(s)
- Daniel R. Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan P. Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Amber M. Aeilts
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, OH, USA
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Nadine Andrieu
- Inserm U900, Paris, France
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
- PSL Research University, Paris, France
| | - Irene L. Andrulis
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Adalgeir Arason
- Department of Pathology, Landspitali - the National University Hospital of Iceland, Reykjavik, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Banu K. Arun
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Department of Medical Oncology, University Hospital of Vall d’Hebron, Barcelona, Spain
| | - Elisa V. Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Rosa B. Barkardottir
- Department of Pathology, Landspitali - the National University Hospital of Iceland, Reykjavik, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Lieke P.V. Berger
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, The Netherlands
| | | | - Pascaline Berthet
- Département de Biopathologie, Centre François Baclesse, Caen, France
| | - Katarzyna Białkowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Line Bjørge
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Amie M. Blanco
- Cancer Genetics and Prevention Program, University of California San Francisco, San Francisco, CA, USA
| | - Marinus J. Blok
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Kristie A. Bobolis
- City of Hope Clinical Cancer Genetics Community Research Network, Duarte, CA, USA
| | - Natalia V. Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - James D. Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Henriett Butz
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
- National Tumour Biology Laboratory, National Institute of Oncology, Budapest, Hungary
- Department of Oncology Biobank, National Institute of Oncology, Budapest, Hungary
| | - Saundra S. Buys
- Department of Medicine, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, UT, USA
| | | | - Ian Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Carmen Castillo
- Hereditary Cancer Program, IDIBELL (Bellvitge Biomedical Research Institute), Catalan Institute of Oncology, Barcelona, Spain
| | - Kathleen B.M. Claes
- Centre for Medical Genetics, Ghent University, Gent, Belgium
- Department of Biomolecular Medicine, University of Ghent, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | | | - EMBRACE Collaborators
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Sarah V. Colonna
- Department of Internal Medicine, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, UT, USA
| | - Linda S. Cook
- Department of Epidemiology, Colorado School of Public Health, University of Colorado, Aurora, CO, USA
| | - Mary B. Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Agnieszka Dansonka-Mieszkowska
- Department of Pathology and Laboratory Medicine, Institute of Oncology and Maria Sklodowska-Curie Cancer Center, Warsaw, Poland
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Anna deFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, New South Wales, Australia
| | - Allison DePersia
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL, USA
- The University of Chicago Pritzker School of Medicine, Chicago, IL, USA
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Susan M. Domchek
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Zakaria Einbeigi
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - D. Gareth Evans
- Genomic Medicine, Division of Evolution and Genomic Sciences, The University of Manchester, Manchester Academic Health Science Centre, Manchester Universities Foundation Trust, St. Mary’s Hospital, Manchester, UK
- Genomic Medicine, North West Genomics hub, Manchester Academic Health Science Centre, Manchester Universities Foundation Trust, St. Mary’s Hospital, Manchester, UK
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Renée T. Fortner
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research ‘Demokritos’, Athens, Greece
| | | | - Eitan Friedman
- Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
- The Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Ramat Gan, Israel
- Assuta Medical Center, Tel-Aviv, Israel
| | - Megan N. Frone
- National Cancer Institute, Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Patricia A. Ganz
- Schools of Medicine and Public Health, Division of Cancer Prevention & Control Research, Jonsson Comprehensive Cancer Centre, UCLA, Los Angeles, CA, USA
| | - Aleksandra Gentry-Maharaj
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, University College London, London, UK
| | - Gord Glendon
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre, Madrid, Spain
- Spanish Network on Rare Diseases, Madrid, Spain
| | - Mark H. Greene
- National Cancer Institute, Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Aliana Guerrieri-Gonzaga
- Division of Cancer Prevention and Genetics, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas v.O. Hansen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Holly R. Harris
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Jan Hauke
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, Essen, Germany
| | - Frans B.L. Hogervorst
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Maartje J. Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David G. Huntsman
- British Columbia’s Ovarian Cancer Research (OVCARE) Program, BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Evgeny N. Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
| | - kConFab Investigators
- Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Louise Izatt
- Clinical Genetics, Guy’s and St Thomas’ NHS Foundation Trust, London, UK
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Paul A. James
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Center and the Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ramunas Janavicius
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
- Hematology, Oncology and Transfusion Medicine Center, Oncogenetics Unit, Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Esther M. John
- Department of Epidemiology & Population Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine (Oncology), Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Siddhartha Kar
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Beth Y. Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, USA
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Catherine J. Kennedy
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research ‘Demokritos’, Athens, Greece
| | - Jolanta Kupryjanczyk
- Department of Pathology and Laboratory Medicine, Institute of Oncology and Maria Sklodowska-Curie Cancer Center, Warsaw, Poland
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Ofer Lavie
- Technion-Israel Institute of Technology, Haifa, Israel
- Carmel Medical Center, Haifa, Israel
| | - Kate Lawrenson
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Women’s Cancer Program at the Samuel Oschin Cancer Institute Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jenny Lester
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, USA
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Fabienne Lesueur
- Inserm U900, Paris, France
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
- PSL Research University, Paris, France
| | - Carlos Lopez-Pleguezuelos
- Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
- Escola de Doutoramento Internacional, Universidade de Santiago, Santiago de Compostela, Spain
| | - Phuong L. Mai
- Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Taymaa May
- Princess Margaret Cancer Center, Toronto, Canada
| | - Iain A. McNeish
- Division of Cancer and Ovarian Cancer Action Research Centre, Department Surgery & Cancer, Imperial College London, London, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Usha Menon
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, University College London, London, UK
| | - Roger L. Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Francesmary Modugno
- Womens Cancer Research Center, Magee-Womens Research Institute and Hillman Cancer Center, Pittsburgh, PA, USA
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jennifer M. Mongiovi
- Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | | | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Finn C. Nielsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Catherine Noguès
- Département d’Anticipation et de Suivi des Cancers, Oncogénétique Clinique, Institut Paoli-Calmettes, Marseille, France
- Aix Marseille Université, INSERM, IRD, SESSTIM, Marseille, France
| | - Edit Oláh
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | | | - Ana Osorio
- Spanish Network on Rare Diseases, Madrid, Spain
- Familial Cancer Clinical Unit, Human Cancer Genetics Programme, Madrid, Spain
| | - Laura Papi
- Department of Experimental and Clinical Biomedical Sciences ‘Mario Serio’, Medical Genetics Unit, University of Florence, Florence, Italy
| | - Harsh Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Celeste L. Pearce
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Inge S. Pedersen
- Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Ana Peixoto
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Tanja Pejovic
- Department of Obstetrics & Gynecology, Providence Medical Center, Medford, OR, USA
- Providence Cancer Center, Medford, OR, USA
| | - Pei-Chen Peng
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Beth N. Peshkin
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
- Jess and Mildred Fisher Center for Hereditary Cancer and Clinical Genomics Research, Georgetown University, Washington, DC, USA
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM - the FIRC Institute of Molecular Oncology, Milan, Italy
| | - C. Bethan Powell
- Hereditary Cancer Program, Kaiser Permanente Northern California, San Francisco, CA, USA
| | | | - Miquel Angel Pujana
- ProCURE, IDIBELL (Bellvitge Biomedical Research Institute), Catalan Institute of Oncology, Barcelona, Spain
- ProCURE, IDIBGI (Girona Biomedical Research Institute), Catalan Institute of Oncology, Girona, Spain
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Muhammad U. Rashid
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore, Pakistan
| | - Gad Rennert
- Technion-Israel Institute of Technology, Haifa, Israel
- The Association for Promotion of Research in Precision Medicine, Haifa, Israel
| | - George Richenberg
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Dale P. Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Rockville, MD, USA
| | - Naoko Sasamoto
- Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA
| | - Veronica W. Setiawan
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Priyanka Sharma
- Department of Internal Medicine, Division of Medical Oncology, University of Kansas Medical Center, Westwood, KS, USA
| | - Weiva Sieh
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christian F. Singer
- Dept of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Katie Snape
- Medical Genetics Unit, St George’s, University of London, London, UK
| | - Anna P. Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec – Université Laval Research Center, Québec City, QC, Canada
| | - Melissa C. Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, Melbourne Medical School, University of Melbourne, Parkville, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, East Melbourne, Victoria, Australia
| | - Dominique Stoppa-Lyonnet
- Genetics Department, Institut Curie, Paris, France
- Unité INSERM U830, Paris, France
- Université Paris Cité, Paris, France
| | - Rebecca Sutphen
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Christian Sutter
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Manuel R. Teixeira
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Kathryn L. Terry
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Liv Cecilie V. Thomsen
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
- Medical Birth Registry of Norway, Norwegian Institute of Public Health, Norway
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montréal, QC, Canada
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Amanda E. Toland
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, OH, USA
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Toon Van Gorp
- Division of Gynecologic Oncology, University Hospital Leuven, Leuven, Belgium
- Leuven Cancer Institute, University of Leuven, Leuven, Belgium
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Digna R. Velez Edwards
- Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Penelope M. Webb
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Alice S. Whittemore
- Department of Epidemiology & Population Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Stacey J. Winham
- Department of Quantitative Health Sciences, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Anna H. Wu
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Argyrios Ziogas
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Andrew Berchuck
- Department of Gynecologic Oncology, Duke University Hospital, Durham, NC, USA
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ellen L. Goode
- Department of Quantitative Health Sciences, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Marc T. Goodman
- Samuel Oschin Comprehensive Cancer Institute, Cancer Prevention and Genetics Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alvaro N. Monteiro
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- AnaNeo Therapeutics, New York, NY, USA
| | - Susan J. Ramus
- School of Clinical Medicine, Faculty of Medicine and Health, University of NSW Sydney, Sydney, New South Wales, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, University of NSW Sydney, Sydney, New South Wales, Australia
| | - Harvey A. Risch
- Chronic Disease Epidemiology, Yale School of Medicine, New Haven, CT, USA
| | | | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec – Université Laval Research Center, Québec City, QC, Canada
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Québec City, QC, Canada
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, 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
| | - Michelle R. Jones
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Simon A. Gayther
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Paul D.P. Pharoah
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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Jain S, Bakolitsa C, Brenner SE, Radivojac P, Moult J, Repo S, Hoskins RA, Andreoletti G, Barsky D, Chellapan A, Chu H, Dabbiru N, Kollipara NK, Ly M, Neumann AJ, Pal LR, Odell E, Pandey G, Peters-Petrulewicz RC, Srinivasan R, Yee SF, Yeleswarapu SJ, Zuhl M, Adebali O, Patra A, Beer MA, Hosur R, Peng J, Bernard BM, Berry M, Dong S, Boyle AP, Adhikari A, Chen J, Hu Z, Wang R, Wang Y, Miller M, Wang Y, Bromberg Y, Turina P, Capriotti E, Han JJ, Ozturk K, Carter H, Babbi G, Bovo S, Di Lena P, Martelli PL, Savojardo C, Casadio R, Cline MS, De Baets G, Bonache S, Díez O, Gutiérrez-Enríquez S, Fernández A, Montalban G, Ootes L, Özkan S, Padilla N, Riera C, De la Cruz X, Diekhans M, Huwe PJ, Wei Q, Xu Q, Dunbrack RL, Gotea V, Elnitski L, Margolin G, Fariselli P, Kulakovskiy IV, Makeev VJ, Penzar DD, Vorontsov IE, Favorov AV, Forman JR, Hasenahuer M, Fornasari MS, Parisi G, Avsec Z, Çelik MH, Nguyen TYD, Gagneur J, Shi FY, Edwards MD, Guo Y, Tian K, Zeng H, Gifford DK, Göke J, Zaucha J, Gough J, Ritchie GRS, Frankish A, Mudge JM, Harrow J, Young EL, Yu Y, Huff CD, Murakami K, Nagai Y, Imanishi T, Mungall CJ, Jacobsen JOB, Kim D, Jeong CS, Jones DT, Li MJ, Guthrie VB, Bhattacharya R, Chen YC, Douville C, Fan J, Kim D, Masica D, Niknafs N, Sengupta S, Tokheim C, Turner TN, Yeo HTG, Karchin R, Shin S, Welch R, Keles S, Li Y, Kellis M, Corbi-Verge C, Strokach AV, Kim PM, Klein TE, Mohan R, Sinnott-Armstrong NA, Wainberg M, Kundaje A, Gonzaludo N, Mak ACY, Chhibber A, Lam HYK, Dahary D, Fishilevich S, Lancet D, Lee I, Bachman B, Katsonis P, Lua RC, Wilson SJ, Lichtarge O, Bhat RR, Sundaram L, Viswanath V, Bellazzi R, Nicora G, Rizzo E, Limongelli I, Mezlini AM, Chang R, Kim S, Lai C, O’Connor R, Topper S, van den Akker J, Zhou AY, Zimmer AD, Mishne G, Bergquist TR, Breese MR, Guerrero RF, Jiang Y, Kiga N, Li B, Mort M, Pagel KA, Pejaver V, Stamboulian MH, Thusberg J, Mooney SD, Teerakulkittipong N, Cao C, Kundu K, Yin Y, Yu CH, Kleyman M, Lin CF, Stackpole M, Mount SM, Eraslan G, Mueller NS, Naito T, Rao AR, Azaria JR, Brodie A, Ofran Y, Garg A, Pal D, Hawkins-Hooker A, Kenlay H, Reid J, Mucaki EJ, Rogan PK, Schwarz JM, Searls DB, Lee GR, Seok C, Krämer A, Shah S, Huang CV, Kirsch JF, Shatsky M, Cao Y, Chen H, Karimi M, Moronfoye O, Sun Y, Shen Y, Shigeta R, Ford CT, Nodzak C, Uppal A, Shi X, Joseph T, Kotte S, Rana S, Rao A, Saipradeep VG, Sivadasan N, Sunderam U, Stanke M, Su A, Adzhubey I, Jordan DM, Sunyaev S, Rousseau F, Schymkowitz J, Van Durme J, Tavtigian SV, Carraro M, Giollo M, Tosatto SCE, Adato O, Carmel L, Cohen NE, Fenesh T, Holtzer T, Juven-Gershon T, Unger R, Niroula A, Olatubosun A, Väliaho J, Yang Y, Vihinen M, Wahl ME, Chang B, Chong KC, Hu I, Sun R, Wu WKK, Xia X, Zee BC, Wang MH, Wang M, Wu C, Lu Y, Chen K, Yang Y, Yates CM, Kreimer A, Yan Z, Yosef N, Zhao H, Wei Z, Yao Z, Zhou F, Folkman L, Zhou Y, Daneshjou R, Altman RB, Inoue F, Ahituv N, Arkin AP, Lovisa F, Bonvini P, Bowdin S, Gianni S, Mantuano E, Minicozzi V, Novak L, Pasquo A, Pastore A, Petrosino M, Puglisi R, Toto A, Veneziano L, Chiaraluce R, Ball MP, Bobe JR, Church GM, Consalvi V, Cooper DN, Buckley BA, Sheridan MB, Cutting GR, Scaini MC, Cygan KJ, Fredericks AM, Glidden DT, Neil C, Rhine CL, Fairbrother WG, Alontaga AY, Fenton AW, Matreyek KA, Starita LM, Fowler DM, Löscher BS, Franke A, Adamson SI, Graveley BR, Gray JW, Malloy MJ, Kane JP, Kousi M, Katsanis N, Schubach M, Kircher M, Mak ACY, Tang PLF, Kwok PY, Lathrop RH, Clark WT, Yu GK, LeBowitz JH, Benedicenti F, Bettella E, Bigoni S, Cesca F, Mammi I, Marino-Buslje C, Milani D, Peron A, Polli R, Sartori S, Stanzial F, Toldo I, Turolla L, Aspromonte MC, Bellini M, Leonardi E, Liu X, Marshall C, McCombie WR, Elefanti L, Menin C, Meyn MS, Murgia A, Nadeau KCY, Neuhausen SL, Nussbaum RL, Pirooznia M, Potash JB, Dimster-Denk DF, Rine JD, Sanford JR, Snyder M, Cote AG, Sun S, Verby MW, Weile J, Roth FP, Tewhey R, Sabeti PC, Campagna J, Refaat MM, Wojciak J, Grubb S, Schmitt N, Shendure J, Spurdle AB, Stavropoulos DJ, Walton NA, Zandi PP, Ziv E, Burke W, Chen F, Carr LR, Martinez S, Paik J, Harris-Wai J, Yarborough M, Fullerton SM, Koenig BA, McInnes G, Shigaki D, Chandonia JM, Furutsuki M, Kasak L, Yu C, Chen R, Friedberg I, Getz GA, Cong Q, Kinch LN, Zhang J, Grishin NV, Voskanian A, Kann MG, Tran E, Ioannidis NM, Hunter JM, Udani R, Cai B, Morgan AA, Sokolov A, Stuart JM, Minervini G, Monzon AM, Batzoglou S, Butte AJ, Greenblatt MS, Hart RK, Hernandez R, Hubbard TJP, Kahn S, O’Donnell-Luria A, Ng PC, Shon J, Veltman J, Zook JM. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biol 2024; 25:53. [PMID: 38389099 PMCID: PMC10882881 DOI: 10.1186/s13059-023-03113-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 11/17/2023] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors. RESULTS Performance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic. CONCLUSIONS Results show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.
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Lawrence ES, Gu W, Bohlender RJ, Anza-Ramirez C, Cole AM, Yu JJ, Hu H, Heinrich EC, O’Brien KA, Vasquez CA, Cowan QT, Bruck PT, Mercader K, Alotaibi M, Long T, Hall JE, Moya EA, Bauk MA, Reeves JJ, Kong MC, Salem RM, Vizcardo-Galindo G, Macarlupu JL, Figueroa-Mujíca R, Bermudez D, Corante N, Gaio E, Fox KP, Salomaa V, Havulinna AS, Murray AJ, Malhotra A, Powel FL, Jain M, Komor AC, Cavalleri GL, Huff CD, Villafuerte FC, Simonson TS. Functional EPAS1/ HIF2A missense variant is associated with hematocrit in Andean highlanders. Sci Adv 2024; 10:eadj5661. [PMID: 38335297 PMCID: PMC10857371 DOI: 10.1126/sciadv.adj5661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
Hypoxia-inducible factor pathway genes are linked to adaptation in both human and nonhuman highland species. EPAS1, a notable target of hypoxia adaptation, is associated with relatively lower hemoglobin concentration in Tibetans. We provide evidence for an association between an adaptive EPAS1 variant (rs570553380) and the same phenotype of relatively low hematocrit in Andean highlanders. This Andean-specific missense variant is present at a modest frequency in Andeans and absent in other human populations and vertebrate species except the coelacanth. CRISPR-base-edited human cells with this variant exhibit shifts in hypoxia-regulated gene expression, while metabolomic analyses reveal both genotype and phenotype associations and validation in a lowland population. Although this genocopy of relatively lower hematocrit in Andean highlanders parallels well-replicated findings in Tibetans, it likely involves distinct pathway responses based on a protein-coding versus noncoding variants, respectively. These findings illuminate how unique variants at EPAS1 contribute to the same phenotype in Tibetans and a subset of Andean highlanders despite distinct evolutionary trajectories.
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Affiliation(s)
- Elijah S. Lawrence
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Wanjun Gu
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ryan J. Bohlender
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cecilia Anza-Ramirez
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Amy M. Cole
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - James J. Yu
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hao Hu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erica C. Heinrich
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Katie A. O’Brien
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Carlos A. Vasquez
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Quinn T. Cowan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Patrick T. Bruck
- Department of Anthropology and Global Health, University of California, San Diego, La Jolla, CA, USA
| | - Kysha Mercader
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Mona Alotaibi
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Tao Long
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Sapient Bioanalytics, LLC, San Diego, CA, USA
| | - James E. Hall
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Esteban A. Moya
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Marco A. Bauk
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer J. Reeves
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mitchell C. Kong
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Rany M. Salem
- Herbert Wertheim School of Public Health and Longevity Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Gustavo Vizcardo-Galindo
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jose-Luis Macarlupu
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Rómulo Figueroa-Mujíca
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Daniela Bermudez
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Noemi Corante
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Eduardo Gaio
- Laboratório de Fisiologia Respiratória, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
| | - Keolu P. Fox
- Department of Anthropology and Global Health, University of California, San Diego, La Jolla, CA, USA
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Aki S. Havulinna
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM-HiLIFE), Helsinki, Finland
| | - Andrew J. Murray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Atul Malhotra
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Frank L. Powel
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mohit Jain
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Sapient Bioanalytics, LLC, San Diego, CA, USA
| | - Alexis C. Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Gianpiero L. Cavalleri
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Francisco C. Villafuerte
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Tatum S. Simonson
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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Wang A, Shen J, Rodriguez AA, Saunders EJ, Chen F, Janivara R, Darst BF, Sheng X, Xu Y, Chou AJ, Benlloch S, Dadaev T, Brook MN, Plym A, Sahimi A, Hoffman TJ, Takahashi A, Matsuda K, Momozawa Y, Fujita M, Laisk T, Figuerêdo J, Muir K, Ito S, Liu X, Uchio Y, Kubo M, Kamatani Y, Lophatananon A, Wan P, Andrews C, Lori A, Choudhury PP, Schleutker J, Tammela TL, Sipeky C, Auvinen A, Giles GG, Southey MC, MacInnis RJ, Cybulski C, Wokolorczyk D, Lubinski J, Rentsch CT, Cho K, Mcmahon BH, Neal DE, Donovan JL, Hamdy FC, Martin RM, Nordestgaard BG, Nielsen SF, Weischer M, Bojesen SE, Røder A, Stroomberg HV, Batra J, Chambers S, Horvath L, Clements JA, Tilly W, Risbridger GP, Gronberg H, Aly M, Szulkin R, Eklund M, Nordstrom T, Pashayan N, Dunning AM, Ghoussaini M, Travis RC, Key TJ, Riboli E, Park JY, Sellers TA, Lin HY, Albanes D, Weinstein S, Cook MB, Mucci LA, Giovannucci E, Lindstrom S, Kraft P, Hunter DJ, Penney KL, Turman C, Tangen CM, Goodman PJ, Thompson IM, Hamilton RJ, Fleshner NE, Finelli A, Parent MÉ, Stanford JL, Ostrander EA, Koutros S, Beane Freeman LE, Stampfer M, Wolk A, Håkansson N, Andriole GL, Hoover RN, Machiela MJ, Sørensen KD, Borre M, Blot WJ, Zheng W, Yeboah ED, Mensah JE, Lu YJ, Zhang HW, Feng N, Mao X, Wu Y, Zhao SC, Sun Z, Thibodeau SN, McDonnell SK, Schaid DJ, West CM, Barnett G, Maier C, Schnoeller T, Luedeke M, Kibel AS, Drake BF, Cussenot O, Cancel-Tassin G, Menegaux F, Truong T, Koudou YA, John EM, Grindedal EM, Maehle L, Khaw KT, Ingles SA, Stern MC, Vega A, Gómez-Caamaño A, Fachal L, Rosenstein BS, Kerns SL, Ostrer H, Teixeira MR, Paulo P, Brandão A, Watya S, Lubwama A, Bensen JT, Butler EN, Mohler JL, Taylor JA, Kogevinas M, Dierssen-Sotos T, Castaño-Vinyals G, Cannon-Albright L, Teerlink CC, Huff CD, Pilie P, Yu Y, Bohlender RJ, Gu J, Strom SS, Multigner L, Blanchet P, Brureau L, Kaneva R, Slavov C, Mitev V, Leach RJ, Brenner H, Chen X, Holleczek B, Schöttker B, Klein EA, Hsing AW, Kittles RA, Murphy AB, Logothetis CJ, Kim J, Neuhausen SL, Steele L, Ding YC, Isaacs WB, Nemesure B, Hennis AJ, Carpten J, Pandha H, Michael A, Ruyck KD, Meerleer GD, Ost P, Xu J, Razack A, Lim J, Teo SH, Newcomb LF, Lin DW, Fowke JH, Neslund-Dudas CM, Rybicki BA, Gamulin M, Lessel D, Kulis T, Usmani N, Abraham A, Singhal S, Parliament M, Claessens F, Joniau S, den Broeck TV, Gago-Dominguez M, Castelao JE, Martinez ME, Larkin S, Townsend PA, Aukim-Hastie C, Bush WS, Aldrich MC, Crawford DC, Srivastava S, Cullen J, Petrovics G, Casey G, Wang Y, Tettey Y, Lachance J, Tang W, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Yamoah K, Govindasami K, Chokkalingam AP, Keaton JM, Hellwege JN, Clark PE, Jalloh M, Gueye SM, Niang L, Ogunbiyi O, Shittu O, Amodu O, Adebiyi AO, Aisuodionoe-Shadrach OI, Ajibola HO, Jamda MA, Oluwole OP, Nwegbu M, Adusei B, Mante S, Darkwa-Abrahams A, Diop H, Gundell SM, Roobol MJ, Jenster G, van Schaik RH, Hu JJ, Sanderson M, Kachuri L, Varma R, McKean-Cowdin R, Torres M, Preuss MH, Loos RJ, Zawistowski M, Zöllner S, Lu Z, Van Den Eeden SK, Easton DF, Ambs S, Edwards TL, Mägi R, Rebbeck TR, Fritsche L, Chanock SJ, Berndt SI, Wiklund F, Nakagawa H, Witte JS, Gaziano JM, Justice AC, Mancuso N, Terao C, Eeles RA, Kote-Jarai Z, Madduri RK, Conti DV, Haiman CA. Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants. Nat Genet 2023; 55:2065-2074. [PMID: 37945903 PMCID: PMC10841479 DOI: 10.1038/s41588-023-01534-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 09/15/2023] [Indexed: 11/12/2023]
Abstract
The transferability and clinical value of genetic risk scores (GRSs) across populations remain limited due to an imbalance in genetic studies across ancestrally diverse populations. Here we conducted a multi-ancestry genome-wide association study of 156,319 prostate cancer cases and 788,443 controls of European, African, Asian and Hispanic men, reflecting a 57% increase in the number of non-European cases over previous prostate cancer genome-wide association studies. We identified 187 novel risk variants for prostate cancer, increasing the total number of risk variants to 451. An externally replicated multi-ancestry GRS was associated with risk that ranged from 1.8 (per standard deviation) in African ancestry men to 2.2 in European ancestry men. The GRS was associated with a greater risk of aggressive versus non-aggressive disease in men of African ancestry (P = 0.03). Our study presents novel prostate cancer susceptibility loci and a GRS with effective risk stratification across ancestry groups.
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Affiliation(s)
- Anqi Wang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jiayi Shen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Fei Chen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rohini Janivara
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Burcu F. Darst
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Xin Sheng
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yili Xu
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alisha J. Chou
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sara Benlloch
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology,University of Cambridge, Cambridge, UK
| | | | | | - Anna Plym
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Urology Division, Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ali Sahimi
- Department of Population and Public Health Sciences, Keck School of Medicine,University of Southern California, Los Angeles, CA, USA
| | - Thomas J. Hoffman
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Atushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Genomic Medicine, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Koichi Matsuda
- Department of Computational Biology and Medical Sciences, Laboratory of Clinical Genome Sequencing,Graduate school of Frontier Sciences,The University of Tokyo, Tokyo, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jéssica Figuerêdo
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Shuji Ito
- Department of Orthopaedics, Shimane University, Izumo, Shimane, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - The Biobank Japan Project
- Corresponding Author: Christopher A. Haiman, Harlyne J. Norris Cancer Research Tower, USC Norris Comprehensive Cancer Center, 1450 Biggy Street, Rm 1504, Los Angeles, CA 90033 or
| | - Yuji Uchio
- Department of Orthopaedics, Shimane University, Izumo, Shimane, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, Manchester, UK
| | - Peggy Wan
- Department of Population and Public Health Sciences, Keck School of Medicine,University of Southern California, Los Angeles, CA, USA
| | - Caroline Andrews
- Harvard TH Chan School of Public Health and Division of Population Sciences,Dana Farber Cancer Institute, Boston, MA, USA
| | - Adriana Lori
- Department of Population Science, American Cancer Society, Kennesaw, GA, USA
| | | | - Johanna Schleutker
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, Turku, Finland
| | | | - Csilla Sipeky
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Anssi Auvinen
- Unit of Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Graham G. Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health,The University of Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Melissa C. Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Robert J. MacInnis
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health,The University of Melbourne, Victoria, Australia
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Dominika Wokolorczyk
- 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
| | - Christopher T. Rentsch
- Yale School of Medicine, New Haven, CT, USA
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Kelly Cho
- Division of Aging, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | | | - David E. Neal
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
- University of Cambridge, Department of Oncology, Addenbrooke’s Hospital, Cambridge, UK
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Jenny L. Donovan
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Freddie C. Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Faculty of Medical Science, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Richard M. Martin
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre at University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Borge G. Nordestgaard
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
| | - Sune F. Nielsen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
| | - Maren Weischer
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
| | - Stig E. Bojesen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
| | - Andreas Røder
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Hein V. Stroomberg
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | | | - Lisa Horvath
- Chris O’Brien Lifehouse (COBLH), Camperdown, Sydney, NSW, Australia, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
| | - Judith A. Clements
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | - Wayne Tilly
- Dame Roma Mitchell Cancer Research Laboratories, University of Adelaide, Adelaide, Australia
| | - Gail P. Risbridger
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Prostate Cancer Translational Research Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Markus Aly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, and Department of Urology, Karolinska University Hospital, Solna, Stockholm, Sweden
- Department of Urology, Karolinska University Hospital, Stockholm, Sweden
| | - Robert Szulkin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- SDS Life Sciences, Stockholm, Sweden
| | - Martin Eklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Tobias Nordstrom
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Sciences at Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Nora Pashayan
- University College London, Department of Applied Health Research, London, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Cambridge, UK
- Department of Applied Health Research, University College London, London, UK
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Cambridge, UK
| | - Maya Ghoussaini
- Open Targets, Wellcome Sanger Institute, Hinxton, Saffron Walden, Hinxton, UK
| | - Ruth C. Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Tim J. Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Jong Y. Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Thomas A. Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Hui-Yi Lin
- School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael B. Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH,, Bethesda, MD, USA
| | - Lorelei A. Mucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sara Lindstrom
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - David J. Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Kathryn L. Penney
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA, USA
| | - Constance Turman
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Catherine M. Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Phyllis J. Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ian M. Thompson
- CHRISTUS Santa Rosa Hospital – Medical Center, San Antonio, TX, USA
| | - Robert J. Hamilton
- Dept. of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, Canada
- Dept. of Surgery (Urology), University of Toronto, Toronto, Canada
| | - Neil E. Fleshner
- Dept. of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, Canada
| | - Antonio Finelli
- Division of Urology, Princess Margaret Cancer Centre, Toronto, Canada
| | - Marie-Élise Parent
- Epidemiology and Biostatistics Unit, Centre Armand-Frappier Santé Biotechnologie, Laval, QC, Canada
| | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elaine A. Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Laura E. Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Meir Stampfer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA, USA
| | - Alicja Wolk
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Niclas Håkansson
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Gerald L. Andriole
- Brady Urological Institute in National Capital Region, Johns Hopkins University, Baltimore, MD, USA
| | - Robert N. Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Mitchell J. Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Karina Dalsgaard Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Michael Borre
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - William J. Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- International Epidemiology Institute, Rockville, MD, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - James E. Mensah
- University of Ghana Medical School, Accra, Ghana
- Korle Bu Teaching Hospital, Accra, Ghana
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | | | - Ninghan Feng
- Wuxi Second Hospital, Nanjing Medical University, Wuxi, Jiangzhu Province, China
| | - Xueying Mao
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Yudong Wu
- Department of Urology, First Affiliated Hospital, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Shan-Chao Zhao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zan Sun
- The People’s Hospital of Liaoning Proviouce, The People’s Hospital of China Medical University, Shenyang, China, Shenyang, China
| | - Stephen N. Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Daniel J. Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Catharine M.L. West
- Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Radiotherapy Related Research, The Christie Hospital NHS Foundation Trust, Manchester, UK
| | - Gill Barnett
- University of Cambridge Department of Oncology, Oncology Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | - Adam S. Kibel
- Division of Urologic Surgery, Brigham and Womens Hospital, Boston, MA, USA
| | | | - Olivier Cussenot
- GRC 5 Predictive Onco-Urology, Sorbonne Université, Paris, France
- CeRePP, Paris, France
| | | | - Florence Menegaux
- Exposome and Heredity, CESP (UMR 1018), Paris-Saclay Medical School, Paris-Saclay University, Inserm, Gustave Roussy, Villejuif, France
| | - Thérèse Truong
- Exposome and Heredity, CESP (UMR 1018), Paris-Saclay Medical School, Paris-Saclay University, Inserm, Gustave Roussy, Villejuif, France
| | - Yves Akoli Koudou
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif Cédex, France
| | - Esther M. John
- Department of Medicine, Stanford Cancer Institute,Stanford University School of Medicine, Stanford, CA, USA
| | | | - Lovise Maehle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, UK
| | - Sue A. Ingles
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Mariana C Stern
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Ana Vega
- Fundación Pública Galega Medicina Xenómica, Santiago De Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago De Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Spain
| | - Antonio Gómez-Caamaño
- Department of Radiation Oncology, Complexo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - Laura Fachal
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago De Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Spain
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
- Fundación Pública Galega Medicina Xenómica, Santiago de Compostela, Spain
| | - Barry S. Rosenstein
- Department of Radiation Oncology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah L. Kerns
- Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Harry Ostrer
- Professor of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Manuel R. Teixeira
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Paula Paulo
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Andreia Brandão
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | | | | | - Jeannette T. Bensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ebonee N. Butler
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - James L. Mohler
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Urology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jack A. Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Manolis Kogevinas
- ISGlobal, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Trinidad Dierssen-Sotos
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- University of Cantabria-IDIVAL, Santander, Spain
| | - Gemma Castaño-Vinyals
- ISGlobal, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Lisa Cannon-Albright
- Division of Epidemiology, Department of Internal Medicine, 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
| | - Craig C. Teerlink
- Division of Epidemiology, Department of Internal Medicine, 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
| | - Chad D. Huff
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Patrick Pilie
- Department of Genitourinary Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Yao Yu
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Ryan J. Bohlender
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Jian Gu
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Sara S. Strom
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Luc Multigner
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Rennes, France
| | - Pascal Blanchet
- CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, France
| | - Laurent Brureau
- CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, France
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia, Bulgaria
| | - Chavdar Slavov
- Department of Urology and Alexandrovska University Hospital, Medical University of Sofia, Sofia, Bulgaria
| | - Vanio Mitev
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia, Bulgaria
| | - Robin J. Leach
- Department of Cell Systems and Anatomy and Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Hermann Brenner
- 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
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Xuechen Chen
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eric A. Klein
- Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
- Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ann W. Hsing
- Department of Medicine and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Adam B. Murphy
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - Christopher J. Logothetis
- The University of Texas M. D. Anderson Cancer Center, Department of Genitourinary Medical Oncology, Houston, TX, USA
| | - Jeri Kim
- The University of Texas M. D. Anderson Cancer Center, Department of Genitourinary Medical Oncology, Houston, TX, USA
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - William B. Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Anselm J.M. Hennis
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
- Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies, Bridgetown, Barbados
| | - John Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Kim De Ruyck
- Ghent University, Faculty of Medicine and Health Sciences, Basic Medical Sciences, Ghent, Belgium
| | - Gert De Meerleer
- Ghent University Hospital, Department of Radiotherapy, Ghent, Belgium
| | - Piet Ost
- Ghent University Hospital, Department of Radiotherapy, Ghent, Belgium
| | - Jianfeng Xu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Azad Razack
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jasmine Lim
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Soo-Hwang Teo
- Cancer Research Malaysia (CRM), Outpatient Centre, Subang Jaya Medical Centre, Subang Jaya, Selangor, Malaysia
| | - Lisa F. Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Daniel W. Lin
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Jay H. Fowke
- Department of Preventive Medicine, Division of Epidemiology,The University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Benjamin A. Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, Detroit, MI, USA
| | - Marija Gamulin
- Division of Medical Oncology, Urogenital Unit, Department of Oncology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tomislav Kulis
- Department of Urology, University Hospital Center Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Nawaid Usmani
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Aswin Abraham
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Sandeep Singhal
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Matthew Parliament
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Steven Joniau
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Thomas Van den Broeck
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, Servicio Galego de Saúde, SERGAS, Santiago de Compostela, Spain
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Jose Esteban Castelao
- Genetic Oncology Unit, CHUVI Hospital, Complexo Hospitalario Universitario de Vigo, Instituto de Investigación Biomédica Galicia Sur (IISGS), Vigo (Pontevedra), Spain
| | - Maria Elena Martinez
- University of California San Diego, Moores Cancer Center, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Samantha Larkin
- Scientific Education Support, Thames Ditton, Surrey, Formerly Cancer Sciences, University of Southampton, Southampton, UK
| | - Paul A. Townsend
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Surrey, UK
| | | | - William S. Bush
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Melinda C. Aldrich
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dana C. Crawford
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Shiv Srivastava
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Jennifer Cullen
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
- Department of Surgery, Center for Prostate Disease Research,Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Gyorgy Petrovics
- Department of Surgery, Center for Prostate Disease Research,Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Graham Casey
- Department of Public Health Science, Center for Public Health Genomics,University of Virginia, Charlottesville, VA, USA
| | - Ying Wang
- Department of Population Science, American Cancer Society, Kennesaw, GA, USA
| | - Yao Tettey
- Korle Bu Teaching Hospital, Accra, Ghana
- Department of Pathology, University of Ghana, Accra, Ghana
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Andrew A. Adjei
- Department of Pathology, University of Ghana Medical School, Accra, Ghana
| | - Evelyn Tay
- Korle Bu Teaching Hospital, Accra, Ghana
| | | | | | - Kosj Yamoah
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | | | | | - Jacob M. Keaton
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jacklyn N. Hellwege
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Nashville, TN, USA
| | - Peter E. Clark
- Atrium Health/Levine Cancer Institute, Charlotte, NC, USA
| | | | | | | | - Olufemi Ogunbiyi
- Department of Pathology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olayiwola Shittu
- Department of Surgery, College of Medicine, University of Ibadan and Univerity College Hospital, Ibadan, Nigeria
| | - Olukemi Amodu
- Institute of Child Health, College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Akindele O. Adebiyi
- Clinical Epidemiology Unit, Department of Community Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oseremen I. Aisuodionoe-Shadrach
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Hafees O. Ajibola
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Mustapha A. Jamda
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Olabode P. Oluwole
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Maxwell Nwegbu
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | | | | | | | - Halimatou Diop
- Laboratoires Bacteriologie et Virologie, Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Susan M. Gundell
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Monique J. Roobol
- Department of Urology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Ron H.N. van Schaik
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jennifer J. Hu
- The University of Miami School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford Cancer Institute, Stanford, CA, USA
| | - Rohit Varma
- Southern California Eye Institute, CHA Hollywood Presbyterian Medical Center, Los Angeles, CA, USA
| | - Roberta McKean-Cowdin
- Department of Population and Public Health Sciences, Keck School of Medicine,University of Southern California, Los Angeles, CA, USA
| | - Mina Torres
- Southern California Eye Institute, CHA Hollywood Presbyterian Medical Center, Los Angeles, CA, USA
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew Zawistowski
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Sebastian 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
| | - Zeyun Lu
- Department of Population and Public Health Sciences, Keck School of Medicine,University of Southern California, Los Angeles, CA, USA
| | | | - Douglas F. Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology,, Cambridge, UK
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Todd L. Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Timothy R. Rebbeck
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA, USA
| | - Lars Fritsche
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - John S. Witte
- Department of Epidemiology and Population Health, Stanford Cancer Institute, Stanford, CA, USA
- Departments of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - J. Michael Gaziano
- Division of Aging, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | | | - Nick Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, School of Pharmaceutical Sciences, Shizuoka, Japan
| | - Rosalind A. Eeles
- The Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | | | | | - David V. Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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6
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Lancaster MC, Chen HH, Shoemaker MB, Fleming MR, Baker JT, Evans G, Polikowsky HG, Samuels DC, Huff CD, Roden DM, Below JE. Detection of distant relatedness in biobanks for identification of undiagnosed carriers of a Mendelian disease variant: application to Long QT Syndrome. Res Sq 2023:rs.3.rs-3314860. [PMID: 37790303 PMCID: PMC10543295 DOI: 10.21203/rs.3.rs-3314860/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Rare genetic diseases are typically studied in referral populations, resulting in underdiagnosis and biased assessment of penetrance and phenotype. To address this, we developed a generalizable method of genotype inference based on distant relatedness and deployed this to identify undiagnosed Type 5 Long QT Syndrome (LQT5) rare variant carriers in a non-referral population. We identified 9 LQT5 families referred to a single specialty clinic, each carrying p.Asp76Asn, the most common LQT5 variant. We uncovered recent common ancestry and a single shared haplotype among probands. Application to a non-referral population of 69,819 BioVU biobank subjects identified 22 additional subjects sharing this haplotype, subsequently confirmed to carry p.Asp76Asn. Referral and non-referral carriers had prolonged QTc compared to controls, and, among carriers, QTc polygenic score additively associated with QTc prolongation. Thus, our novel analysis of shared chromosomal segments identified undiagnosed cases of genetic disease and refined the understanding of LQT5 penetrance and phenotype.
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Affiliation(s)
- Megan C Lancaster
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - Hung-Hsin Chen
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - M Benjamin Shoemaker
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - Matthew R Fleming
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - James T Baker
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - Grahame Evans
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - Hannah G Polikowsky
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - David C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, 37232, U.S.A
| | - Chad D Huff
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, U.S.A
| | - Dan M Roden
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - Jennifer E Below
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
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7
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Chen F, Madduri RK, Rodriguez AA, Darst BF, Chou A, Sheng X, Wang A, Shen J, Saunders EJ, Rhie SK, Bensen JT, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Stanford JL, Zheng W, Sanderson M, John EM, Park JY, Xu J, Wang Y, Berndt SI, Huff CD, Yeboah ED, Tettey Y, Lachance J, Tang W, Rentsch CT, Cho K, Mcmahon BH, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Sellers TA, Yamoah K, Murphy AB, Crawford DC, Patel AV, Bush WS, Aldrich MC, Cussenot O, Petrovics G, Cullen J, Neslund-Dudas CM, Stern MC, Kote-Jarai Z, Govindasami K, Cook MB, Chokkalingam AP, Hsing AW, Goodman PJ, Hoffmann TJ, Drake BF, Hu JJ, Keaton JM, Hellwege JN, Clark PE, Jalloh M, Gueye SM, Niang L, Ogunbiyi O, Idowu MO, Popoola O, Adebiyi AO, Aisuodionoe-Shadrach OI, Ajibola HO, Jamda MA, Oluwole OP, Nwegbu M, Adusei B, Mante S, Darkwa-Abrahams A, Mensah JE, Diop H, Van Den Eeden SK, Blanchet P, Fowke JH, Casey G, Hennis AJ, Lubwama A, Thompson IM, Leach R, Easton DF, Preuss MH, Loos RJ, Gundell SM, Wan P, Mohler JL, Fontham ET, Smith GJ, Taylor JA, Srivastava S, Eeles RA, Carpten JD, Kibel AS, Multigner L, Parent MÉ, Menegaux F, Cancel-Tassin G, Klein EA, Andrews C, Rebbeck TR, Brureau L, Ambs S, Edwards TL, Watya S, Chanock SJ, Witte JS, Blot WJ, Michael Gaziano J, Justice AC, Conti DV, Haiman CA. Evidence of Novel Susceptibility Variants for Prostate Cancer and a Multiancestry Polygenic Risk Score Associated with Aggressive Disease in Men of African Ancestry. Eur Urol 2023; 84:13-21. [PMID: 36872133 PMCID: PMC10424812 DOI: 10.1016/j.eururo.2023.01.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 06/21/2022] [Revised: 12/14/2022] [Accepted: 01/24/2023] [Indexed: 03/06/2023]
Abstract
BACKGROUND Genetic factors play an important role in prostate cancer (PCa) susceptibility. OBJECTIVE To discover common genetic variants contributing to the risk of PCa in men of African ancestry. DESIGN, SETTING, AND PARTICIPANTS We conducted a meta-analysis of ten genome-wide association studies consisting of 19378 cases and 61620 controls of African ancestry. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Common genotyped and imputed variants were tested for their association with PCa risk. Novel susceptibility loci were identified and incorporated into a multiancestry polygenic risk score (PRS). The PRS was evaluated for associations with PCa risk and disease aggressiveness. RESULTS AND LIMITATIONS Nine novel susceptibility loci for PCa were identified, of which seven were only found or substantially more common in men of African ancestry, including an African-specific stop-gain variant in the prostate-specific gene anoctamin 7 (ANO7). A multiancestry PRS of 278 risk variants conferred strong associations with PCa risk in African ancestry studies (odds ratios [ORs] >3 and >5 for men in the top PRS decile and percentile, respectively). More importantly, compared with men in the 40-60% PRS category, men in the top PRS decile had a significantly higher risk of aggressive PCa (OR = 1.23, 95% confidence interval = 1.10-1.38, p = 4.4 × 10-4). CONCLUSIONS This study demonstrates the importance of large-scale genetic studies in men of African ancestry for a better understanding of PCa susceptibility in this high-risk population and suggests a potential clinical utility of PRS in differentiating between the risks of developing aggressive and nonaggressive disease in men of African ancestry. PATIENT SUMMARY In this large genetic study in men of African ancestry, we discovered nine novel prostate cancer (PCa) risk variants. We also showed that a multiancestry polygenic risk score was effective in stratifying PCa risk, and was able to differentiate risk of aggressive and nonaggressive disease.
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Affiliation(s)
- Fei Chen
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Burcu F Darst
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alisha Chou
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xin Sheng
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anqi Wang
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jiayi Shen
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jeannette T Bensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sue A Ingles
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rick A Kittles
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Sara S Strom
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - William B Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN, USA
| | - Esther M John
- Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Ying Wang
- Department of Population Science, American Cancer Society, Kennesaw, GA, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | | | - Yao Tettey
- Department of Pathology, University of Ghana, Accra, Ghana; Korle Bu Teaching Hospital, Accra, Ghana
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Christopher T Rentsch
- Yale School of Medicine, New Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Kelly Cho
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Jamaica Plain, MA, USA
| | - Benjamin H Mcmahon
- Theoretical Biology Division, Los Alamos National Lab, Los Alamos, NM, USA
| | | | - Andrew A Adjei
- Department of Pathology, University of Ghana Medical School, Accra, Ghana
| | - Evelyn Tay
- Korle Bu Teaching Hospital, Accra, Ghana
| | | | | | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Kosj Yamoah
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA; Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Adam B Murphy
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - Dana C Crawford
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Alpa V Patel
- Department of Population Science, American Cancer Society, Kennesaw, GA, USA
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Melinda C Aldrich
- Division of Epidemiology, Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Olivier Cussenot
- Department of Urology and Predictive Onco-Urology Group, Sorbonne Université, GRC 5 Predictive Onco-Urology, APHP-Sorbonne Université, Paris, France; CeRePP, Tenon Hospital, Paris, France
| | - Gyorgy Petrovics
- Department of Surgery, Center for Prostate Disease Research, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jennifer Cullen
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA; Department of Surgery, Center for Prostate Disease Research, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | - Mariana C Stern
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Michael B Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Ann W Hsing
- Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Bettina F Drake
- Division of Public Health Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Jennifer J Hu
- The University of Miami School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Jacob M Keaton
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jacklyn N Hellwege
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Nashville, TN, USA
| | - Peter E Clark
- Atrium Health/Levine Cancer Institute, Charlotte, NC, USA
| | | | | | | | - Olufemi Ogunbiyi
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Michael O Idowu
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Olufemi Popoola
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Akindele O Adebiyi
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Oseremen I Aisuodionoe-Shadrach
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Hafees O Ajibola
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Mustapha A Jamda
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Olabode P Oluwole
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Maxwell Nwegbu
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | | | | | | | | | - Halimatou Diop
- Laboratoires Bacteriologie et Virologie, Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente, Northern California, Oakland, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Pascal Blanchet
- CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, Guadeloupe, France
| | - Jay H Fowke
- Department of Preventive Medicine, Division of Epidemiology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Graham Casey
- Department of Public Health Science, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Anselm J Hennis
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | | | - Ian M Thompson
- CHRISTUS Santa Rosa Medical Center Hospital, San Antonio, TX, USA
| | - Robin Leach
- Department of Urology, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susan M Gundell
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Peggy Wan
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - James L Mohler
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Elizabeth T Fontham
- School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Gary J Smith
- Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA; Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Shiv Srivastava
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Rosaline A Eeles
- The Institute of Cancer Research, London, UK; Royal Marsden NHS Foundation Trust, London, UK
| | - John D Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Adam S Kibel
- Department of Urology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Luc Multigner
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Rennes, France
| | - Marie-Élise Parent
- Epidemiology and Biostatistics Unit, Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, Canada
| | - Florence Menegaux
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif Cédex, France; Paris-Sud University, Villejuif Cédex, France
| | - Geraldine Cancel-Tassin
- Department of Urology and Predictive Onco-Urology Group, Sorbonne Université, GRC 5 Predictive Onco-Urology, APHP-Sorbonne Université, Paris, France; CeRePP, Tenon Hospital, Paris, France
| | - Eric A Klein
- Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Caroline Andrews
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA, USA; Glickman Urological & Kidney Institute, Cleveland, OH, USA
| | - Timothy R Rebbeck
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA, USA
| | - Laurent Brureau
- CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, Guadeloupe, France
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; International Epidemiology Institute, Rockville, MD, USA
| | - J Michael Gaziano
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA
| | - Amy C Justice
- Yale School of Medicine, New Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA
| | - David V Conti
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher A Haiman
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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8
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Martin-Giacalone BA, Richard MA, Scheurer ME, Khan J, Sok P, Shetty PB, Chanock SJ, Li SA, Yeager M, Marquez-Do DA, Barkauskas DA, Hall D, McEvoy MT, Brown AL, Sabo A, Scheet P, Huff CD, Skapek SX, Hawkins DS, Venkatramani R, Mirabello L, Lupo PJ. Germline genetic variants and pediatric rhabdomyosarcoma outcomes: a report from the Children's Oncology Group. J Natl Cancer Inst 2023; 115:733-741. [PMID: 36951526 PMCID: PMC10248851 DOI: 10.1093/jnci/djad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/15/2023] [Accepted: 03/09/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Relative to other pediatric cancers, survival for rhabdomyosarcoma (RMS) has not improved in recent decades, suggesting the need to enhance risk stratification. Therefore, we conducted a genome-wide association study for event-free survival (EFS) and overall survival (OS) to identify genetic variants associated with outcomes in individuals with RMS. METHODS The study included 920 individuals with newly diagnosed RMS who were enrolled in Children's Oncology Group protocols. To assess the association of each single nucleotide polymorphism (SNP) with EFS and OS, we estimated hazard ratios (HRs) and 95% confidence intervals (CIs) using multivariable Cox proportional hazards models, adjusted for clinical covariates. All statistical tests were two sided. We also performed stratified analyses by histological subtype (alveolar and embryonal RMS) and carried out sensitivity analyses of statistically significant SNPs by PAX3/7-FOXO1 fusion status and genetic ancestry group. RESULTS We identified that rs17321084 was associated with worse EFS (HR = 2.01, 95% CI = 1.59 to 2.53, P = 5.39 × 10-9) and rs10094840 was associated with worse OS (HR = 1.84, 95% CI = 1.48 to 2.27, P = 2.13 × 10-8). Using publicly available data, we found that rs17321084 lies in a binding region for transcription factors GATA2 and GATA3, and rs10094840 is associated with SPAG1 and RNF19A expression. We also identified that CTNNA3 rs2135732 (HR = 3.75, 95% CI = 2.34 to 5.99, P = 3.54 × 10-8) and MED31 rs74504320 (HR = 3.21, 95% CI = 2.12 to 4.86, P = 3.60 × 10-8) were associated with worse OS among individuals with alveolar RMS. CONCLUSIONS We demonstrated that common germline variants are associated with EFS and OS among individuals with RMS. Additional replication and investigation of these SNP effects may further support their consideration in risk stratification protocols.
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Affiliation(s)
- Bailey A Martin-Giacalone
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Melissa A Richard
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Michael E Scheurer
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Pagna Sok
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Priya B Shetty
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Meredith Yeager
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Deborah A Marquez-Do
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Donald A Barkauskas
- Department of Population and Public Health Sciences, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- QuadW Childhood Sarcoma Biostatistics and Annotation Office, Children’s Oncology Group, Monrovia, CA, USA
| | - David Hall
- QuadW Childhood Sarcoma Biostatistics and Annotation Office, Children’s Oncology Group, Monrovia, CA, USA
| | - Matthew T McEvoy
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Austin L Brown
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephen X Skapek
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Douglas S Hawkins
- Division of Hematology-Oncology, Department of Pediatrics, Seattle Children’s Hospital, University of Washington, Seattle, WA, USA
| | - Rajkumar Venkatramani
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Lisa Mirabello
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MA, USA
| | - Philip J Lupo
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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9
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Lancaster MC, Chen HH, Shoemaker MB, Fleming MR, Baker JT, Polikowsky HG, Samuels DC, Huff CD, Roden DM, Below JE. Detection of distant familial relatedness in biobanks for identification of undiagnosed carriers of a Mendelian disease variant: application to Long QT syndrome. medRxiv 2023:2023.04.19.23288831. [PMID: 37163006 PMCID: PMC10168417 DOI: 10.1101/2023.04.19.23288831] [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] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Importance The diagnosis and study of rare genetic disease is often limited to referral populations, leading to underdiagnosis and a biased assessment of penetrance and phenotype. Objective To develop a generalizable method of genotype inference based on distant relatedness and to deploy this to identify undiagnosed Type 5 Long QT Syndrome (LQT5) rare variant carriers in a non-referral population. Participants We identified 9 LQT5 probands and 3 first-degree relatives referred to a single Genetic Arrhythmia clinic, each carrying D76N (p.Asp76Asn), the most common variant implicated in LQT5. The non-referral population consisted of 69,879 ancestry-matched subjects in BioVU, a large biobank that links electronic health records to dense array data. Participants were enrolled from 2007-2022. Data analysis was performed in 2022. Exposures We developed and applied a novel approach to genotype inference (Distant Relatedness for Identification and Variant Evaluation, or DRIVE) to identify shared, identical-by-descent (IBD) large chromosomal segments in array data. Main Outcomes and Measures We sought to establish genetic relatedness among the probands and to use genomic segments underlying D76N to identify other potential carriers in BioVU. We then further studied the role of D76N in LQT5 pathogenesis. Results Genetic reconstruction of pedigrees and distant relatedness detection among clinic probands using DRIVE revealed shared recent common ancestry and identified a single long shared haplotype. Interrogation of the non-referral population in BioVU identified a further 23 subjects sharing this haplotype, and sequencing confirmed D76N carrier status in 22, all previously undiagnosed with LQT5. The QTc was prolonged in D76N carriers compared to BioVU controls, with 40% penetrance of QTc ≥ 480 msec. Among D76N carriers, a QTc polygenic score was additively associated with QTc prolongation. Conclusions and Relevance Detection of IBD shared chromosomal segments around D76N enabled identification of distantly related and previously undiagnosed rare-variant carriers, demonstrated the contribution of polygenic risk to monogenic disease penetrance, and further established LQT5 as a primary arrhythmia disorder. Analysis of shared chromosomal regions spanning disease-causing mutations can identify undiagnosed cases of genetic diseases.
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Affiliation(s)
| | - Hung-Hsin Chen
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | | | - James T Baker
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | | | - Chad D Huff
- University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dan M Roden
- Vanderbilt University Medical Center, Nashville, Tennessee
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10
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Wang A, Xu Y, Sheng X, Hughley R, Adusei B, Jalloh M, Gueye SM, Adjei AA, Mensah J, Fernandez PW, Adebiyi AO, Aisuodionoe-Shadrach OI, Petersen L, Joffe M, Bensen JT, Mohler JL, Taylor JA, Butler EN, Ingles SA, Rybicki BA, Stanford JL, Zheng W, Berndt SI, Huff CD, Lachance J, Multigner L, Andrews C, Rebbeck TR, Brureau L, Chanock SJ, de Smith A, Chen F, Darst BF, Conti DV, Haiman CA. Abstract 3508: Association between clonal hematopoiesis and risk of prostate cancer in a large sample of African ancestry men. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3508] [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: 04/07/2023]
Abstract
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) has been associated with inflammation, which is a risk factor for cancer, including prostate cancer. We previously reported weak evidence of an association between CHIP and prostate cancer risk in men of European ancestry. However, little is known for African ancestry populations. We investigated the association of age-related CHIP with overall and aggressive prostate cancer risk in a large whole-exome sequencing study of 12,049 African ancestry men, including 7,176 prostate cancer cases (of which 3,283 had aggressive disease and 1,074 had metastatic disease) and 4,873 controls. Somatic variant calling was carried out using GATK Mutect2, and only variants with minor allele frequencies (MAF) <0.1% and a variant allelic fraction (VAF) >5% were included. Variants with a MAF ≥0.1% in gnomAD were excluded. CHIP variants were identified from a list of pre-specified mutations in 74 genes. Associations were tested using regression models adjusting for age, sub-study, and top 10 principal components, with statistical significance tested by the likelihood ratio test and applying a Bonferroni correction to account for multiple testing. In total, 998 variants in 57 CHIP genes were identified. Consistent with previous results, we observed a strong association between CHIP and age at blood draw. CHIP genes in aggregate were not statistically significantly associated with risks of total (OR=1.12, 95% CI=0.97-1.28), aggressive (OR=1.14, 95% CI=0.92-1.43) or metastatic (OR=1.17, 95% CI=0.91-1.49) prostate cancer. We observed that carriers of variants in DNMT3A, which is the gene that harbors the most CHIP driver mutations, had a nominally elevated risk of prostate cancer compared to non-carriers (OR=1.35, 95% CI=1.08-1.68, p=0.007). Additionally, carriers of variants in EZH2, which is implicated in cancer progression, showed a suggestive association with aggressive prostate cancer (OR=7.33, 95% CI=1.01-53.21, p=0.029). After adjusting for age at blood draw, CHIP genes in aggregate were not associated with age at prostate cancer diagnosis. However, we found that EZH2 variants carriers were diagnosed 12.9 years earlier on average than non-carriers (95% CI=6.1-19.7, adjusted p=0.01). A prostate cancer polygenic risk score (PRS) constructed using 269 risk variants was not associated with CHIP carrier status in aggregate (OR=0.99, 95% CI=0.92-1.06, p=0.70) or with any individual gene (all adjusted p>0.05). In summary, overall CHIP is not likely to be a risk factor of prostate cancer or aggressive disease in men of African ancestry. However, our results do confirm the association of CHIP in DNMT3A with prostate cancer risk as reported in previous studies in men of European ancestry. Future work will be needed to evaluate the biological causality of DNMT3A- and EZH2- related CHIP on prostate cancer.
Citation Format: Anqi Wang, Yili Xu, Xin Sheng, Raymond Hughley, Ben Adusei, Mohamed Jalloh, Serigne Magueye Gueye, Andrew A Adjei, James Mensah, Pedro W. Fernandez, Akin Olupelumi Adebiyi, Oseremen Inokhoife Aisuodionoe-Shadrach, Lindsay Petersen, Maureen Joffe, Jeannette T. Bensen, James L. Mohler, Jack A. Taylor, Eboneé N. Butler, Sue A. Ingles, Benjamin A. Rybicki, Janet L. Stanford, Wei Zheng, Sonja I. Berndt, Chad D. Huff, Joseph Lachance, Luc Multigner, Caroline Andrews, Timothy R. Rebbeck, Laurent Brureau, Stephen J. Chanock, Adam de Smith, Fei Chen, Burcu F. Darst, David V. Conti, Christopher A. Haiman. Association between clonal hematopoiesis and risk of prostate cancer in a large sample of African ancestry men [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3508.
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Affiliation(s)
- Anqi Wang
- 1University of Southern California, Los Angeles, CA
| | - Yili Xu
- 1University of Southern California, Los Angeles, CA
| | - Xin Sheng
- 1University of Southern California, Los Angeles, CA
| | | | | | | | | | | | | | | | | | | | | | - Maureen Joffe
- 10Wits Health Consortium, Johannesburg, South Africa
| | | | | | - Jack A. Taylor
- 13National Institute of Environmental Health Sciences, Research Triangle Park, NC
| | | | | | | | | | - Wei Zheng
- 16Vanderbilt University Medical Center, Nashville, TN
| | | | - Chad D. Huff
- 18University of Texas M.D. Anderson Cancer Center, Huston, TX
| | - Joseph Lachance
- 19Georgia Institute of Technology, School of Biological Sciences, GA
| | - Luc Multigner
- 20Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Rennes, France
| | | | | | - Laurent Brureau
- 22CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, France
| | | | | | - Fei Chen
- 1University of Southern California, Los Angeles, CA
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11
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Xu A, Liu M, Huang MF, Zhang Y, Hu R, Gingold JA, Liu Y, Zhu D, Chien CS, Wang WC, Liao Z, Yuan F, Hsu CW, Tu J, Yu Y, Rosen T, Xiong F, Jia P, Yang YP, Bazer DA, Chen YW, Li W, Huff CD, Zhu JJ, Aguilo F, Chiou SH, Boles NC, Lai CC, Hung MC, Zhao Z, Van Nostrand EL, Zhao R, Lee DF. Rewired m 6A epitranscriptomic networks link mutant p53 to neoplastic transformation. Nat Commun 2023; 14:1694. [PMID: 36973285 PMCID: PMC10042811 DOI: 10.1038/s41467-023-37398-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 10/07/2022] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
N6-methyladenosine (m6A), one of the most prevalent mRNA modifications in eukaryotes, plays a critical role in modulating both biological and pathological processes. However, it is unknown whether mutant p53 neomorphic oncogenic functions exploit dysregulation of m6A epitranscriptomic networks. Here, we investigate Li-Fraumeni syndrome (LFS)-associated neoplastic transformation driven by mutant p53 in iPSC-derived astrocytes, the cell-of-origin of gliomas. We find that mutant p53 but not wild-type (WT) p53 physically interacts with SVIL to recruit the H3K4me3 methyltransferase MLL1 to activate the expression of m6A reader YTHDF2, culminating in an oncogenic phenotype. Aberrant YTHDF2 upregulation markedly hampers expression of multiple m6A-marked tumor-suppressing transcripts, including CDKN2B and SPOCK2, and induces oncogenic reprogramming. Mutant p53 neoplastic behaviors are significantly impaired by genetic depletion of YTHDF2 or by pharmacological inhibition using MLL1 complex inhibitors. Our study reveals how mutant p53 hijacks epigenetic and epitranscriptomic machinery to initiate gliomagenesis and suggests potential treatment strategies for LFS gliomas.
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Affiliation(s)
- An Xu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Mo Liu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Mo-Fan Huang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Yang Zhang
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, 518055, China
| | - Ruifeng Hu
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Julian A Gingold
- Department of Obstetrics & Gynecology and Women's Health, Einstein/Montefiore Medical Center, Bronx, NY, 10461, USA
| | - Ying Liu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Dandan Zhu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Chian-Shiu Chien
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, 112, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan
| | - Wei-Chen Wang
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Zian Liao
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fei Yuan
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jian Tu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Yao Yu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Taylor Rosen
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Feng Xiong
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Yi-Ping Yang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, 112, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan
| | - Danielle A Bazer
- Department of Neurology, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY, 11794, USA
| | - Ya-Wen Chen
- Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Institute for Airway Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Wenbo Li
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Chad D Huff
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jay-Jiguang Zhu
- Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Francesca Aguilo
- Wallenberg Centre for Molecular Medicine (WCMM), Umea University, SE-901 85, Umea, Sweden
- Department of Molecular Biology, Umea University, SE-901 85, Umea, Sweden
| | - Shih-Hwa Chiou
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, 112, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan
| | | | - Chien-Chen Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227, Taiwan
- Graduate institute of Chinese Medical Science, China Medical University, Taichung, 40402, Taiwan
- Ph.D. Program in Translational Medicine and Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences and Center for Molecular Medicine, and Office of the President, China Medical University, Taichung, 404, Taiwan
- Department of Biotechnology, Asia University, Taichung, 413, Taiwan
| | - Zhongming Zhao
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Eric L Van Nostrand
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ruiying Zhao
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
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12
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Yu Y, Alvarado R, Petty LE, Bohlender RJ, Shaw DM, Below JE, Bejar N, Ruiz OE, Tandon B, Eisenhoffer GT, Kiss DL, Huff CD, Letra A, Hecht JT. Polygenic risk impacts PDGFRA mutation penetrance in non-syndromic cleft lip and palate. Hum Mol Genet 2022; 31:2348-2357. [PMID: 35147171 PMCID: PMC9307317 DOI: 10.1093/hmg/ddac037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 11/12/2022] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common, severe craniofacial malformation that imposes significant medical, psychosocial and financial burdens. NSCL/P is a multifactorial disorder with genetic and environmental factors playing etiologic roles. Currently, only 25% of the genetic variation underlying NSCL/P has been identified by linkage, candidate gene and genome-wide association studies. In this study, whole-genome sequencing and genome-wide genotyping followed by polygenic risk score (PRS) and linkage analyses were used to identify the genetic etiology of NSCL/P in a large three-generation family. We identified a rare missense variant in PDGFRA (c.C2740T; p.R914W) as potentially etiologic in a gene-based association test using pVAAST (P = 1.78 × 10-4) and showed decreased penetrance. PRS analysis suggested that variant penetrance was likely modified by common NSCL/P risk variants, with lower scores found among unaffected carriers. Linkage analysis provided additional support for PRS-modified penetrance, with a 7.4-fold increase in likelihood after conditioning on PRS. Functional characterization experiments showed that the putatively causal variant was null for signaling activity in vitro; further, perturbation of pdgfra in zebrafish embryos resulted in unilateral orofacial clefting. Our findings show that a rare PDGFRA variant, modified by additional common NSCL/P risk variants, have a profound effect on NSCL/P risk. These data provide compelling evidence for multifactorial inheritance long postulated to underlie NSCL/P and may explain some unusual familial patterns.
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Affiliation(s)
- Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rolando Alvarado
- Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Lauren E Petty
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ryan J Bohlender
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Douglas M Shaw
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nada Bejar
- Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Oscar E Ruiz
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bhavna Tandon
- Department of Pediatrics and Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX 77030, USA
| | - George T Eisenhoffer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Daniel L Kiss
- Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ariadne Letra
- Department of Diagnostic and Biomedical Sciences, UTHealth School of Dentistry at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, UTHealth School of Dentistry at Houston, Houston 77054, TX, USA
| | - Jacqueline T Hecht
- Department of Pediatrics and Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX 77030, USA
- Center for Craniofacial Research, UTHealth School of Dentistry at Houston, Houston 77054, TX, USA
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13
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Huynh-Le MP, Karunamuni R, Fan CC, Asona L, Thompson WK, Martinez ME, Eeles RA, Kote-Jarai Z, Muir KR, Lophatananon A, Schleutker J, Pashayan N, Batra J, Grönberg H, Neal DE, Nordestgaard BG, Tangen CM, MacInnis RJ, Wolk A, Albanes D, Haiman CA, Travis RC, Blot WJ, Stanford JL, Mucci LA, West CML, Nielsen SF, Kibel AS, Cussenot O, Berndt SI, Koutros S, Sørensen KD, Cybulski C, Grindedal EM, Menegaux F, Park JY, Ingles SA, Maier C, Hamilton RJ, Rosenstein BS, Lu YJ, Watya S, Vega A, Kogevinas M, Wiklund F, Penney KL, Huff CD, Teixeira MR, Multigner L, Leach RJ, Brenner H, John EM, Kaneva R, Logothetis CJ, Neuhausen SL, De Ruyck K, Ost P, Razack A, Newcomb LF, Fowke JH, Gamulin M, Abraham A, Claessens F, Castelao JE, Townsend PA, Crawford DC, Petrovics G, van Schaik RHN, Parent MÉ, Hu JJ, Zheng W, Mills IG, Andreassen OA, Dale AM, Seibert TM. Prostate cancer risk stratification improvement across multiple ancestries with new polygenic hazard score. Prostate Cancer Prostatic Dis 2022; 25:755-761. [PMID: 35152271 PMCID: PMC9372232 DOI: 10.1038/s41391-022-00497-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/12/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND Prostate cancer risk stratification using single-nucleotide polymorphisms (SNPs) demonstrates considerable promise in men of European, Asian, and African genetic ancestries, but there is still need for increased accuracy. We evaluated whether including additional SNPs in a prostate cancer polygenic hazard score (PHS) would improve associations with clinically significant prostate cancer in multi-ancestry datasets. METHODS In total, 299 SNPs previously associated with prostate cancer were evaluated for inclusion in a new PHS, using a LASSO-regularized Cox proportional hazards model in a training dataset of 72,181 men from the PRACTICAL Consortium. The PHS model was evaluated in four testing datasets: African ancestry, Asian ancestry, and two of European Ancestry-the Cohort of Swedish Men (COSM) and the ProtecT study. Hazard ratios (HRs) were estimated to compare men with high versus low PHS for association with clinically significant, with any, and with fatal prostate cancer. The impact of genetic risk stratification on the positive predictive value (PPV) of PSA testing for clinically significant prostate cancer was also measured. RESULTS The final model (PHS290) had 290 SNPs with non-zero coefficients. Comparing, for example, the highest and lowest quintiles of PHS290, the hazard ratios (HRs) for clinically significant prostate cancer were 13.73 [95% CI: 12.43-15.16] in ProtecT, 7.07 [6.58-7.60] in African ancestry, 10.31 [9.58-11.11] in Asian ancestry, and 11.18 [10.34-12.09] in COSM. Similar results were seen for association with any and fatal prostate cancer. Without PHS stratification, the PPV of PSA testing for clinically significant prostate cancer in ProtecT was 0.12 (0.11-0.14). For the top 20% and top 5% of PHS290, the PPV of PSA testing was 0.19 (0.15-0.22) and 0.26 (0.19-0.33), respectively. CONCLUSIONS We demonstrate better genetic risk stratification for clinically significant prostate cancer than prior versions of PHS in multi-ancestry datasets. This is promising for implementing precision-medicine approaches to prostate cancer screening decisions in diverse populations.
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Affiliation(s)
- Minh-Phuong Huynh-Le
- Radiation Oncology, George Washington University, Washington, DC, USA
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA, USA
| | - Roshan Karunamuni
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA, USA
| | - Chun Chieh Fan
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA, USA
| | - Lui Asona
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA
| | - Wesley K Thompson
- Division of Biostatistics and Halicioğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Maria Elena Martinez
- University of California San Diego, Moores Cancer Center, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093-0012, USA
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | | | - Kenneth R Muir
- Division of Population Health, Health Services Research and Primary Care, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Johanna Schleutker
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, PO Box 52, 20521, Turku, Finland
| | - Nora Pashayan
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge, CB1 8RN, UK
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, 4059, Australia
- Translational Research Institute, Brisbane, QLD, 4102, Australia
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, SE-171 77, Stockholm, Sweden
| | - David E Neal
- Nuffield Department of Surgical Sciences, University of Oxford, Room 6603, Level 6, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- University of Cambridge, Department of Oncology, Box 279, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Børge G Nordestgaard
- Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, 2200, Copenhagen, Denmark
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert J MacInnis
- Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Grattan Street, Parkville, VIC, 3010, Australia
| | - Alicja Wolk
- Department of Surgical Sciences, Uppsala University, 75185, Uppsala, Sweden
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90015, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 800, Nashville, TN, 37232, USA
- International Epidemiology Institute, Rockville, MD, 20850, USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, 98195, USA
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Catharine M L West
- Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Radiotherapy Related Research, The Christie Hospital NHS Foundation Trust, Manchester, M13 9PL, UK
| | - Sune F Nielsen
- Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, 2200, Copenhagen, Denmark
| | - Adam S Kibel
- Division of Urologic Surgery, Brigham and Womens Hospital, 75 Francis Street, Boston, MA, 02115, USA
| | - Olivier Cussenot
- Sorbonne Universite, GRC n°5, AP-HP, Tenon Hospital, 4 rue de la Chine, F-45020, Paris, France
- CeRePP, Tenon Hospital, F-75020, Paris, France
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Karina Dalsgaard Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensen Boulevard 99, 8200, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, DK, 8200, Aarhus N, Denmark
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-115, Szczecin, Poland
| | - Eli Marie Grindedal
- Department of Medical Genetics, Oslo University Hospital, 0424, Oslo, Norway
| | - Florence Menegaux
- Exposome and Heredity, CESP (UMR 1018), Faculté de Médecine, Université Paris-Saclay, Inserm, Gustave Roussy, Villejuif, France
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90015, USA
| | - Christiane Maier
- Humangenetik Tuebingen, Paul-Ehrlich-Str 23, D-72076, Tuebingen, Germany
| | - Robert J Hamilton
- Dept. of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, ON, M5G 2M9, Canada
- Dept. of Surgery (Urology), University of Toronto, Toronto, Canada
| | - Barry S Rosenstein
- Department of Radiation Oncology and Department of Genetics and Genomic Sciences, Box 1236, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Yong-Jie Lu
- Centre for Cancer Biomarker and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | | | - Ana Vega
- Fundación Pública Galega Medicina Xenómica, Santiago de Compostela, 15706, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago De Compostela, 15706, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Santiago De Compostela, Spain
| | - Manolis Kogevinas
- ISGlobal, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, SE-171 77, Stockholm, Sweden
| | - Kathryn L Penney
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, MA, 02115, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), 4200-072, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, 4050-313, Porto, Portugal
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), 4200-072, Porto, Portugal
| | - Luc Multigner
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Robin J Leach
- Department of Cell Systems and Anatomy, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
| | - Esther M John
- Departments of Epidemiology & Population Health and of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia, 2 Zdrave Str., 1431, Sofia, Bulgaria
| | - Christopher J Logothetis
- The University of Texas M. D. Anderson Cancer Center, Department of Genitourinary Medical Oncology, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Kim De Ruyck
- Ghent University, Faculty of Medicine and Health Sciences, Basic Medical Sciences, Proeftuinstraat 86, B-9000, Gent, Belgium
| | - Piet Ost
- Ghent University Hospital, Department of Radiotherapy, De Pintelaan 185, B-9000, Gent, Belgium
| | - Azad Razack
- Department of Surgery, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Lisa F Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
- Department of Urology, University of Washington, 1959 NE Pacific Street, Box 356510, Seattle, WA, 98195, USA
| | - Jay H Fowke
- Division of Epidemiology, Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Marija Gamulin
- Department of Oncology, University Hospital Centre Zagreb, University of Zagreb, School of Medicine, 10 000, Zagreb, Croatia
| | - Aswin Abraham
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, AB, T6G 1Z2, Canada
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, BE-3000, Belgium
| | - Jose Esteban Castelao
- Genetic Oncology Unit, CHUVI Hospital, Complexo Hospitalario Universitario de Vigo, Instituto de Investigación Biomédica Galicia Sur (IISGS), 36204, Vigo (Pontevedra), Spain
| | - Paul A Townsend
- Division of Cancer Sciences, Manchester Cancer Research Centre, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Research Centre, Health Innovation Manchester, Univeristy of Manchester, Manchester, M13 9WL, UK
- The University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Dana C Crawford
- Case Western Reserve University, Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, 2103 Cornell Road, Wolstein Research Building, Suite 2527, Cleveland, OH, 44106, USA
| | - Gyorgy Petrovics
- Uniformed Services University, 4301 Jones Bridge Rd, Bethesda, MD, 20814, USA
- Center for Prostate Disease Research, 6720A Rockledge Drive, Suite 300, Bethesda, MD, 20817, USA
| | - Ron H N van Schaik
- Department of Clinical Chemistry, Erasmus University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | - Marie-Élise Parent
- Epidemiology and Biostatistics Unit, Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
- Department of Social and Preventive Medicine, School of Public Health, University of Montreal, Montreal, QC, Canada
| | - Jennifer J Hu
- The University of Miami School of Medicine, Sylvester Comprehensive Cancer Center, 1120 NW 14th Street, CRB 1511, Miami, FL, 33136, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 800, Nashville, TN, 37232, USA
| | - Ian G Mills
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Ole A Andreassen
- NORMENT, KG Jebsen Centre, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Anders M Dale
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA, USA
- NORMENT, KG Jebsen Centre, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Radiology, University of California San Diego, La Jolla, CA, USA
| | - Tyler M Seibert
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA, USA.
- NORMENT, KG Jebsen Centre, Oslo University Hospital and University of Oslo, Oslo, Norway.
- Department of Radiology, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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14
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Yu Y, Chang K, Chen JS, Bohlender RJ, Fowler J, Zhang D, Huang M, Chang P, Li Y, Wong J, Wang H, Gu J, Wu X, Schildkraut J, Cannon-Albright L, Ye Y, Zhao H, Hildebrandt MAT, Permuth JB, Li D, Scheet P, Huff CD. A whole-exome case-control association study to characterize the contribution of rare coding variation to pancreatic cancer risk. HGG Adv 2022; 3:100078. [PMID: 35047863 PMCID: PMC8756505 DOI: 10.1016/j.xhgg.2021.100078] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/08/2021] [Indexed: 10/26/2022] Open
Abstract
Pancreatic cancer is a deadly disease that accounts for approximately 5% of cancer deaths worldwide, with a dismal 5-year survival rate of 10%. Known genetic risk factors explain only a modest proportion of the heritable risk of pancreatic cancer. We conducted a whole-exome case-control sequencing study in 1,591 pancreatic cancer cases and 2,134 cancer-free controls of European ancestry. In our gene-based analysis, ATM ranked first, with a genome-wide significant p value of 1 × 10-8. The odds ratio for protein-truncating variants in ATM was 24, which is substantially higher than prior estimates, although ours includes a broad 95% confidence interval (4.0-1000). SIK3 was the second highest ranking gene (p = 3.84 × 10-6, false discovery rate or FDR = 0.032). We observed nominally significant association signals in several genes of a priori interest, including BRCA2 (p = 4.3 × 10-4), STK11 (p = 0.003), PALB2 (p = 0.019), and TP53 (p = 0.037), and reported risk estimates for known pathogenic variants and variants of uncertain significance (VUS) in these genes. The rare variants in established susceptibility genes explain approximately 24% of log familial relative risk, which is comparable to the contribution from established common susceptibility variants (17%). In conclusion, this study provides new insights into the genetic susceptibility of pancreatic cancer, refining rare variant risk estimates in known pancreatic cancer susceptibility genes and identifying SIK3 as a novel candidate susceptibility gene. This study highlights the prominent importance of ATM truncating variants and the underappreciated role of VUS in pancreatic cancer etiology.
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Affiliation(s)
- Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kyle Chang
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jiun-Sheng Chen
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ryan J Bohlender
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jerry Fowler
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Di Zhang
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maosheng Huang
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ping Chang
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yanan Li
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Justin Wong
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Huamin Wang
- Department of Anatomical Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jian Gu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xifeng Wu
- Center for Clinical Big Data and Analytics, Bioinformatics and Big Data, The Second Affiliated Hospital and School of Public Health, Zhejiang University School of Medicine, PR China
| | - Joellen Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Lisa Cannon-Albright
- Genetic Epidemiology, Department of Internal Medicine, 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.,Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Yuanqing Ye
- Center for Clinical Big Data and Analytics, Bioinformatics and Big Data, The Second Affiliated Hospital and School of Public Health, Zhejiang University School of Medicine, PR China
| | - Hua Zhao
- Department of Family Medicine and Population Health, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Michelle A T Hildebrandt
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer B Permuth
- Departments of Cancer Epidemiology and Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Scheet
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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15
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Darst BF, Hughley R, Pfennig A, Hazra U, Fan C, Wan P, Sheng X, Xia L, Andrews C, Chen F, Berndt SI, Kote-Jarai Z, Govindasami K, Bensen JT, Ingles SA, Rybicki BA, Nemesure B, John EM, Fowke JH, Huff CD, Strom SS, Isaacs WB, Park JY, Zheng W, Ostrander EA, Walsh PC, Carpten J, Sellers TA, Yamoah K, Murphy AB, Sanderson M, Crawford DC, Gapstur SM, Bush WS, Aldrich MC, Cussenot O, Petrovics G, Cullen J, Neslund-Dudas C, Kittles RA, Xu J, Stern MC, Chokkalingam AP, Multigner L, Parent ME, Menegaux F, Cancel-Tassin G, Kibel AS, Klein EA, Goodman PJ, Stanford JL, Drake BF, Hu JJ, Clark PE, Blanchet P, Casey G, Hennis AJM, Lubwama A, Thompson IM, Leach RJ, Gundell SM, Pooler L, Mohler JL, Fontham ETH, Smith GJ, Taylor JA, Brureau L, Blot WJ, Biritwum R, Tay E, Truelove A, Niwa S, Tettey Y, Varma R, McKean-Cowdin R, Torres M, Jalloh M, Magueye Gueye S, Niang L, Ogunbiyi O, Oladimeji Idowu M, Popoola O, Adebiyi AO, Aisuodionoe-Shadrach OI, Nwegbu M, Adusei B, Mante S, Darkwa-Abrahams A, Yeboah ED, Mensah JE, Anthony Adjei A, Diop H, Cook MB, Chanock SJ, Watya S, Eeles RA, Chiang CWK, Lachance J, Rebbeck TR, Conti DV, Haiman CA. A Rare Germline HOXB13 Variant Contributes to Risk of Prostate Cancer in Men of African Ancestry. Eur Urol 2022; 81:458-462. [PMID: 35031163 PMCID: PMC9018520 DOI: 10.1016/j.eururo.2021.12.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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: 09/09/2021] [Revised: 12/06/2021] [Accepted: 12/22/2021] [Indexed: 11/17/2022]
Abstract
A rare African ancestry-specific germline deletion variant in HOXB13 (X285K, rs77179853) was recently reported in Martinican men with early-onset prostate cancer. Given the role of HOXB13 germline variation in prostate cancer, we investigated the association between HOXB13 X285K and prostate cancer risk in a large sample of 22 361 African ancestry men, including 11 688 prostate cancer cases. The risk allele was present only in men of West African ancestry, with an allele frequency in men that ranged from 0.40% in Ghana and 0.31% in Nigeria to 0% in Uganda and South Africa, with a range of frequencies in men with admixed African ancestry from North America and Europe (0-0.26%). HOXB13 X285K was associated with 2.4-fold increased odds of prostate cancer (95% confidence interval [CI] = 1.5-3.9, p = 2 × 10-4), with greater risk observed for more aggressive and advanced disease (Gleason ≥8: odds ratio [OR] = 4.7, 95% CI = 2.3-9.5, p = 2 × 10-5; stage T3/T4: OR = 4.5, 95% CI = 2.0-10.0, p = 2 × 10-4; metastatic disease: OR = 5.1, 95% CI = 1.9-13.7, p = 0.001). We estimated that the allele arose in West Africa 1500-4600 yr ago. Further analysis is needed to understand how the HOXB13 X285K variant impacts the HOXB13 protein and function in the prostate. Understanding who carries this mutation may inform prostate cancer screening in men of West African ancestry. PATIENT SUMMARY: A rare African ancestry-specific germline deletion in HOXB13, found only in men of West African ancestry, was reported to be associated with an increased risk of overall and advanced prostate cancer. Understanding who carries this mutation may help inform screening for prostate cancer in men of West African ancestry.
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Affiliation(s)
- Burcu F Darst
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
| | - Raymond Hughley
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Aaron Pfennig
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ujani Hazra
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Caoqi Fan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Peggy Wan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xin Sheng
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lucy Xia
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Caroline Andrews
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA, USA
| | - Fei Chen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | | | - Koveela Govindasami
- The Institute of Cancer Research, Sutton, London, UK; Royal Marsden NHS Foundation Trust, London, UK
| | - Jeannette T Bensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sue A Ingles
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Esther M John
- Department of Epidemiology & Population Health and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jay H Fowke
- Division of Epidemiology, Department of Preventive Medicine, The University of Tennessee Health Science Center, TN, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Sara S Strom
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - William B Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Patrick C Walsh
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - John Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Kosj Yamoah
- Department of Radiation Oncology and Cancer Epidemiology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Adam B Murphy
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN, USA
| | - Dana C Crawford
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - William S Bush
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Olivier Cussenot
- CeRePP & Sorbonne Universite, GRC n° 5, AP-HP, Tenon Hospital, Paris, France
| | - Gyorgy Petrovics
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jennifer Cullen
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Rick A Kittles
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Mariana C Stern
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | | | - Luc Multigner
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) -UMR_S 1085, Rennes, France
| | - Marie-Elise Parent
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, University of Quebec, Laval, Quebec, Canada
| | - Florence Menegaux
- Université Paris-Saclay, Université Paris-Sud, CESP (Center for Research in Epidemiology and Population Health), Inserm, Team Cancer-Environment, Villejuif, France
| | | | - Adam S Kibel
- Division of Urology, Brigham and Women's Hospital/Dana-Farber Cancer Institute, Boston, MA, USA; Washington University, St. Louis, MO, USA
| | - Eric A Klein
- Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Bettina F Drake
- Department of Surgery, Division of Public Health Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Jennifer J Hu
- Sylvester Comprehensive Cancer Center and Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Peter E Clark
- Atrium Health/Levine Cancer Institute, Charlotte, NC, USA
| | - Pascal Blanchet
- CHU de Guadeloupe, Univ Antilles, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) -UMR_S 1085, Rennes, France
| | - Graham Casey
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Anselm J M Hennis
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA; George Alleyne Chronic Disease Research Centre and Faculty of Medical Sciences, The University of the West Indies, Bridgetown, Barbados
| | - Alexander Lubwama
- School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - Ian M Thompson
- CHRISTUS Santa Rosa Health System and The University of Texas Health Science Center, San Antonio, TX, USA
| | - Robin J Leach
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Susan M Gundell
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Loreall Pooler
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - James L Mohler
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Elizabeth T H Fontham
- School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Gary J Smith
- Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jack A Taylor
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA; Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Laurent Brureau
- CHU de Guadeloupe, Univ Antilles, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) -UMR_S 1085, Rennes, France
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Evelyn Tay
- Korle Bu Teaching Hospital, Accra, Ghana
| | | | | | - Yao Tettey
- Korle Bu Teaching Hospital, Accra, Ghana; University of Ghana Medical School, Accra, Ghana
| | - Rohit Varma
- Southern California Eye Institute, CHA Hollywood Presbyterian Medical Center, Los Angeles, CA, USA
| | - Roberta McKean-Cowdin
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Mina Torres
- Southern California Eye Institute, CHA Hollywood Presbyterian Medical Center, Los Angeles, CA, USA
| | | | | | | | - Olufemi Ogunbiyi
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | | | - Olufemi Popoola
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Akindele O Adebiyi
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Oseremen I Aisuodionoe-Shadrach
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Maxwell Nwegbu
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | | | | | | | - Edward D Yeboah
- Korle Bu Teaching Hospital, Accra, Ghana; University of Ghana Medical School, Accra, Ghana
| | | | | | - Halimatou Diop
- Laboratoires Bacteriologie et Virologie, Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Michael B Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Stephen Watya
- School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda; Uro Care, Kampala, Uganda
| | - Rosalind A Eeles
- The Institute of Cancer Research, Sutton, London, UK; Royal Marsden NHS Foundation Trust, London, UK
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Timothy R Rebbeck
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA, USA
| | - David V Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
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16
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Thompson BA, Snow AK, Koptiuch C, Kohlmann WK, Mooney R, Johnson S, Huff CD, Yu Y, Teerlink CC, Feng BJ, Neklason DW, Cannon-Albright LA, Tavtigian SV. A novel ribosomal protein S20 variant in a family with unexplained colorectal cancer and polyposis. Clin Genet 2021; 97:943-944. [PMID: 32424863 DOI: 10.1111/cge.13757] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/21/2020] [Accepted: 02/23/2020] [Indexed: 01/23/2023]
Affiliation(s)
- Bryony A Thompson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Department of Pathology, Royal Melbourne Hospital, Melbourne, Australia.,Department of Clinical Pathology, University of Melbourne, Melbourne, Australia
| | - Angela K Snow
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Cathryn Koptiuch
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Wendy K Kohlmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Ryan Mooney
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Sara Johnson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Craig C Teerlink
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Bing-Jian Feng
- Department of Dermatology, University of Utah, Salt Lake City, Utah, USA
| | - Deborah W Neklason
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Lisa A Cannon-Albright
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA.,Research and Development Service, George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, USA
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah, USA
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17
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Petty LE, Phillippi-Falkenstein K, Kubisch HM, Raveendran M, Harris RA, Vallender EJ, Huff CD, Bohm RP, Rogers J, Below JE. Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta). Mol Ecol Resour 2021; 21:1333-1346. [PMID: 33386679 PMCID: PMC8247968 DOI: 10.1111/1755-0998.13317] [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] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/13/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022]
Abstract
A primary challenge in the analysis of free‐ranging animal populations is the accurate estimation of relatedness among individuals. Many aspects of population analysis rely on knowledge of relatedness patterns, including socioecology, demography, heritability and gene mapping analyses, wildlife conservation and the management of breeding colonies. Methods for determining relatedness using genome‐wide data have improved our ability to determine kinship and reconstruct pedigrees in humans. However, methods for reconstructing complex pedigree structures and estimating distant relatedness (beyond third‐degree) have not been widely applied to other species. We sequenced the genomes of 150 male rhesus macaques from the Tulane National Primate Research Center colony to estimate pairwise relatedness, reconstruct closely related pedigrees, estimate more distant relationships and augment colony records. Methods for determining relatedness developed for human genetic data were applied and evaluated in the analysis of nonhuman primates, including identity‐by‐descent‐based methods for pedigree reconstruction and shared segment‐based inference of more distant relatedness. We compared the genotype‐based pedigrees and estimated relationships to available colony pedigree records and found high concordance (95.5% agreement) between expected and identified relationships for close relatives. In addition, we detected distant relationships not captured in colony records, including some as distant as twelfth‐degree. Furthermore, while deep sequence coverage is preferable, we show that this approach can also provide valuable information when only low‐coverage (5×) sequence data is available. Our findings demonstrate the value of these methods for determination of relatedness in various animal populations, with diverse applications to conservation biology, evolutionary and ecological research and biomedical studies.
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Affiliation(s)
- Lauren E Petty
- Vanderbilt Genetics Institute and Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - H Michael Kubisch
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Eric J Vallender
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA.,Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rudolf P Bohm
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute and Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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18
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Chen HH, Shaw DM, Petty LE, Graff M, Bohlender RJ, Polikowsky HG, Zhong X, Kim D, Buchanan VL, Preuss MH, Shuey MM, Loos RJF, Huff CD, Cox NJ, Bastarache JA, Bastarache L, North KE, Below JE. Host genetic effects in pneumonia. Am J Hum Genet 2021; 108:194-201. [PMID: 33357513 PMCID: PMC7820802 DOI: 10.1016/j.ajhg.2020.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/02/2020] [Indexed: 01/05/2023] Open
Abstract
Given the coronavirus disease 2019 (COVID-19) pandemic, investigations into host susceptibility to infectious diseases and downstream sequelae have never been more relevant. Pneumonia is a lung disease that can cause respiratory failure and hypoxia and is a common complication of infectious diseases, including COVID-19. Few genome-wide association studies (GWASs) of host susceptibility and severity of pneumonia have been conducted. We performed GWASs of pneumonia susceptibility and severity in the Vanderbilt University biobank (BioVU) with linked electronic health records (EHRs), including Illumina Expanded Multi-Ethnic Global Array (MEGAEX)-genotyped European ancestry (EA, n= 69,819) and African ancestry (AA, n = 15,603) individuals. Two regions of large effect were identified: the CFTR locus in EA (rs113827944; OR = 1.84, p value = 1.2 × 10-36) and HBB in AA (rs334 [p.Glu7Val]; OR = 1.63, p value = 3.5 × 10-13). Mutations in these genes cause cystic fibrosis (CF) and sickle cell disease (SCD), respectively. After removing individuals diagnosed with CF and SCD, we assessed heterozygosity effects at our lead variants. Further GWASs after removing individuals with CF uncovered an additional association in R3HCC1L (rs10786398; OR = 1.22, p value = 3.5 × 10-8), which was replicated in two independent datasets: UK Biobank (n = 459,741) and 7,985 non-overlapping BioVU subjects, who are genotyped on arrays other than MEGAEX. This variant was also validated in GWASs of COVID-19 hospitalization and lung function. Our results highlight the importance of the host genome in infectious disease susceptibility and severity and offer crucial insight into genetic effects that could potentially influence severity of COVID-19 sequelae.
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Affiliation(s)
- Hung-Hsin Chen
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Douglas M Shaw
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lauren E Petty
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Misa Graff
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Ryan J Bohlender
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Hannah G Polikowsky
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Xue Zhong
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Daeeun Kim
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Victoria L Buchanan
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Megan M Shuey
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Nancy J Cox
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Julie A Bastarache
- Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kari E North
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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19
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Conti DV, Darst BF, Moss LC, Saunders EJ, Sheng X, Chou A, Schumacher FR, Olama AAA, Benlloch S, Dadaev T, Brook MN, Sahimi A, Hoffmann TJ, Takahashi A, Matsuda K, Momozawa Y, Fujita M, Muir K, Lophatananon A, Wan P, Le Marchand L, Wilkens LR, Stevens VL, Gapstur SM, Carter BD, Schleutker J, Tammela TLJ, Sipeky C, Auvinen A, Giles GG, Southey MC, MacInnis RJ, Cybulski C, Wokołorczyk D, Lubiński J, Neal DE, Donovan JL, Hamdy FC, Martin RM, Nordestgaard BG, Nielsen SF, Weischer M, Bojesen SE, Røder MA, Iversen P, Batra J, Chambers S, Moya L, Horvath L, Clements JA, Tilley W, Risbridger GP, Gronberg H, Aly M, Szulkin R, Eklund M, Nordström T, Pashayan N, Dunning AM, Ghoussaini M, Travis RC, Key TJ, Riboli E, Park JY, Sellers TA, Lin HY, Albanes D, Weinstein SJ, Mucci LA, Giovannucci E, Lindstrom S, Kraft P, Hunter DJ, Penney KL, Turman C, Tangen CM, Goodman PJ, Thompson IM, Hamilton RJ, Fleshner NE, Finelli A, Parent MÉ, Stanford JL, Ostrander EA, Geybels MS, Koutros S, Freeman LEB, Stampfer M, Wolk A, Håkansson N, Andriole GL, Hoover RN, Machiela MJ, Sørensen KD, Borre M, Blot WJ, Zheng W, Yeboah ED, Mensah JE, Lu YJ, Zhang HW, Feng N, Mao X, Wu Y, Zhao SC, Sun Z, Thibodeau SN, McDonnell SK, Schaid DJ, West CML, Burnet N, Barnett G, Maier C, Schnoeller T, Luedeke M, Kibel AS, Drake BF, Cussenot O, Cancel-Tassin G, Menegaux F, Truong T, Koudou YA, John EM, Grindedal EM, Maehle L, Khaw KT, Ingles SA, Stern MC, Vega A, Gómez-Caamaño A, Fachal L, Rosenstein BS, Kerns SL, Ostrer H, Teixeira MR, Paulo P, Brandão A, Watya S, Lubwama A, Bensen JT, Fontham ETH, Mohler J, Taylor JA, Kogevinas M, Llorca J, Castaño-Vinyals G, Cannon-Albright L, Teerlink CC, Huff CD, Strom SS, Multigner L, Blanchet P, Brureau L, Kaneva R, Slavov C, Mitev V, Leach RJ, Weaver B, Brenner H, Cuk K, Holleczek B, Saum KU, Klein EA, Hsing AW, Kittles RA, Murphy AB, Logothetis CJ, Kim J, Neuhausen SL, Steele L, Ding YC, Isaacs WB, Nemesure B, Hennis AJM, Carpten J, Pandha H, Michael A, De Ruyck K, De Meerleer G, Ost P, Xu J, Razack A, Lim J, Teo SH, Newcomb LF, Lin DW, Fowke JH, Neslund-Dudas C, Rybicki BA, Gamulin M, Lessel D, Kulis T, Usmani N, Singhal S, Parliament M, Claessens F, Joniau S, Van den Broeck T, Gago-Dominguez M, Castelao JE, Martinez ME, Larkin S, Townsend PA, Aukim-Hastie C, Bush WS, Aldrich MC, Crawford DC, Srivastava S, Cullen JC, Petrovics G, Casey G, Roobol MJ, Jenster G, van Schaik RHN, Hu JJ, Sanderson M, Varma R, McKean-Cowdin R, Torres M, Mancuso N, Berndt SI, Van Den Eeden SK, Easton DF, Chanock SJ, Cook MB, Wiklund F, Nakagawa H, Witte JS, Eeles RA, Kote-Jarai Z, Haiman CA. Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction. Nat Genet 2021; 53:65-75. [PMID: 33398198 PMCID: PMC8148035 DOI: 10.1038/s41588-020-00748-0] [Citation(s) in RCA: 205] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 11/05/2020] [Indexed: 01/28/2023]
Abstract
Prostate cancer is a highly heritable disease with large disparities in incidence rates across ancestry populations. We conducted a multiancestry meta-analysis of prostate cancer genome-wide association studies (107,247 cases and 127,006 controls) and identified 86 new genetic risk variants independently associated with prostate cancer risk, bringing the total to 269 known risk variants. The top genetic risk score (GRS) decile was associated with odds ratios that ranged from 5.06 (95% confidence interval (CI), 4.84-5.29) for men of European ancestry to 3.74 (95% CI, 3.36-4.17) for men of African ancestry. Men of African ancestry were estimated to have a mean GRS that was 2.18-times higher (95% CI, 2.14-2.22), and men of East Asian ancestry 0.73-times lower (95% CI, 0.71-0.76), than men of European ancestry. These findings support the role of germline variation contributing to population differences in prostate cancer risk, with the GRS offering an approach for personalized risk prediction.
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Affiliation(s)
- David V Conti
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Burcu F Darst
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Lilit C Moss
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | | | - Xin Sheng
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Alisha Chou
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
| | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Sara Benlloch
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | | | | | - Ali Sahimi
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Atushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Genomic Medicine, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
- Biobank, Tokyo, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Peggy Wan
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Lynne R Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Victoria L Stevens
- Behavioral and Epidemiology Research Group, Research Program, American Cancer Society, Atlanta, GA, USA
| | - Susan M Gapstur
- Behavioral and Epidemiology Research Group, Research Program, American Cancer Society, Atlanta, GA, USA
| | - Brian D Carter
- Behavioral and Epidemiology Research Group, Research Program, American Cancer Society, Atlanta, GA, USA
| | - Johanna Schleutker
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, Turku, Finland
| | - Teuvo L J Tammela
- Department of Urology, Tampere University Hospital and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Csilla Sipeky
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Anssi Auvinen
- Unit of Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Robert J MacInnis
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Dominika Wokołorczyk
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubiński
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - David E Neal
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
- University of Cambridge, Department of Oncology, Addenbrooke's Hospital, Cambridge, UK
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Jenny L Donovan
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Faculty of Medical Science, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Richard M Martin
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- National Institute for Health Research (NIHR) Biomedical Research Centre, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Børge G Nordestgaard
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Sune F Nielsen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Maren Weischer
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Stig E Bojesen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Martin Andreas Røder
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Peter Iversen
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | | | - Leire Moya
- Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | - Lisa Horvath
- Chris O'Brien Lifehouse (COBLH), Camperdown, Sydney, New South Wales, Australia
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Judith A Clements
- Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | - Wayne Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Gail P Risbridger
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Prostate Cancer Translational Research Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Markus Aly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, and Department of Urology, Karolinska University Hospital, Solna, Stockholm, Sweden
- Department of Urology, Karolinska University Hospital, Stockholm, Sweden
| | - Robert Szulkin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- SDS Life Science, Danderyd, Sweden
| | - Martin Eklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Tobias Nordström
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Sciences at Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Nora Pashayan
- Department of Applied Health Research, University College London, London, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Cambridge, UK
- Department of Applied Health Research, University College London, London, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Cambridge, UK
| | | | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Tim J Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Hui-Yi Lin
- School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sara Lindstrom
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - David J Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Kathryn L Penney
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, MA, USA
| | - Constance Turman
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ian M Thompson
- CHRISTUS Santa Rosa Hospital - Medical Center, San Antonio, TX, USA
| | - Robert J Hamilton
- Department of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Surgery (Urology), University of Toronto, Toronto, Ontario, Canada
| | - Neil E Fleshner
- Department of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Antonio Finelli
- Division of Urology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Marie-Élise Parent
- Epidemiology and Biostatistics Unit, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
- Department of Social and Preventive Medicine, School of Public Health, University of Montreal, Montreal, Quebec, Canada
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Milan S Geybels
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Meir Stampfer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, MA, USA
| | - Alicja Wolk
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Niclas Håkansson
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Karina Dalsgaard Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Michael Borre
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- International Epidemiology Institute, Rockville, MD, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Edward D Yeboah
- University of Ghana Medical School, Accra, Ghana
- Korle Bu Teaching Hospital, Accra, Ghana
| | - James E Mensah
- University of Ghana Medical School, Accra, Ghana
- Korle Bu Teaching Hospital, Accra, Ghana
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | | | - Ninghan Feng
- Wuxi Second Hospital, Nanjing Medical University, Wuxi, China
| | - Xueying Mao
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Yudong Wu
- Department of Urology, First Affiliated Hospital, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Shan-Chao Zhao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zan Sun
- The People's Hospital of Liaoning Province, The People's Hospital of China Medical University, Shenyang, China
| | - Stephen N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Shannon K McDonnell
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Daniel J Schaid
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Catharine M L West
- Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Radiotherapy Related Research, The Christie Hospital NHS Foundation Trust, Manchester, UK
| | - Neil Burnet
- Division of Cancer Sciences, University of Manchester, Manchester Cancer Research Centre, Manchester Academic Health Science Centre, and The Christie NHS Foundation Trust, Manchester, UK
| | - Gill Barnett
- University of Cambridge Department of Oncology, Oncology Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | - Adam S Kibel
- Division of Urologic Surgery, Brigham and Womens Hospital, Boston, MA, USA
| | | | | | | | - Florence Menegaux
- Exposome and Heredity, CESP (UMR 1018), Paris-Saclay Medical School, Paris-Saclay University, Inserm, Gustave Roussy, Villejuif, France
| | - Thérèse Truong
- Exposome and Heredity, CESP (UMR 1018), Paris-Saclay Medical School, Paris-Saclay University, Inserm, Gustave Roussy, Villejuif, France
| | - Yves Akoli Koudou
- CESP (UMR 1018), Paris-Saclay Medical School, Paris-Saclay University, Inserm, Villejuif, France
| | - Esther M John
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Lovise Maehle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, UK
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Mariana C Stern
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Ana Vega
- Fundación Pública Galega Medicina Xenómica, Santiago De Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago De Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Antonio Gómez-Caamaño
- Department of Radiation Oncology, Complexo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - Laura Fachal
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
- Fundación Pública Galega Medicina Xenómica, Santiago De Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago De Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Barry S Rosenstein
- Department of Radiation Oncology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah L Kerns
- Department of Radiation Oncology, University of Rochester Medical Center, Rochester, NY, USA
| | - Harry Ostrer
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Paula Paulo
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Andreia Brandão
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | | | | | - Jeannette T Bensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth T H Fontham
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - James Mohler
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Manolis Kogevinas
- ISGlobal, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Javier Llorca
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- University of Cantabria-IDIVAL, Santander, Spain
| | - Gemma Castaño-Vinyals
- ISGlobal, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Lisa Cannon-Albright
- Division of Epidemiology, Department of Internal Medicine, 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
| | - Craig C Teerlink
- Division of Epidemiology, Department of Internal Medicine, 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
| | - Chad D Huff
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Sara S Strom
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Luc Multigner
- University of Rennes, Inserm, EHESP, Irset (Research Institute for Environmental and Occupational Health), Rennes, France
| | - Pascal Blanchet
- CHU de Pointe-à-Pitre, University of the French Antilles, University of Rennes, Inserm, EHESP, Irset (Research Institute for Environmental and Occupational Health), Pointe-à-Pitre, France
| | - Laurent Brureau
- CHU de Pointe-à-Pitre, University of the French Antilles, University of Rennes, Inserm, EHESP, Irset (Research Institute for Environmental and Occupational Health), Pointe-à-Pitre, France
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia, Bulgaria
| | - Chavdar Slavov
- Department of Urology and Alexandrovska University Hospital, Medical University of Sofia, Sofia, Bulgaria
| | - Vanio Mitev
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia, Bulgaria
| | - Robin J Leach
- Department of Urology, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Brandi Weaver
- Department of Urology, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Hermann Brenner
- 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
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Katarina Cuk
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Kai-Uwe Saum
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eric A Klein
- Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
- Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ann W Hsing
- Department of Medicine and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Rick A Kittles
- Division of Health Equities, Department of Population Sciences, City of Hope, Duarte, CA, USA
| | - Adam B Murphy
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - Christopher J Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Jeri Kim
- Department of Genitourinary Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - William B Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Anselm J M Hennis
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
- Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies, Bridgetown, Barbados
| | - John Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hardev Pandha
- Faculty of Health and Medical Sciences, The University of Surrey, Guildford, UK
| | - Agnieszka Michael
- Faculty of Health and Medical Sciences, The University of Surrey, Guildford, UK
| | - Kim De Ruyck
- Department of Basic Medical Sciences, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Gert De Meerleer
- Department of Radiotherapy, Ghent University Hospital, Gent, Belgium
| | - Piet Ost
- Department of Radiotherapy, Ghent University Hospital, Gent, Belgium
| | - Jianfeng Xu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Azad Razack
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jasmine Lim
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Soo-Hwang Teo
- Cancer Research Malaysia (CRM), Outpatient Centre, Subang Jaya Medical Centre, Subang Jaya, Malaysia
| | - Lisa F Newcomb
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Daniel W Lin
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Jay H Fowke
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | - Marija Gamulin
- Department of Oncology, University Hospital Centre Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tomislav Kulis
- Department of Urology, University Hospital Center Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Nawaid Usmani
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Sandeep Singhal
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Matthew Parliament
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Steven Joniau
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Thomas Van den Broeck
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, Servicio Galego de Saúde, SERGAS, Santiago de Compostela, Spain
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Jose Esteban Castelao
- Genetic Oncology Unit, CHUVI Hospital, Complexo Hospitalario Universitario de Vigo, Instituto de Investigación Biomédica Galicia Sur (IISGS), Vigo, Spain
| | - Maria Elena Martinez
- Moores Cancer Center, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Samantha Larkin
- The University of Southampton, Southampton General Hospital, Southampton, UK
| | - Paul A Townsend
- Faculty of Health and Medical Sciences, The University of Surrey, Guildford, UK
- Division of Cancer Sciences, Manchester Cancer Research Centre, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Research Centre, Health Innovation Manchester, University of Manchester, Manchester, UK
| | - Claire Aukim-Hastie
- Faculty of Health and Medical Sciences, The University of Surrey, Guildford, UK
| | - William S Bush
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dana C Crawford
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Shiv Srivastava
- Center for Prostate Disease Research, Uniformed Services University, Bethesda, MD, USA
| | - Jennifer C Cullen
- Center for Prostate Disease Research, Uniformed Services University, Bethesda, MD, USA
| | - Gyorgy Petrovics
- Center for Prostate Disease Research, Uniformed Services University, Bethesda, MD, USA
| | - Graham Casey
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Monique J Roobol
- Department of Urology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ron H N van Schaik
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jennifer J Hu
- The University of Miami School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN, USA
| | - Rohit Varma
- Southern California Eye Institute, CHA Hollywood Presbyterian Medical Center, Los Angeles, CA, USA
| | - Roberta McKean-Cowdin
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Mina Torres
- Southern California Eye Institute, CHA Hollywood Presbyterian Medical Center, Los Angeles, CA, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente, Northern California, Oakland, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael B Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | | | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA.
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20
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Darst BF, Wan P, Sheng X, Bensen JT, Ingles SA, Rybicki BA, Nemesure B, John EM, Fowke JH, Stevens VL, Berndt SI, Huff CD, Strom SS, Park JY, Zheng W, Ostrander EA, Walsh PC, Srivastava S, Carpten J, Sellers TA, Yamoah K, Murphy AB, Sanderson M, Crawford DC, Gapstur SM, Bush WS, Aldrich MC, Cussenot O, Yeager M, Petrovics G, Cullen J, Neslund-Dudas C, Kittles RA, Xu J, Stern MC, Kote-Jarai Z, Govindasami K, Chokkalingam AP, Multigner L, Parent ME, Menegaux F, Cancel-Tassin G, Kibel AS, Klein EA, Goodman PJ, Drake BF, Hu JJ, Clark PE, Blanchet P, Casey G, Hennis AJM, Lubwama A, Thompson IM, Leach R, Gundell SM, Pooler L, Xia L, Mohler JL, Fontham ETH, Smith GJ, Taylor JA, Eeles RA, Brureau L, Chanock SJ, Watya S, Stanford JL, Mandal D, Isaacs WB, Cooney K, Blot WJ, Conti DV, Haiman CA. A Germline Variant at 8q24 Contributes to Familial Clustering of Prostate Cancer in Men of African Ancestry. Eur Urol 2020; 78:316-320. [PMID: 32409115 PMCID: PMC7805560 DOI: 10.1016/j.eururo.2020.04.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 01/24/2020] [Accepted: 04/23/2020] [Indexed: 01/15/2023]
Abstract
Although men of African ancestry have a high risk of prostate cancer (PCa), no genes or mutations have been identified that contribute to familial clustering of PCa in this population. We investigated whether the African ancestry-specific PCa risk variant at 8q24, rs72725854, is enriched in men with a PCa family history in 9052 cases, 143 cases from high-risk families, and 8595 controls of African ancestry. We found the risk allele to be significantly associated with earlier age at diagnosis, more aggressive disease, and enriched in men with a PCa family history (32% of high-risk familial cases carried the variant vs 23% of cases without a family history and 12% of controls). For cases with two or more first-degree relatives with PCa who had at least one family member diagnosed at age <60 yr, the odds ratios for TA heterozygotes and TT homozygotes were 3.92 (95% confidence interval [CI] = 2.13-7.22) and 33.41 (95% CI = 10.86-102.84), respectively. Among men with a PCa family history, the absolute risk by age 60 yr reached 21% (95% CI = 17-25%) for TA heterozygotes and 38% (95% CI = 13-65%) for TT homozygotes. We estimate that in men of African ancestry, rs72725854 accounts for 32% of the total familial risk explained by all known PCa risk variants. PATIENT SUMMARY: We found that rs72725854, an African ancestry-specific risk variant, is more common in men with a family history of prostate cancer and in those diagnosed with prostate cancer at younger ages. Men of African ancestry may benefit from the knowledge of their carrier status for this genetic risk variant to guide decisions about prostate cancer screening.
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Affiliation(s)
- Burcu F Darst
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Peggy Wan
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xin Sheng
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jeannette T Bensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sue A Ingles
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | - Barbara Nemesure
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Esther M John
- Department of Epidemiology and Population Health and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jay H Fowke
- Division of Epidemiology, Department of Preventive Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Victoria L Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Sara S Strom
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Patrick C Walsh
- The James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - Shiv Srivastava
- Department of Surgery, Center for Prostate Disease Research, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - John Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Kosj Yamoah
- Department of Radiation Oncology and Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Adam B Murphy
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN, USA
| | - Dana C Crawford
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - William S Bush
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Olivier Cussenot
- CeRePP and Sorbonne Universite, GRC n° 5, AP-HP, Tenon Hospital, Paris, France
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Gyorgy Petrovics
- Department of Surgery, Center for Prostate Disease Research, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jennifer Cullen
- Department of Surgery, Center for Prostate Disease Research, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | - Rick A Kittles
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Mariana C Stern
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | | | - Koveela Govindasami
- Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Sutton, London, UK
| | | | | | - Marie-Elise Parent
- INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, University of Quebec, Laval, Quebec, Canada
| | - Florence Menegaux
- INSERM, Center for Research in Epidemiology and Population Health, Team Cancer-Environment, Université Paris-Saclay, Université Paris-Sud, Villejuif, France
| | | | - Adam S Kibel
- Division of Urology, Brigham and Women's Hospital/Dana-Farber Cancer Institute, Boston, MA, USA; Washington University, St. Louis, MO, USA
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bettina F Drake
- Department of Surgery, Division of Public Health Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Jennifer J Hu
- Sylvester Comprehensive Cancer Center and Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Peter E Clark
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Pascal Blanchet
- Inserm U1085-IRSET, Rennes, France; University Hospital of Pointe-à-Pitre, Guadeloupe, FWI, France; French West Indies University, Pointe-à-Pitre, Guadeloupe, FWI, France
| | - Graham Casey
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Anselm J M Hennis
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA; Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies, Bridgetown, Barbados
| | - Alexander Lubwama
- School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - Ian M Thompson
- Department of Urology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Robin Leach
- Department of Urology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Susan M Gundell
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Loreall Pooler
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lucy Xia
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - James L Mohler
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Elizabeth T H Fontham
- School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Gary J Smith
- Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jack A Taylor
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA; Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Rosalind A Eeles
- The Institute of Cancer Research, Sutton, London, UK; Royal Marsden NHS Foundation Trust, London, UK
| | - Laurent Brureau
- Inserm U1085-IRSET, Rennes, France; University Hospital of Pointe-à-Pitre, Guadeloupe, FWI, France; French West Indies University, Pointe-à-Pitre, Guadeloupe, FWI, France
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Stephen Watya
- School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda; Uro Care, Kampala, Uganda
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Diptasri Mandal
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - William B Isaacs
- The James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - Kathleen Cooney
- Department of Medicine, Duke University of Medicine, Durham, NC, USA
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David V Conti
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
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21
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Darst BF, Bensen JT, Ingles SA, Rybicki BA, Nemesure B, John EM, Fowke JH, Stevens VL, Berndt SI, Huff CD, Park JY, Zheng W, Ostrander EA, Srivastava S, Carpten J, Sellers TA, Sanderson M, Crawford DC, Cussenot O, Cullen J, Kittles RA, Xu J, Kote-Jarai Z, Multigner L, Parent ME, Menegaux F, Cancel-Tassin G, Kibel AS, Klein EA, Goodman PJ, Hu JJ, Casey G, Hennis AJ, Thompson IM, Leach R, Mohler JL, Fontham ET, Smith GJ, Taylor JA, Eeles RA, Brureau L, Chanock SJ, Watya S, Stanford JL, Mandal D, Isaacs WB, Cooney KA, Blot WJ, Conti DV, Haiman CA. Abstract 3517: A germline variant at 8q24 contributes to familial clustering of prostate cancer in men of African ancestry. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3517] [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
Germline variation at 8q24 is the strongest risk factor for prostate cancer (PCa) across all racial and ethnic populations. While most 8q24 associations have been observed across populations, rs72725854 [T risk allele frequency ~6%] is only found in men of African ancestry and is the strongest known genome-wide association signal for PCa in this population. We investigated whether the T allele of rs72725854 is associated with PCa family history and age at diagnosis, characteristics known to have a strong genetic component. Analyses were performed using a sample of 9,052 cases and 8,595 controls from the African Ancestry Prostate Cancer (AAPC) GWAS Consortium and the ELLIPSE/PRACTICAL OncoArray Consortium. Participants were unselected for PCa family history. Among cases, 23.7% carried at least one copy of the T allele versus 11.6% of controls. The OR was 2.29 (95% CI=2.10–2.49) for TA heterozygotes and 5.04 (95% CI=3.36–7.55) for TT homozygotes. The percentage of cases carrying the T allele was significantly greater for men with a PCa family history (27.4% vs. 22.7% without a family history, p=0.002) and for men diagnosed <60 (28.2% vs. 21.6% if over ≥60, p=0.002). The mean age at diagnosis for men with the TT genotype was 61.1 years (sd=8.7), compared to 62.7 (sd=9.1) for TA heterozygotes and 64.3 (sd=8.9) for AA homozygotes (p=5.7E-14). Carrier frequency was highest among men with both a positive family history and an early diagnosis (30.8%). The T allele was also over-represented in cases with more advanced PCa, with carrier frequencies ranging from 26% for lethal PCa (metastatic disease, PSA>100 ng/ml or death from PCa), 25.4% for high-risk disease (stage T3/T4, Gleason 8-10, or PSA=20-100 ng/ml), 24.6% for intermediate-risk disease (Gleason=7, stage T1/T2, and PSA=10-20 ng/ml), and 21.4% for low-risk disease (Gleason<7, stage T1/T2, and PSA<10 ng/ml) (p=0.026). We also examined whether the risk allele is over-represented in 144 men from PCa families, with multiple first- and/or second-degree relatives with PCa or men diagnosed with PCa ≤55 years old. Among affected probands, 32.7% carried the risk allele, with 3.5% being homozygous carriers. The OR for TA heterozygotes and TT homozygotes was 3.41 (95% CI=2.33–4.98) and 11.06 (95% CI=3.92–31.18), respectively. Among men without a family history, the absolute risk for PCa by age 60 for non-risk allele carriers was 4.3%, compared to 9.0% and 15.6% for TA heterozygotes and TT homozygotes, respectively. Absolute risks by age 60 were higher among men with a family history of prostate cancer, reaching 9.0% for non-risk allele carriers, compared to 20.8% and 37.7% for TA heterozygotes and TT homozygotes, respectively. Given the high PCa risk conveyed by rs72725854 and the greater frequency of the allele in men with more aggressive and lethal disease, carriers of the risk allele would benefit from earlier and more regular PSA screening.
Citation Format: Burcu F. Darst, Jeannette T. Bensen, Sue A. Ingles, Benjamin A. Rybicki, Barbara Nemesure, Esther M. John, Jay H. Fowke, Victoria L. Stevens, Sonja I. Berndt, Chad D. Huff, Jong Y. Park, Wei Zheng, Elaine A. Ostrander, Shiv Srivastava, John Carpten, Thomas A. Sellers, Maureen Sanderson, Dana C. Crawford, Olivier Cussenot, Jennifer Cullen, Rick A. Kittles, Jianfeng Xu, Zsofia Kote-Jarai, Luc Multigner, Marie-Elise Parent, Florence Menegaux, Geraldine Cancel-Tassin, Adam S. Kibel, Eric A. Klein, Phyllis J. Goodman, Jennifer J. Hu, Graham Casey, Anselm J. Hennis, Ian M. Thompson, Robin Leach, James L. Mohler, Elizabeth T. Fontham, Gary J. Smith, Jack A. Taylor, Rosalind A. Eeles, Laurent Brureau, Stephen J. Chanock, Stephen Watya, Janet L. Stanford, Diptasri Mandal, William B. Isaacs, Kathleen A. Cooney, William J. Blot, David V. Conti, Christopher A. Haiman. A germline variant at 8q24 contributes to familial clustering of prostate cancer in men of African ancestry [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3517.
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Affiliation(s)
| | | | | | | | | | - Esther M. John
- 5California Prevention Institute of California, Fremont, CA
| | - Jay H. Fowke
- 6Vanderbilt University Medical Center, Nashville, TN
| | | | - Sonja I. Berndt
- 8National Cancer Institute, National Institute of Health, Bethesda, MD
| | - Chad D. Huff
- 9University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Jong Y. Park
- 10Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Wei Zheng
- 11Vanderbilt University School of Medicine, Nashville, TN
| | - Elaine A. Ostrander
- 12National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Shiv Srivastava
- 13Uniformed Services University of the Health Sciences, Bethesda, MD
| | - John Carpten
- 1University of Southern California, Los Angeles, CA
| | | | | | | | | | - Jennifer Cullen
- 13Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Rick A. Kittles
- 17University of Arizona College of Medicine and University of Arizona Cancer Center, Tucson, AZ
| | - Jianfeng Xu
- 18NorthShore University HealthSystem, Evanston, IL
| | | | | | | | - Florence Menegaux
- 22Université Paris-Saclay, Université Paris-Sud, CESP (Center for Research in Epidemiology and Population Health), Inserm, Team Cancer-Environment, Villejuif, France
| | | | - Adam S. Kibel
- 23Brigham and Women's Hospital/Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Jennifer J. Hu
- 26University of Miami Miller School of Medicine, Miami, FL
| | | | | | - Ian M. Thompson
- 28University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Robin Leach
- 29University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - James L. Mohler
- 2University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Jack A. Taylor
- 32National Institute of Environmental Health Sciences, Research Triangle Park, NC
| | | | | | | | - Stephen Watya
- 35Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Diptasri Mandal
- 30Louisiana State University Health Sciences Center, New Orleans, LA
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Hu F, Yu Y, Chen JS, Hu H, Scheet P, Huff CD. Integrated case-control and somatic-germline interaction analyses of soft-tissue sarcoma. J Med Genet 2020; 58:145-153. [PMID: 32447321 DOI: 10.1136/jmedgenet-2019-106814] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/02/2020] [Accepted: 04/05/2020] [Indexed: 11/04/2022]
Abstract
PURPOSE The contribution of rare genetic variation in the development of soft-tissue sarcoma (STS) remains underexplored. To address this gap, we conducted a whole-exome case-control and somatic-germline interaction study to identify and characterise STS susceptible genes. METHODS The study involved 219 STS cases from The Cancer Genome Atlas and 3507 controls. All cases and controls were matched genetically onEuropean ancestry based on the 1000 Genomes project. Cross-platform technological stratification was performed with XPAT and gene-based association tests with VAAST 2. RESULTS NF1 exhibited the strongest genome-wide signal across the six subtypes, with p=1×10-5. We also observed nominally significant association signals for three additional genes of interest, TP53 (p=0.0025), RB1 (p=0.0281), and MSH2 (p=0.0085). BAG1, which has not previously been implicated in STS, exhibited the strongest genome-wide signal after NF1, with p=6×10-5. The association signals for NF1 and MSH2 were driven primarily by truncating variants, with ORs of 39 (95% CI: 7.1 to 220) for NF1 and 33 (95% CI: 2.4 to 460) for MSH2. In contrast, the association signals for RB1 and BAG1 were driven primarily by predicted damaging missense variants, with estimated ORs of 12 (95% CI: 2.4 to 59) for RB1 and 20 (95% CI: 1.4 to 300) for BAG1. CONCLUSIONS Our results confirm that pathogenic variants in NF1, RB1 and TP53 confer large increases in the risk of developing multiple STS subtypes, provide support for the role of MSH2 in STS susceptibility and identify BAG1 as a novel candidate STS risk gene.
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Affiliation(s)
- Fulan Hu
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, China.,Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jiun-Sheng Chen
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hao Hu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Paul Scheet
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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23
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Jakubek YA, Chang K, Sivakumar S, Yu Y, Giordano MR, Fowler J, Huff CD, Kadara H, Vilar E, Scheet P. Large-scale analysis of acquired chromosomal alterations in non-tumor samples from patients with cancer. Nat Biotechnol 2020; 38:90-96. [PMID: 31685958 PMCID: PMC8082517 DOI: 10.1038/s41587-019-0297-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 01/28/2019] [Accepted: 09/25/2019] [Indexed: 01/21/2023]
Abstract
Mosaicism, the presence of subpopulations of cells bearing somatic mutations, is associated with disease and aging and has been detected in diverse tissues, including apparently normal cells adjacent to tumors. To analyze mosaicism on a large scale, we surveyed haplotype-specific somatic copy number alterations (sCNAs) in 1,708 normal-appearing adjacent-to-tumor (NAT) tissue samples from 27 cancer sites and in 7,149 blood samples from The Cancer Genome Atlas. We find substantial variation across tissues in the rate, burden and types of sCNAs, including those spanning entire chromosome arms. We document matching sCNAs in the NAT tissue and the adjacent tumor, suggesting a shared clonal origin, as well as instances in which both NAT tissue and tumor tissue harbor a gain of the same oncogene arising in parallel from distinct parental haplotypes. These results shed light on pan-tissue mutations characteristic of field cancerization, the presence of oncogenic processes adjacent to cancer cells.
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Affiliation(s)
- Y A Jakubek
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - K Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - S Sivakumar
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Y Yu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M R Giordano
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Fowler
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - C D Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - H Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - E Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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24
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Voskanian A, Katsonis P, Lichtarge O, Pejaver V, Radivojac P, Mooney SD, Capriotti E, Bromberg Y, Wang Y, Miller M, Martelli PL, Savojardo C, Babbi G, Casadio R, Cao Y, Sun Y, Shen Y, Garg A, Pal D, Yu Y, Huff CD, Tavtigian SV, Young E, Neuhausen SL, Ziv E, Pal LR, Andreoletti G, Brenner S, Kann MG. Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer. Hum Mutat 2019; 40:1612-1622. [PMID: 31241222 PMCID: PMC6744287 DOI: 10.1002/humu.23849] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 02/25/2019] [Revised: 05/23/2019] [Accepted: 06/21/2019] [Indexed: 01/22/2023]
Abstract
The availability of disease-specific genomic data is critical for developing new computational methods that predict the pathogenicity of human variants and advance the field of precision medicine. However, the lack of gold standards to properly train and benchmark such methods is one of the greatest challenges in the field. In response to this challenge, the scientific community is invited to participate in the Critical Assessment for Genome Interpretation (CAGI), where unpublished disease variants are available for classification by in silico methods. As part of the CAGI-5 challenge, we evaluated the performance of 18 submissions and three additional methods in predicting the pathogenicity of single nucleotide variants (SNVs) in checkpoint kinase 2 (CHEK2) for cases of breast cancer in Hispanic females. As part of the assessment, the efficacy of the analysis method and the setup of the challenge were also considered. The results indicated that though the challenge could benefit from additional participant data, the combined generalized linear model analysis and odds of pathogenicity analysis provided a framework to evaluate the methods submitted for SNV pathogenicity identification and for comparison to other available methods. The outcome of this challenge and the approaches used can help guide further advancements in identifying SNV-disease relationships.
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Affiliation(s)
- Alin Voskanian
- Department of Biological Sciences, University of Maryland, Baltimore County, MD, U.S.A
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, U.S.A
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, U.S.A
- Department of Pharmacology, Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Vikas Pejaver
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, U.S.A
- The eScience Institute, University of Washington, Seattle, Washington, U.S.A
| | - Predrag Radivojac
- Khoury College of Computer and Information Sciences, Northeastern University, Boston, Massachusetts, U.S.A
| | - Sean D. Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, U.S.A
| | - Emidio Capriotti
- BioFolD Unit, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, U.S.A
- Department of Genetics, Rutgers University, New Brunswick, New Jersey, U.S.A
- Technical University of Munich Institute for Advanced Study, (TUM-IAS), Lichtenbergstr. 2a, 85748 Garching/Munich, Germany
| | - Yanran Wang
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, U.S.A
| | - Max Miller
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, U.S.A
| | - Pier Luigi Martelli
- Biocomputing Group, BiGeA/Giorgio Prodi Interdepartmental Center for Cancer Research, University of Bologna, Via F. Selmi 3, Bologna, 40126, Italy
| | - Castrense Savojardo
- Biocomputing Group, BiGeA/Giorgio Prodi Interdepartmental Center for Cancer Research, University of Bologna, Via F. Selmi 3, Bologna, 40126, Italy
| | - Giulia Babbi
- Biocomputing Group, BiGeA/Giorgio Prodi Interdepartmental Center for Cancer Research, University of Bologna, Via F. Selmi 3, Bologna, 40126, Italy
| | - Rita Casadio
- Biocomputing Group, BiGeA/Giorgio Prodi Interdepartmental Center for Cancer Research, University of Bologna, Via F. Selmi 3, Bologna, 40126, Italy
| | - Yue Cao
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843-3128, U.S.A
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843-3128, U.S.A
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843-3128, U.S.A
| | - Aditi Garg
- Department of Computational and Data Sciences Indian Institute of Science, Bengaluru 560 012, India
| | - Debnath Pal
- Department of Computational and Data Sciences Indian Institute of Science, Bengaluru 560 012, India
| | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, U.S.A
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, U.S.A
| | - Sean V. Tavtigian
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84132, U.S.A
| | - Erin Young
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84132, U.S.A
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010 U.S.A
| | - 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,U.S.A
| | - Lipika R. Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Gaia Andreoletti
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Steven Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Maricel G. Kann
- Department of Biological Sciences, University of Maryland, Baltimore County, MD, U.S.A
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25
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Lupo PJ, Schraw JM, Desrosiers TA, Nembhard WN, Langlois PH, Canfield MA, Copeland G, Meyer RE, Brown AL, Chambers TM, Sok P, Danysh HE, Carozza SE, Sisoudiya SD, Hilsenbeck SG, Janitz AE, Oster ME, Scheuerle AE, Schiffman JD, Luo C, Mian A, Mueller BA, Huff CD, Rasmussen SA, Scheurer ME, Plon SE. Association Between Birth Defects and Cancer Risk Among Children and Adolescents in a Population-Based Assessment of 10 Million Live Births. JAMA Oncol 2019; 5:1150-1158. [PMID: 31219523 DOI: 10.1001/jamaoncol.2019.1215] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance Birth defects affect approximately 1 in 33 children. Some birth defects are known to be strongly associated with childhood cancer (eg, trisomy 21 and acute leukemia). However, comprehensive evaluations of childhood cancer risk in those with birth defects have been limited in previous studies by insufficient sample sizes. Objectives To identify specific birth defect-childhood cancer (BD-CC) associations and characterize cancer risk in children by increasing number of nonchromosomal birth defects. Design, Setting, and Participants This multistate, population-based registry linkage study pooled statewide data on births, birth defects, and cancer from Texas, Arkansas, Michigan, and North Carolina on 10 181 074 children born from January 1, 1992, to December 31, 2013. Children were followed up to 18 years of age for a diagnosis of cancer. Data were retrieved between September 26, 2016, and September 21, 2017, and data analysis was performed from September 2, 2017, to March 21, 2019. Exposures Birth defects diagnoses (chromosomal anomalies and nonchromosomal birth defects) recorded by statewide, population-based birth defects registries. Main Outcomes and Measures Cancer diagnosis before age 18 years, as recorded in state cancer registries. Cox regression models were used to generate hazard ratios (HRs) and 95% CIs to evaluate BD-CC associations and the association between number of nonchromosomal defects and cancer risk. Results Compared with children without any birth defects, children with chromosomal anomalies were 11.6 (95% CI, 10.4-12.9) times more likely to be diagnosed with cancer, whereas children with nonchromosomal birth defects were 2.5 (95% CI, 2.4-2.6) times more likely to be diagnosed with cancer before 18 years of age. An increasing number of nonchromosomal birth defects was associated with a corresponding increase in the risk of cancer. Children with 4 or more major birth defects were 5.9 (95% CI, 5.3-6.4) times more likely to be diagnosed with cancer compared with those without a birth defect. In the analysis of 72 specific BD-CC patterns, 40 HRs were statistically significant (adjusted P < .05) after accounting for multiple comparisons. Cancers most frequently associated with nonchromosomal defects were hepatoblastoma and neuroblastoma. Conclusions and Relevance Several significant and novel associations were observed between specific birth defects and cancers. Among children with nonchromosomal birth defects, the number of major birth defects diagnosed was significantly and directly associated with cancer risk. These findings could inform clinical treatment for children with birth defects and may elucidate mechanisms that lead to these complex outcomes.
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Affiliation(s)
- Philip J Lupo
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Cancer Center, Texas Children's Hospital, Houston
| | - Jeremy M Schraw
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | | | - Wendy N Nembhard
- Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock.,Arkansas Children's Research Institute, Little Rock
| | - Peter H Langlois
- Birth Defects Epidemiology and Surveillance Branch,Texas Department of State Health Services, Austin
| | - Mark A Canfield
- Birth Defects Epidemiology and Surveillance Branch,Texas Department of State Health Services, Austin
| | - Glenn Copeland
- Division for Vital Records and Health Statistics, Michigan Department of Health and Human Services, Lansing, Michigan
| | - Robert E Meyer
- Department of Maternal and Child Health, University of North Carolina at Chapel Hill
| | - Austin L Brown
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Cancer Center, Texas Children's Hospital, Houston
| | - Tiffany M Chambers
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Cancer Center, Texas Children's Hospital, Houston
| | - Pagna Sok
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Cancer Center, Texas Children's Hospital, Houston
| | - Heather E Danysh
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Cancer Center, Texas Children's Hospital, Houston
| | - Susan E Carozza
- School of Biological and Population Health Sciences, Oregon State University, Corvallis
| | - Saumya D Sisoudiya
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Amanda E Janitz
- Department of Biostatistics and Epidemiology, Hudson College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City
| | - Matthew E Oster
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Angela E Scheuerle
- Birth Defects Epidemiology and Surveillance Branch,Texas Department of State Health Services, Austin.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas
| | - Joshua D Schiffman
- Division of Hematology and Oncology, Department of Pediatrics, Huntsman Cancer Institute, University of Utah, Salt Lake City
| | - Chunqiao Luo
- Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock
| | - Amir Mian
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock
| | - Beth A Mueller
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Chad D Huff
- Department of Epidemiology, MD Anderson Cancer Center, Houston, Texas
| | - Sonja A Rasmussen
- Department of Pediatrics, University of Florida College of Medicine Gainsville.,Department of Epidemiology, University of Florida College of Medicine and College of Public Health and Health Professions, Gainesville
| | - Michael E Scheurer
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Cancer Center, Texas Children's Hospital, Houston
| | - Sharon E Plon
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Cancer Center, Texas Children's Hospital, Houston.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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26
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Petty LE, Highland HM, Gamazon ER, Hu H, Karhade M, Chen HH, de Vries PS, Grove ML, Aguilar D, Bell GI, Huff CD, Hanis CL, Doddapaneni H, Munzy DM, Gibbs RA, Ma J, Parra EJ, Cruz M, Valladares-Salgado A, Arking DE, Barbeira A, Im HK, Morrison AC, Boerwinkle E, Below JE. Functionally oriented analysis of cardiometabolic traits in a trans-ethnic sample. Hum Mol Genet 2019; 28:1212-1224. [PMID: 30624610 PMCID: PMC6423424 DOI: 10.1093/hmg/ddy435] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 11/13/2018] [Accepted: 11/20/2018] [Indexed: 01/02/2023] Open
Abstract
Interpretation of genetic association results is difficult because signals often lack biological context. To generate hypotheses of the functional genetic etiology of complex cardiometabolic traits, we estimated the genetically determined component of gene expression from common variants using PrediXcan (1) and determined genes with differential predicted expression by trait. PrediXcan imputes tissue-specific expression levels from genetic variation using variant-level effect on gene expression in transcriptome data. To explore the value of imputed genetically regulated gene expression (GReX) models across different ancestral populations, we evaluated imputed expression levels for predictive accuracy genome-wide in RNA sequence data in samples drawn from European-ancestry and African-ancestry populations and identified substantial predictive power using European-derived models in a non-European target population. We then tested the association of GReX on 15 cardiometabolic traits including blood lipid levels, body mass index, height, blood pressure, fasting glucose and insulin, RR interval, fibrinogen level, factor VII level and white blood cell and platelet counts in 15 755 individuals across three ancestry groups, resulting in 20 novel gene-phenotype associations reaching experiment-wide significance across ancestries. In addition, we identified 18 significant novel gene-phenotype associations in our ancestry-specific analyses. Top associations were assessed for additional support via query of S-PrediXcan (2) results derived from publicly available genome-wide association studies summary data. Collectively, these findings illustrate the utility of transcriptome-based imputation models for discovery of cardiometabolic effect genes in a diverse dataset.
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Affiliation(s)
- Lauren E Petty
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Heather M Highland
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Eric R Gamazon
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Clare Hall, University of Cambridge, Cambridge, UK
| | - Hao Hu
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | - Mandar Karhade
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hung-Hsin Chen
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Paul S de Vries
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Megan L Grove
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - David Aguilar
- Department of Cardiology, Baylor College of Medicine Houston, TX, USA
| | - Graeme I Bell
- Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Chad D Huff
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | - Craig L Hanis
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Donna M Munzy
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jianzhong Ma
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Miguel Cruz
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, IMSS, Mexico City, Mexico
| | - Adan Valladares-Salgado
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, IMSS, Mexico City, Mexico
| | - Dan E Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alvaro Barbeira
- Section of Genetic Medicine, Department of Medicine, University of Chicago, IL, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, IL, USA
| | - Alanna C Morrison
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
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27
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Williams LB, Javed A, Sabri A, Morgan DJ, Huff CD, Grigg JR, Heng XT, Khng AJ, Hollink IHIM, Morrison MA, Owen LA, Anderson K, Kinard K, Greenlees R, Novacic D, Nida Sen H, Zein WM, Rodgers GM, Vitale AT, Haider NB, Hillmer AM, Ng PC, Shankaracharya, Cheng A, Zheng L, Gillies MC, van Slegtenhorst M, van Hagen PM, Missotten TOAR, Farley GL, Polo M, Malatack J, Curtin J, Martin F, Arbuckle S, Alexander SI, Chircop M, Davila S, Digre KB, Jamieson RV, DeAngelis MM. ALPK1 missense pathogenic variant in five families leads to ROSAH syndrome, an ocular multisystem autosomal dominant disorder. Genet Med 2019; 21:2103-2115. [PMID: 30967659 PMCID: PMC6752478 DOI: 10.1038/s41436-019-0476-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/25/2019] [Indexed: 01/07/2023] Open
Abstract
Purpose To identify the molecular cause in five unrelated families with a distinct autosomal dominant ocular systemic disorder we called ROSAH syndrome due to clinical features of retinal dystrophy, optic nerve edema, splenomegaly, anhidrosis, and migraine headache. Methods Independent discovery exome and genome sequencing in families 1, 2, and 3, and confirmation in families 4 and 5. Expression of wild-type messenger RNA and protein in human and mouse tissues and cell lines. Ciliary assays in fibroblasts from affected and unaffected family members. Results We found the heterozygous missense variant in the ɑ-kinase gene, ALPK1, (c.710C>T, [p.Thr237Met]), segregated with disease in all five families. All patients shared the ROSAH phenotype with additional low-grade ocular inflammation, pancytopenia, recurrent infections, and mild renal impairment in some. ALPK1 was notably expressed in retina, retinal pigment epithelium, and optic nerve, with immunofluorescence indicating localization to the basal body of the connecting cilium of the photoreceptors, and presence in the sweat glands. Immunocytofluorescence revealed expression at the centrioles and spindle poles during metaphase, and at the base of the primary cilium. Affected family member fibroblasts demonstrated defective ciliogenesis. Conclusion Heterozygosity for ALPK1, p.Thr237Met leads to ROSAH syndrome, an autosomal dominant ocular systemic disorder.
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Affiliation(s)
- Lloyd B Williams
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Asif Javed
- Genome Institute of Singapore, Singapore, Singapore.,School of Biomedical Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Amin Sabri
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Save Sight Institute, University of Sydney, Sydney, NSW, Australia
| | - Denise J Morgan
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Chad D Huff
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA.,Department of Epidemiology, Division of OVP, Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John R Grigg
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Save Sight Institute, University of Sydney, Sydney, NSW, Australia.,Discipline of Ophthalmology, University of Sydney, Sydney, NSW, Australia
| | | | | | | | - Margaux A Morrison
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Leah A Owen
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Krista Kinard
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Rebecca Greenlees
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Save Sight Institute, University of Sydney, Sydney, NSW, Australia
| | - Danica Novacic
- National Institutes of Health, National Human Genome Research Institute, Undiagnosed Diseases Network, Bethesda, MD, USA
| | - H Nida Sen
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wadih M Zein
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - George M Rodgers
- Department of Hematology, Utah Health Sciences Center, Salt Lake City, UT, USA
| | - Albert T Vitale
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Neena B Haider
- Department of Ophthalmology, Schepens Eye Research Institute/Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | | | - Pauline C Ng
- Genome Institute of Singapore, Singapore, Singapore
| | - Shankaracharya
- Department of Epidemiology, Division of OVP, Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anson Cheng
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Save Sight Institute, University of Sydney, Sydney, NSW, Australia
| | - Linda Zheng
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Save Sight Institute, University of Sydney, Sydney, NSW, Australia
| | - Mark C Gillies
- Discipline of Ophthalmology, University of Sydney, Sydney, NSW, Australia
| | | | | | | | | | - Michael Polo
- Drs. Farley, Polo and Ho, Colonial Heights, VA, USA
| | - James Malatack
- Nemours/Alfred I. DuPont Hospital for Children, Wilmington, DE, USA
| | - Julie Curtin
- Department of Haematology, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Frank Martin
- Department of Ophthalmology, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Susan Arbuckle
- Department of Pathology, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Stephen I Alexander
- Department of Nephrology, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Megan Chircop
- Cell Cycle Unit, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia
| | - Sonia Davila
- Genome Institute of Singapore, Singapore, Singapore
| | - Kathleen B Digre
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Robyn V Jamieson
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Save Sight Institute, University of Sydney, Sydney, NSW, Australia. .,Disciplines of Genomic Medicine, and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia. .,Department of Clinical Genetics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney Children's Hospitals Network, Sydney, NSW, Australia.
| | - Margaret M DeAngelis
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA. .,Department of Pharmacotherapy, College of Pharmacy, University of Utah, Salt Lake City, UT, USA. .,Department of Population Health Sciences, University of Utah School of Medicine, Salt Lake City, UT, USA.
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28
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Vickrey AI, Bruders R, Kronenberg Z, Mackey E, Bohlender RJ, Maclary ET, Maynez R, Osborne EJ, Johnson KP, Huff CD, Yandell M, Shapiro MD. Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon. eLife 2018; 7:e34803. [PMID: 30014848 PMCID: PMC6050045 DOI: 10.7554/elife.34803] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 06/05/2018] [Indexed: 12/17/2022] Open
Abstract
Birds and other vertebrates display stunning variation in pigmentation patterning, yet the genes controlling this diversity remain largely unknown. Rock pigeons (Columba livia) are fundamentally one of four color pattern phenotypes, in decreasing order of melanism: T-check, checker, bar (ancestral), or barless. Using whole-genome scans, we identified NDP as a candidate gene for this variation. Allele-specific expression differences in NDP indicate cis-regulatory divergence between ancestral and melanistic alleles. Sequence comparisons suggest that derived alleles originated in the speckled pigeon (Columba guinea), providing a striking example of introgression. In contrast, barless rock pigeons have an increased incidence of vision defects and, like human families with hereditary blindness, carry start-codon mutations in NDP. In summary, we find that both coding and regulatory variation in the same gene drives wing pattern diversity, and post-domestication introgression supplied potentially advantageous melanistic alleles to feral populations of this ubiquitous urban bird.
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Affiliation(s)
- Anna I Vickrey
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Rebecca Bruders
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Zev Kronenberg
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Emma Mackey
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Ryan J Bohlender
- Department of Epidemiology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Emily T Maclary
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Raquel Maynez
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Edward J Osborne
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research InstituteUniversity of Illinois Urbana-ChampaignChampaignUnited States
| | - Chad D Huff
- Department of Epidemiology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Mark Yandell
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Michael D Shapiro
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
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29
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Yu Y, Hu H, Bohlender RJ, Hu F, Chen JS, Holt C, Fowler J, Guthery SL, Scheet P, Hildebrandt MAT, Yandell M, Huff CD. XPAT: a toolkit to conduct cross-platform association studies with heterogeneous sequencing datasets. Nucleic Acids Res 2018; 46:e32. [PMID: 29294048 PMCID: PMC5888834 DOI: 10.1093/nar/gkx1280] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 07/06/2017] [Revised: 12/07/2017] [Accepted: 12/20/2017] [Indexed: 12/12/2022] Open
Abstract
High-throughput sequencing data are increasingly being made available to the research community for secondary analyses, providing new opportunities for large-scale association studies. However, heterogeneity in target capture and sequencing technologies often introduce strong technological stratification biases that overwhelm subtle signals of association in studies of complex traits. Here, we introduce the Cross-Platform Association Toolkit, XPAT, which provides a suite of tools designed to support and conduct large-scale association studies with heterogeneous sequencing datasets. XPAT includes tools to support cross-platform aware variant calling, quality control filtering, gene-based association testing and rare variant effect size estimation. To evaluate the performance of XPAT, we conducted case-control association studies for three diseases, including 783 breast cancer cases, 272 ovarian cancer cases, 205 Crohn disease cases and 3507 shared controls (including 1722 females) using sequencing data from multiple sources. XPAT greatly reduced Type I error inflation in the case-control analyses, while replicating many previously identified disease-gene associations. We also show that association tests conducted with XPAT using cross-platform data have comparable performance to tests using matched platform data. XPAT enables new association studies that combine existing sequencing datasets to identify genetic loci associated with common diseases and other complex traits.
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Affiliation(s)
- Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hao Hu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ryan J Bohlender
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fulan Hu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jiun-Sheng Chen
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- The The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Carson Holt
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Jerry Fowler
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stephen L Guthery
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Paul Scheet
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michelle A T Hildebrandt
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Yu Y, Hu H, Chen JS, Hu F, Fowler J, Scheet P, Zhao H, Huff CD. Integrated case-control and somatic-germline interaction analyses of melanoma susceptibility genes. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2247-2254. [PMID: 29317335 DOI: 10.1016/j.bbadis.2018.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/20/2017] [Accepted: 01/04/2018] [Indexed: 12/18/2022]
Abstract
While a number of genes have been implicated in melanoma susceptibility, the role of protein-coding variation in melanoma development and progression remains underexplored. To better characterize the role of germline coding variation in melanoma, we conducted a whole-exome case-control and somatic-germline interaction study involving 322 skin cutaneous melanoma cases from The Cancer Genome Atlas and 3607 controls of European ancestry. We controlled for cross-platform technological stratification using XPAT and conducted gene-based association tests using VAAST 2. Four established melanoma susceptibility genes achieved nominal statistical significance, MC1R (p = .0014), MITF (p = .0165) BRCA2 (p = .0206), and MTAP (p = .0393). We also observed a suggestive association for FANCA (p = .002), a gene previously implicated in melanoma survival. The association signal for BRCA2 was driven primarily by likely gene disrupting (LGD) variants, with an Odds Ratio (OR) of 5.62 (95% Confidence Interval (CI) 1.03-30.1). In contrast, the association signals for MC1R and MITF were driven primarily by predicted pathogenic missense variants, with estimated ORs of 1.4 to 3.0 for MC1R and 4.1 for MITF. MTAP exhibited an excess of both LGD and predicted damaging missense variants among cases, with ORs of 5.62 and 3.72, respectively, although neither category was significant. For individuals with known or predicted damaging variants, age of disease onset was significantly lower for two of the four genes, MC1R (p = .005) and MTAP (p = .035). In an analysis of germline carrier status and overlapping copy number alterations, we observed no evidence to support a two-hit model of carcinogenesis in any of the four genes. Although MC1R carriers were represented proportionally among the four molecular tumor subtypes, these individuals accounted for 69% of ultraviolet (UV) radiation mutational signatures among triple-wild type tumors (p = .040), highlighting the increased sensitivity to UV exposure among individuals with loss-of-function variants in MC1R.
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Affiliation(s)
- Yao Yu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hao Hu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jiun-Sheng Chen
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Fulan Hu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jerry Fowler
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hua Zhao
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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31
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Lanikova L, Reading NS, Hu H, Tashi T, Burjanivova T, Shestakova A, Siwakoti B, Thakur BK, Pun CB, Sapkota A, Abdelaziz S, Feng BJ, Huff CD, Hashibe M, Prchal JT. Evolutionary selected Tibetan variants of HIF pathway and risk of lung cancer. Oncotarget 2017; 8:11739-11747. [PMID: 28036300 PMCID: PMC5355300 DOI: 10.18632/oncotarget.14340] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/16/2016] [Indexed: 01/09/2023] Open
Abstract
Tibetans existed in high altitude for ~25 thousand years and have evolutionary selected unique haplotypes assumed to be beneficial to hypoxic adaptation. EGLN1/PHD2 and EPAS1/HIF-2α, both crucial components of hypoxia sensing, are the two best-established loci contributing to high altitude adaptation. The co-adapted Tibetan-specific haplotype encoding for PHD2:p.[D4E/C127S] promotes increased HIF degradation under hypoxic conditions. The Tibetan-specific 200 kb EPAS1 haplotype introgressed from an archaic human population related to Denisovans which underwent evolutionary decay; however, the functional variant(s) responsible for high-altitude adaptation at EPAS1/HIF-2α have not yet been identified. Since HIF modulates the behavior of cancer cells, we hypothesized that these Tibetan selected genomic variants may modify cancer risk predisposition. Here, we ascertained the frequencies of EGLN1D4E/C127S and EGLN1C127S variants and ten EPAS1/HIF-2α variants in lung cancer patients and controls in Nepal, whose population consists of people with Indo-Aryan origin and Tibetan-related Mongoloid origin. We observed a significant association between the selected Tibetan EGLN1/PHD2 haplotype and lung cancer (p=0.0012 for D4E, p=0.0002 for C127S), corresponding to a two-fold increase in lung cancer risk. We also observed a two-fold or greater increased risk for two of the ten EPAS1/HIF-2α variants, although the association was not significant after correcting for multiple comparisons (p=0.12). Although these data cannot address the role of these genetic variants on lung cancer initiation or progression, we conclude that some selected Tibetan variants are strongly associated with a modified risk of lung cancer.
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Affiliation(s)
- Lucie Lanikova
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, Utah, USA.,Institute of Molecular Genetics, Academy of Sciences, Prague, Czech Republic
| | - N Scott Reading
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, Utah, USA.,Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Hao Hu
- University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Tsewang Tashi
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Tatiana Burjanivova
- Department of Molecular Biology, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin, Slovak Republic
| | - Anna Shestakova
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Bhola Siwakoti
- B.P. Koirala Memorial Cancer Hospital, Bharatpur, Chitwan, Nepal
| | | | - Chin Bahadur Pun
- B.P. Koirala Memorial Cancer Hospital, Bharatpur, Chitwan, Nepal
| | - Amir Sapkota
- Maryland Institute for Applied Environmental Health, and University of Maryland College Park School of Public Health, Maryland, USA
| | - Sarah Abdelaziz
- Division of Public Health, Department of Family & Preventive Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Bing-Jian Feng
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Chad D Huff
- University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Mia Hashibe
- Division of Public Health, Department of Family & Preventive Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Josef T Prchal
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, Utah, USA.,Department of Pathophysiology and 1st Department of Medicine, 1st Faculty of Medicine, Charles University in Prague, Czech Republic
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32
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Tashi T, Scott Reading N, Wuren T, Zhang X, Moore LG, Hu H, Tang F, Shestakova A, Lorenzo F, Burjanivova T, Koul P, Guchhait P, Wittwer CT, Julian CG, Shah B, Huff CD, Gordeuk VR, Prchal JT, Ge R. Gain-of-function EGLN1 prolyl hydroxylase (PHD2 D4E:C127S) in combination with EPAS1 (HIF-2α) polymorphism lowers hemoglobin concentration in Tibetan highlanders. J Mol Med (Berl) 2017; 95:665-670. [PMID: 28233034 DOI: 10.1007/s00109-017-1519-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 11/06/2016] [Revised: 12/14/2016] [Accepted: 02/07/2017] [Indexed: 12/30/2022]
Abstract
Tibetans have lived at high altitude for generations and are thought to be genetically adapted to hypoxic environments. Most are protected from hypoxia-induced polycythemia, and a haplotype of EPAS1, encoding hypoxia-inducible factor (HIF-2α), has been associated with lower hemoglobin levels. We earlier reported a Tibetan-specific EGLN1 haplotype encoding PHD2 which abrogates HIF augmentation in hypoxia. We genotyped 347 Tibetan individuals from varying altitudes for both the Tibetan-specific EGLN1 haplotype and 10 candidate SNPs in the EPAS1 haplotype and correlated their association with hemoglobin levels. The effect of the EGLN1 haplotype on hemoglobin exhibited age dependency at low altitude, while at higher altitudes, it showed a trend to lower hemoglobin levels in the presence of the Tibetan-selected EPAS1 rs142764723 C/C allele. The observed gene-environment and gene-gene interactions and the moderate effect of the EGLN1 and EPAS1 haplotypes on hemoglobin indicate that other modifiers exist. It remains to be determined whether a blunting of erythropoiesis or other physiological consequences of HIF downregulation are the primary drivers of these genetic adaptations among Tibetans. KEY MESSAGE Most Tibetans are protected from polycythemia while living in high altitude. An EGLN1 co-adapted haplotype, EGLN1 c.12C>G, c.380G>C is uniquely Tibetan. The Tibetan EPAS1 haplotype has introgressed from the Denisovan genome. While EGLN1 and EPAS1 genotypes lower Hb, this study indicates additional Hb modifiers.
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Affiliation(s)
- Tsewang Tashi
- Division of Hematology, University of Utah, Salt Lake City, UT, USA
| | - N Scott Reading
- Division of Hematology, University of Utah, Salt Lake City, UT, USA
- Department of Pathology and ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Tanna Wuren
- Research Center for High-Altitude Medicine, Qinghai University, Xining, China
| | - Xu Zhang
- Division of Hematology and Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Lorna G Moore
- Departments of Medicine and Obstetrics/Gynecology, University of Colorado Denver, Aurora, CO, USA
| | - Hao Hu
- MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Feng Tang
- Research Center for High-Altitude Medicine, Qinghai University, Xining, China
| | - Anna Shestakova
- Department of Pathology and ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Felipe Lorenzo
- Division of Hematology, University of Utah, Salt Lake City, UT, USA
| | - Tatiana Burjanivova
- Division of Hematology, University of Utah, Salt Lake City, UT, USA
- Department of Molecular Biology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Bratislava, Slovakia
| | - Parvaiz Koul
- Sher-i-Kashmir Institute of Medical Sciences, Srinagar, India
| | | | - Carl T Wittwer
- Department of Pathology and ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Colleen G Julian
- Departments of Medicine and Obstetrics/Gynecology, University of Colorado Denver, Aurora, CO, USA
| | - Binal Shah
- Division of Hematology and Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Chad D Huff
- MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Victor R Gordeuk
- Division of Hematology and Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Josef T Prchal
- Division of Hematology, University of Utah, Salt Lake City, UT, USA.
- Department of Pathology and ARUP Laboratories, University of Utah, Salt Lake City, UT, USA.
- Department of Pathophysiology and 1st Department of Medicine, 1st Faculty Medicine, Charles University in Prague, Prague, Czech Republic.
- Hematology, SOM 5C310, University of Utah School of Medicine, Salt Lake City, UT, 84132-2408, USA.
| | - RiLi Ge
- Research Center for High-Altitude Medicine, Qinghai University, Xining, China.
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33
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Hu H, Petousi N, Glusman G, Yu Y, Bohlender R, Tashi T, Downie JM, Roach JC, Cole AM, Lorenzo FR, Rogers AR, Brunkow ME, Cavalleri G, Hood L, Alpatty SM, Prchal JT, Jorde LB, Robbins PA, Simonson TS, Huff CD. Evolutionary history of Tibetans inferred from whole-genome sequencing. PLoS Genet 2017; 13:e1006675. [PMID: 28448578 PMCID: PMC5407610 DOI: 10.1371/journal.pgen.1006675] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [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: 09/12/2016] [Accepted: 03/08/2017] [Indexed: 12/20/2022] Open
Abstract
The indigenous people of the Tibetan Plateau have been the subject of much recent interest because of their unique genetic adaptations to high altitude. Recent studies have demonstrated that the Tibetan EPAS1 haplotype is involved in high altitude-adaptation and originated in an archaic Denisovan-related population. We sequenced the whole-genomes of 27 Tibetans and conducted analyses to infer a detailed history of demography and natural selection of this population. We detected evidence of population structure between the ancestral Han and Tibetan subpopulations as early as 44 to 58 thousand years ago, but with high rates of gene flow until approximately 9 thousand years ago. The CMS test ranked EPAS1 and EGLN1 as the top two positive selection candidates, and in addition identified PTGIS, VDR, and KCTD12 as new candidate genes. The advantageous Tibetan EPAS1 haplotype shared many variants with the Denisovan genome, with an ancient gene tree divergence between the Tibetan and Denisovan haplotypes of about 1 million years ago. With the exception of EPAS1, we observed no evidence of positive selection on Denisovan-like haplotypes.
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Affiliation(s)
- Hao Hu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Nayia Petousi
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gustavo Glusman
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ryan Bohlender
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Tsewang Tashi
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
| | - Jonathan M. Downie
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Jared C. Roach
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Amy M. Cole
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Felipe R. Lorenzo
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
| | - Alan R. Rogers
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary E. Brunkow
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Gianpiero Cavalleri
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Sama M. Alpatty
- Skaggs School of Pharmacy and Pharmaceutical Science, UC San Diego, La Jolla, California, United States of America
| | - Josef T. Prchal
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Peter A. Robbins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Tatum S. Simonson
- Department of Medicine, Division of Physiology, University of California San Diego, La Jolla, California, United States of America
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
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34
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Ng MCY, Graff M, Lu Y, Justice AE, Mudgal P, Liu CT, Young K, Yanek LR, Feitosa MF, Wojczynski MK, Rand K, Brody JA, Cade BE, Dimitrov L, Duan Q, Guo X, Lange LA, Nalls MA, Okut H, Tajuddin SM, Tayo BO, Vedantam S, Bradfield JP, Chen G, Chen WM, Chesi A, Irvin MR, Padhukasahasram B, Smith JA, Zheng W, Allison MA, Ambrosone CB, Bandera EV, Bartz TM, Berndt SI, Bernstein L, Blot WJ, Bottinger EP, Carpten J, Chanock SJ, Chen YDI, Conti DV, Cooper RS, Fornage M, Freedman BI, Garcia M, Goodman PJ, Hsu YHH, Hu J, Huff CD, Ingles SA, John EM, Kittles R, Klein E, Li J, McKnight B, Nayak U, Nemesure B, Ogunniyi A, Olshan A, Press MF, Rohde R, Rybicki BA, Salako B, Sanderson M, Shao Y, Siscovick DS, Stanford JL, Stevens VL, Stram A, Strom SS, Vaidya D, Witte JS, Yao J, Zhu X, Ziegler RG, Zonderman AB, Adeyemo A, Ambs S, Cushman M, Faul JD, Hakonarson H, Levin AM, Nathanson KL, Ware EB, Weir DR, Zhao W, Zhi D, Arnett DK, Grant SFA, Kardia SLR, Oloapde OI, Rao DC, Rotimi CN, Sale MM, Williams LK, Zemel BS, Becker DM, Borecki IB, Evans MK, Harris TB, Hirschhorn JN, Li Y, Patel SR, Psaty BM, Rotter JI, Wilson JG, Bowden DW, Cupples LA, Haiman CA, Loos RJF, North KE. Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium. PLoS Genet 2017; 13:e1006719. [PMID: 28430825 PMCID: PMC5419579 DOI: 10.1371/journal.pgen.1006719] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 05/05/2017] [Accepted: 03/29/2017] [Indexed: 11/20/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified >300 loci associated with measures of adiposity including body mass index (BMI) and waist-to-hip ratio (adjusted for BMI, WHRadjBMI), but few have been identified through screening of the African ancestry genomes. We performed large scale meta-analyses and replications in up to 52,895 individuals for BMI and up to 23,095 individuals for WHRadjBMI from the African Ancestry Anthropometry Genetics Consortium (AAAGC) using 1000 Genomes phase 1 imputed GWAS to improve coverage of both common and low frequency variants in the low linkage disequilibrium African ancestry genomes. In the sex-combined analyses, we identified one novel locus (TCF7L2/HABP2) for WHRadjBMI and eight previously established loci at P < 5×10−8: seven for BMI, and one for WHRadjBMI in African ancestry individuals. An additional novel locus (SPRYD7/DLEU2) was identified for WHRadjBMI when combined with European GWAS. In the sex-stratified analyses, we identified three novel loci for BMI (INTS10/LPL and MLC1 in men, IRX4/IRX2 in women) and four for WHRadjBMI (SSX2IP, CASC8, PDE3B and ZDHHC1/HSD11B2 in women) in individuals of African ancestry or both African and European ancestry. For four of the novel variants, the minor allele frequency was low (<5%). In the trans-ethnic fine mapping of 47 BMI loci and 27 WHRadjBMI loci that were locus-wide significant (P < 0.05 adjusted for effective number of variants per locus) from the African ancestry sex-combined and sex-stratified analyses, 26 BMI loci and 17 WHRadjBMI loci contained ≤ 20 variants in the credible sets that jointly account for 99% posterior probability of driving the associations. The lead variants in 13 of these loci had a high probability of being causal. As compared to our previous HapMap imputed GWAS for BMI and WHRadjBMI including up to 71,412 and 27,350 African ancestry individuals, respectively, our results suggest that 1000 Genomes imputation showed modest improvement in identifying GWAS loci including low frequency variants. Trans-ethnic meta-analyses further improved fine mapping of putative causal variants in loci shared between the African and European ancestry populations. Genome-wide association studies (GWAS) have identified >300 genetic regions that influence body size and shape as measured by body mass index (BMI) and waist-to-hip ratio (WHR), respectively, but few have been identified in populations of African ancestry. We conducted large scale high coverage GWAS and replication of these traits in 52,895 and 23,095 individuals of African ancestry, respectively, followed by additional replication in European populations. We identified 10 genome-wide significant loci in all individuals, and an additional seven loci by analyzing men and women separately. We combined African and European ancestry GWAS and were able to narrow down 43 out of 74 African ancestry associated genetic regions to contain small number of putative causal variants. Our results highlight the improvement of applying high density genome coverage and combining multiple ancestries in the identification and refinement of location of genetic regions associated with adiposity traits.
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Affiliation(s)
- Maggie C. Y. Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Icachn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Anne E. Justice
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Poorva Mudgal
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States of America
| | - Kristin Young
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Lisa R. Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Mary F. Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis MO, United States of America
| | - Mary K. Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis MO, United States of America
| | - Kristin Rand
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, United States of America
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
| | - Latchezar Dimitrov
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
| | - Qing Duan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Leslie A. Lange
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Michael A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States of America
- Data Tecnica International, Glen Echo, MD, United States of America
| | - Hayrettin Okut
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
| | - Salman M. Tajuddin
- National Institute on Aging, National Institutes of Health, Baltimore, MD, United States of America
| | - Bamidele O. Tayo
- Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States of America
| | - Sailaja Vedantam
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, United States of America
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Jonathan P. Bradfield
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Wei-Min Chen
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Alessandra Chesi
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Badri Padhukasahasram
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, MI, United States of America
| | - Jennifer A. Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, United States of America
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | - Matthew A. Allison
- Division of Preventive Medicine, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, United States of America
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, United States of America
| | - Elisa V. Bandera
- Department of Population Science, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States of America
| | - Traci M. Bartz
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States of America
| | - Leslie Bernstein
- Beckman Research Institute of the City of Hope, Duarte, CA, United States of America
| | - William J. Blot
- International Epidemiology Institute, Rockville, MD, United States of America
| | - Erwin P. Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icachn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - John Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States of America
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - David V. Conti
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Richard S. Cooper
- Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States of America
| | - Myriam Fornage
- Center for Human Genetics, University of Texas Health Science Center at Houston, Houston, TX, United States of America
| | - Barry I. Freedman
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
| | - Melissa Garcia
- National Institute on Aging, National Institutes of Health, Baltimore, MD, United States of America
| | - Phyllis J. Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Yu-Han H. Hsu
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, United States of America
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, United States of America
| | - Jennifer Hu
- Sylvester Comprehensive Cancer Center, University of Miami Leonard Miller School of Medicine, Miami, FL, United States of America
- Department of Public Health Sciences, University of Miami Leonard Miller School of Medicine, Miami, FL, United States of America
| | - Chad D. Huff
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States of America
| | - Sue A. Ingles
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
| | - Esther M. John
- Cancer Prevention Institute of California, Fremont, CA, United States of America
- Department of Health Research and Policy (Epidemiology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Rick Kittles
- Division of Urology, Department of Surgery, The University of Arizona, Tucson, AZ, United States of America
| | - Eric Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, United States of America
| | - Jin Li
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, United States of America
| | - Barbara McKnight
- Cardiovascular Health Research Unit, Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Uma Nayak
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Barbara Nemesure
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, United States of America
| | | | - Andrew Olshan
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC, United States of America
| | - Michael F. Press
- Department of Pathology and Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, United States of America
| | - Rebecca Rohde
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Benjamin A. Rybicki
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, United States of America
| | | | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN, United States of America
| | - Yaming Shao
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States of America
| | - David S. Siscovick
- The New York Academy of Medicine, New York, NY, United States of America
| | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Victoria L. Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, United States of America
| | - Alex Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Sara S. Strom
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States of America
| | - Dhananjay Vaidya
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- Department of Epidemiology, Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - John S. Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States of America
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, United States of America
| | - Jie Yao
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Xiaofeng Zhu
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, United States of America
| | - Regina G. Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Alan B. Zonderman
- National Institute on Aging, National Institutes of Health, Baltimore, MD, United States of America
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD, United States of America
| | - Mary Cushman
- Department of Medicine, University of Vermont College of Medicine, Burlington, VT, United States of America
| | - Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, United States of America
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Albert M. Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, United States of America
| | - Katherine L. Nathanson
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Erin B. Ware
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, United States of America
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, United States of America
| | - David R. Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, United States of America
| | - Wei Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, United States of America
| | - Degui Zhi
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, United States of America
| | | | - Donna K. Arnett
- School of Public Health, University of Kentucky, Lexington, KY, United States of America
| | - Struan F. A. Grant
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- Division of Endocrinology, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Sharon L. R. Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, United States of America
| | - Olufunmilayo I. Oloapde
- Center for Clinical Cancer Genetics, Department of Medicine and Human Genetics, University of Chicago, Chicago, IL, United States of America
| | - D. C. Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Michele M. Sale
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - L. Keoki Williams
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, MI, United States of America
- Department of Internal Medicine, Henry Ford Health System, Detroit, MI, United States of America
| | - Babette S. Zemel
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- Division of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Diane M. Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Ingrid B. Borecki
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis MO, United States of America
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Inc, United States of America
| | - Michele K. Evans
- National Institute on Aging, National Institutes of Health, Baltimore, MD, United States of America
| | - Tamara B. Harris
- National Institute on Aging, National Institutes of Health, Baltimore, MD, United States of America
| | - Joel N. Hirschhorn
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, United States of America
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
- Departments of Genetics and Pediatrics, Harvard Medical School, Boston, MA, United States of America
| | - Yun Li
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Sanjay R. Patel
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA, United States of America
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, United States of America
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, United States of America
- Division of Genomic Outcomes, Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Los Angeles, CA, United States of America
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, United States of America
| | - Donald W. Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States of America
- NHLBI Framingham Heart Study, Framingham, MA, United States of America
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
- * E-mail: (CAH); (RJFL); (KEN)
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icachn School of Medicine at Mount Sinai, New York, NY, United States of America
- The Mindich Child Health and Development Institute, Ichan School of Medicine at Mount Sinai, New York, NY, United States of America
- * E-mail: (CAH); (RJFL); (KEN)
| | - Kari E. North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States of America
- * E-mail: (CAH); (RJFL); (KEN)
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Hu H, Coon H, Li M, Yandell M, Huff CD. VARPRISM: incorporating variant prioritization in tests of de novo mutation association. Genome Med 2016; 8:91. [PMID: 27562213 PMCID: PMC4997702 DOI: 10.1186/s13073-016-0341-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 08/02/2016] [Indexed: 12/18/2022] Open
Abstract
Background Patients with certain genetic diseases, such as autism spectrum disorder, have increased rates of de novo mutations within some protein-coding genes. Results We introduce the VARiant PRIoritization SuM (VARPRISM), a software package which incorporates functional variant prioritization information to improve the power to detect de novo mutations influencing disease risk. VARPRISM evaluates the consequence of any given exonic mutation on the protein sequence to estimate the likelihood that the mutation is benign or damaging and conducts a likelihood ratio test on the gene level. We analyzed the Simons Simplex Collection of 2508 parent-offspring autism trios using VARPRISM, replicating 44 genes previously implicated in autism susceptibility and identifying 20 additional candidate genes, including MYO1E, KCND3, PDCD1, DLX3, and TSPAN4 (false discovery rate < 0.3). Conclusion By incorporating functional predictions, VARPRISM improved the statistical power to identify de novo mutations increasing disease risks. VARPRISM is available at http://www.hufflab.org/software/VARPRISM. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0341-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Hu
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Hilary Coon
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA
| | - Man Li
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Mark Yandell
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.
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Simonson TS, Huff CD, Witherspoon DJ, Prchal JT, Jorde LB. Adaptive genetic changes related to haemoglobin concentration in native high-altitude Tibetans. Exp Physiol 2016; 100:1263-8. [PMID: 26454145 DOI: 10.1113/ep085035] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 10/06/2015] [Indexed: 12/17/2022]
Abstract
NEW FINDINGS What is the topic of this review? Tibetans have genetic adaptations that are hypothesized to underlie the distinct set of traits they exhibit at altitude. What advances does it highlight? Several adaptive signatures in the same genomic regions have been identified among Tibetan populations resident throughout the Qinghai-Tibetan Plateau. Many highland Tibetans exhibit a haemoglobin concentration within the range expected at sea level, and this trait is associated with putatively adaptive regions harbouring the hypoxia-inducible factor pathway genes EGLN1, EPAS1 and PPARA. Precise functional variants at adaptive loci and relationships to physiological traits, beyond haemoglobin concentration, are currently being examined in this population. Some native Tibetan, Andean and Ethiopian populations have lived at altitudes ranging from 3000 to >4000 m above sea level for hundreds of generations and exhibit distinct combinations of traits at altitude. It was long hypothesized that genetic factors contribute to adaptive differences in these populations, and recent advances in genomics provide evidence that some of the strongest signatures of positive selection in humans are those identified in Tibetans. Many of the top adaptive genomic regions highlighted thus far harbour genes related to hypoxia sensing and response. Putatively adaptive copies of three hypoxia-inducible factor pathway genes, EPAS1, EGLN1 and PPARA, are associated with sea-level range, rather than elevated, haemoglobin concentration observed in many Tibetans at high altitude, and recent studies provide insight into some of the precise adaptive variants, timing of adaptive events and functional roles. While several studies in highland Tibetans have converged on a few hypoxia-inducible factor pathway genes, additional candidates have been reported in independent studies of Tibetans located throughout the Qinghai-Tibetan Plateau. Various aspects of adaptive significance have yet to be identified, integrated, and fully explored. Given the rapid technological advances and interdisciplinary efforts in genomics, physiology and molecular biology, careful examination of Tibetans and comparisons with other distinctively adapted highland populations will provide valuable insight into evolutionary processes and models for both basic and clinical research.
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Affiliation(s)
- T S Simonson
- Department of Medicine, Division of Physiology, University of California San Diego, La Jolla, CA, USA
| | - C D Huff
- Department of Epidemiology, University of Texas, MD Anderson, Houston, TX, USA
| | - D J Witherspoon
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - J T Prchal
- Department of Medicine, University of Utah, Salt Lake City, UT, USA
| | - L B Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
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Staples J, Witherspoon D, Jorde L, Nickerson D, Below J, Huff C, Huff CD. PADRE: Pedigree-Aware Distant-Relationship Estimation. Am J Hum Genet 2016; 99:154-62. [PMID: 27374771 DOI: 10.1016/j.ajhg.2016.05.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/16/2016] [Indexed: 10/21/2022] Open
Abstract
Accurate estimation of shared ancestry is an important component of many genetic studies; current prediction tools accurately estimate pairwise genetic relationships up to the ninth degree. Pedigree-aware distant-relationship estimation (PADRE) combines relationship likelihoods generated by estimation of recent shared ancestry (ERSA) with likelihoods from family networks reconstructed by pedigree reconstruction and identification of a maximum unrelated set (PRIMUS), improving the power to detect distant relationships between pedigrees. Using PADRE, we estimated relationships from simulated pedigrees and three extended pedigrees, correctly predicting 20% more fourth- through ninth-degree simulated relationships than when using ERSA alone. By leveraging pedigree information, PADRE can even identify genealogical relationships between individuals who are genetically unrelated. For example, although 95% of 13(th)-degree relatives are genetically unrelated, in simulations, PADRE correctly predicted 50% of 13(th)-degree relationships to within one degree of relatedness. The improvement in prediction accuracy was consistent between simulated and actual pedigrees. We also applied PADRE to the HapMap3 CEU samples and report new cryptic relationships and validation of previously described relationships between families. PADRE greatly expands the range of relationships that can be estimated by using genetic data in pedigrees.
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Affiliation(s)
| | | | | | | | | | | | - Chad D Huff
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
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Hu H, Huff CD, Yamamura Y, Wu X, Strom SS. The Relationship between Native American Ancestry, Body Mass Index and Diabetes Risk among Mexican-Americans. PLoS One 2015; 10:e0141260. [PMID: 26501420 PMCID: PMC4621045 DOI: 10.1371/journal.pone.0141260] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/05/2015] [Indexed: 01/19/2023] Open
Abstract
Higher body mass index (BMI) is a well-established risk factor for type 2 diabetes, and rates of obesity and type 2 diabetes are substantially higher among Mexican-Americans relative to non-Hispanic European Americans. Mexican-Americans are genetically diverse, with a highly variable distribution of Native American, European, and African ancestries. Here, we evaluate the role of Native American ancestry on BMI and diabetes risk in a well-defined Mexican-American population. Participants were randomly selected among individuals residing in the Houston area who are enrolled in the Mexican-American Cohort study. Using a custom Illumina GoldenGate Panel, we genotyped DNA from 4,662 cohort participants for 87 Ancestry-Informative Markers. On average, the participants were of 50.2% Native American ancestry, 42.7% European ancestry and 7.1% African ancestry. Using multivariate linear regression, we found BMI and Native American ancestry were inversely correlated; individuals with <20% Native American ancestry were 2.5 times more likely to be severely obese compared to those with >80% Native American ancestry. Furthermore, we demonstrated an interaction between BMI and Native American ancestry in diabetes risk among women; Native American ancestry was a strong risk factor for diabetes only among overweight and obese women (OR = 1.190 for each 10% increase in Native American ancestry). This study offers new insight into the complex relationship between obesity, genetic ancestry, and their respective effects on diabetes risk. Findings from this study may improve the diabetes risk prediction among Mexican-American individuals thereby facilitating targeted prevention strategies.
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Affiliation(s)
- Hao Hu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Yuko Yamamura
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Xifeng Wu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Sara S. Strom
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
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Park DJ, Tao K, Le Calvez-Kelm F, Nguyen-Dumont T, Robinot N, Hammet F, Odefrey F, Tsimiklis H, Teo ZL, Thingholm LB, Young EL, Voegele C, Lonie A, Pope BJ, Roane TC, Bell R, Hu H, Shankaracharya, Huff CD, Ellis J, Li J, Makunin IV, John EM, Andrulis IL, Terry MB, Daly M, Buys SS, Snyder C, Lynch HT, Devilee P, Giles GG, Hopper JL, Feng BJ, Lesueur F, Tavtigian SV, Southey MC, Goldgar DE. Rare mutations in RINT1 predispose carriers to breast and Lynch syndrome-spectrum cancers. Cancer Discov 2014; 4:804-15. [PMID: 25050558 PMCID: PMC4234633 DOI: 10.1158/2159-8290.cd-14-0212] [Citation(s) in RCA: 38] [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] [Indexed: 01/08/2023]
Abstract
UNLABELLED Approximately half of the familial aggregation of breast cancer remains unexplained. A multiple-case breast cancer family exome-sequencing study identified three likely pathogenic mutations in RINT1 (NM_021930.4) not present in public sequencing databases: RINT1 c.343C>T (p.Q115X), c.1132_1134del (p.M378del), and c.1207G>T (p.D403Y). On the basis of this finding, a population-based case-control mutation-screening study was conducted that identified 29 carriers of rare (minor allele frequency < 0.5%), likely pathogenic variants: 23 in 1,313 early-onset breast cancer cases and six in 1,123 frequency-matched controls [OR, 3.24; 95% confidence interval (CI), 1.29-8.17; P = 0.013]. RINT1 mutation screening of probands from 798 multiple-case breast cancer families identified four additional carriers of rare genetic variants. Analysis of the incidence of first primary cancers in families of women carrying RINT1 mutations estimated that carriers were at increased risk of Lynch syndrome-spectrum cancers [standardized incidence ratio (SIR), 3.35; 95% CI, 1.7-6.0; P = 0.005], particularly for relatives diagnosed with cancer under the age of 60 years (SIR, 10.9; 95% CI, 4.7-21; P = 0.0003). SIGNIFICANCE The work described in this study adds RINT1 to the growing list of genes in which rare sequence variants are associated with intermediate levels of breast cancer risk. Given that RINT1 is also associated with a spectrum of cancers with mismatch repair defects, these findings have clinical applications and raise interesting biological questions.
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Affiliation(s)
- Daniel J Park
- Genetic Epidemiology Laboratory, Department of Pathology
| | | | | | | | - Nivonirina Robinot
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon
| | - Fleur Hammet
- Genetic Epidemiology Laboratory, Department of Pathology
| | | | | | - Zhi L Teo
- Genetic Epidemiology Laboratory, Department of Pathology
| | | | | | - Catherine Voegele
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon
| | | | - Bernard J Pope
- Department of Computing and Information Systems; Victorian Life Sciences Computation Initiative
| | | | | | - Hao Hu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shankaracharya
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chad D Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jonathan Ellis
- The QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia; Departments of
| | - Jun Li
- The QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia; Departments of
| | - Igor V Makunin
- The QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia; Departments of
| | - Esther M John
- Cancer Prevention Institute of California, Fremont; Department of Health Research and Policy, Stanford Cancer Institute, Stanford, California
| | - Irene L Andrulis
- Department of Molecular Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Mary B Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Mary Daly
- Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Saundra S Buys
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Carrie Snyder
- Department of Preventive Medicine, Creighton University, Omaha, Nebraska
| | - Henry T Lynch
- Department of Preventive Medicine, Creighton University, Omaha, Nebraska
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands; and
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne; Centre for Cancer Epidemiology, The Cancer Council Victoria, Carlton, Victoria
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne; School of Public Health, Seoul National University, Seoul, Korea
| | - Bing-Jian Feng
- Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine; Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Fabienne Lesueur
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon; Genetic Epidemiology of Cancer Team, Institut National de la Santé et de la Recherche Medicale (INSERM), U900, Institut Curie, Mines ParisTech, Paris, France
| | | | | | - David E Goldgar
- Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine; Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah;
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Hu H, Roach JC, Coon H, Guthery SL, Voelkerding KV, Margraf RL, Durtschi JD, Tavtigian SV, Shankaracharya, Wu W, Scheet P, Wang S, Xing J, Glusman G, Hubley R, Li H, Garg V, Moore B, Hood L, Galas DJ, Srivastava D, Reese MG, Jorde LB, Yandell M, Huff CD. A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nat Biotechnol 2014; 32:663-9. [PMID: 24837662 DOI: 10.1038/nbt.2895] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 04/04/2014] [Indexed: 01/02/2023]
Abstract
High-throughput sequencing of related individuals has become an important tool for studying human disease. However, owing to technical complexity and lack of available tools, most pedigree-based sequencing studies rely on an ad hoc combination of suboptimal analyses. Here we present pedigree-VAAST (pVAAST), a disease-gene identification tool designed for high-throughput sequence data in pedigrees. pVAAST uses a sequence-based model to perform variant and gene-based linkage analysis. Linkage information is then combined with functional prediction and rare variant case-control association information in a unified statistical framework. pVAAST outperformed linkage and rare-variant association tests in simulations and identified disease-causing genes from whole-genome sequence data in three human pedigrees with dominant, recessive and de novo inheritance patterns. The approach is robust to incomplete penetrance and locus heterogeneity and is applicable to a wide variety of genetic traits. pVAAST maintains high power across studies of monogenic, high-penetrance phenotypes in a single pedigree to highly polygenic, common phenotypes involving hundreds of pedigrees.
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Affiliation(s)
- Hao Hu
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Jared C Roach
- Institute for Systems Biology, Seattle, Washington, USA
| | - Hilary Coon
- Department of Psychiatry, University of Utah, Salt Lake City, Utah, USA
| | - Stephen L Guthery
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Karl V Voelkerding
- 1] Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA. [2] ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Rebecca L Margraf
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Jacob D Durtschi
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Shankaracharya
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Wilfred Wu
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Shuoguo Wang
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA
| | | | - Robert Hubley
- Institute for Systems Biology, Seattle, Washington, USA
| | - Hong Li
- Institute for Systems Biology, Seattle, Washington, USA
| | - Vidu Garg
- 1] Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA. [2] Center for Cardiovascular and Pulmonary Research, Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Barry Moore
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, USA
| | - David J Galas
- 1] Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg. [2] Pacific Northwest Diabetes Research Institute, Seattle, Washington, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease and University of California, San Francisco, San Francisco, California, USA
| | | | - Lynn B Jorde
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA
| | - Mark Yandell
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
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Wuren T, Simonson TS, Qin G, Xing J, Huff CD, Witherspoon DJ, Jorde LB, Ge RL. Shared and unique signals of high-altitude adaptation in geographically distinct Tibetan populations. PLoS One 2014; 9:e88252. [PMID: 24642866 PMCID: PMC3958363 DOI: 10.1371/journal.pone.0088252] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 01/06/2014] [Indexed: 01/11/2023] Open
Abstract
Recent studies have used a variety of analytical methods to identify genes targeted by selection in high-altitude populations located throughout the Tibetan Plateau. Despite differences in analytic strategies and sample location, hypoxia-related genes, including EPAS1 and EGLN1, were identified in multiple studies. By applying the same analytic methods to genome-wide SNP information used in our previous study of a Tibetan population (n = 31) from the township of Maduo, located in the northeastern corner of the Qinghai-Tibetan Plateau (4200 m), we have identified common targets of natural selection in a second geographically and linguistically distinct Tibetan population (n = 46) in the Tuo Tuo River township (4500 m). Our analyses provide evidence for natural selection based on iHS and XP-EHH signals in both populations at the p<0.02 significance level for EPAS1, EGLN1, HMOX2, and CYP17A1 and for PKLR, HFE, and HBB and HBG2, which have also been reported in other studies. We highlight differences (i.e., stratification and admixture) in the two distinct Tibetan groups examined here and report selection candidate genes common to both groups. These findings should be considered in the prioritization of selection candidate genes in future genetic studies in Tibet.
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Affiliation(s)
- Tana Wuren
- Research Center for High-Altitude Medicine, Qinghai University Medical School, Xining, Qinghai, People's Republic of China
| | - Tatum S. Simonson
- Division of Physiology, Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Ga Qin
- Research Center for High-Altitude Medicine, Qinghai University Medical School, Xining, Qinghai, People's Republic of China
| | - Jinchuan Xing
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Chad D. Huff
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - David J. Witherspoon
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Ri-Li Ge
- Research Center for High-Altitude Medicine, Qinghai University Medical School, Xining, Qinghai, People's Republic of China
- * E-mail:
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42
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Li H, Glusman G, Hu H, Shankaracharya, Caballero J, Hubley R, Witherspoon D, Guthery SL, Mauldin DE, Jorde LB, Hood L, Roach JC, Huff CD. Relationship estimation from whole-genome sequence data. PLoS Genet 2014; 10:e1004144. [PMID: 24497848 PMCID: PMC3907355 DOI: 10.1371/journal.pgen.1004144] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/09/2013] [Indexed: 12/02/2022] Open
Abstract
The determination of the relationship between a pair of individuals is a fundamental application of genetics. Previously, we and others have demonstrated that identity-by-descent (IBD) information generated from high-density single-nucleotide polymorphism (SNP) data can greatly improve the power and accuracy of genetic relationship detection. Whole-genome sequencing (WGS) marks the final step in increasing genetic marker density by assaying all single-nucleotide variants (SNVs), and thus has the potential to further improve relationship detection by enabling more accurate detection of IBD segments and more precise resolution of IBD segment boundaries. However, WGS introduces new complexities that must be addressed in order to achieve these improvements in relationship detection. To evaluate these complexities, we estimated genetic relationships from WGS data for 1490 known pairwise relationships among 258 individuals in 30 families along with 46 population samples as controls. We identified several genomic regions with excess pairwise IBD in both the pedigree and control datasets using three established IBD methods: GERMLINE, fastIBD, and ISCA. These spurious IBD segments produced a 10-fold increase in the rate of detected false-positive relationships among controls compared to high-density microarray datasets. To address this issue, we developed a new method to identify and mask genomic regions with excess IBD. This method, implemented in ERSA 2.0, fully resolved the inflated cryptic relationship detection rates while improving relationship estimation accuracy. ERSA 2.0 detected all 1(st) through 6(th) degree relationships, and 55% of 9(th) through 11(th) degree relationships in the 30 families. We estimate that WGS data provides a 5% to 15% increase in relationship detection power relative to high-density microarray data for distant relationships. Our results identify regions of the genome that are highly problematic for IBD mapping and introduce new software to accurately detect 1(st) through 9(th) degree relationships from whole-genome sequence data.
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Affiliation(s)
- Hong Li
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Gustavo Glusman
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Hao Hu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Shankaracharya
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Juan Caballero
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Robert Hubley
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - David Witherspoon
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Stephen L. Guthery
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Denise E. Mauldin
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Jared C. Roach
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Chad D. Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
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Hu H, Huff CD. Detecting statistical interaction between somatic mutational events and germline variation from next-generation sequence data. Pac Symp Biocomput 2014:51-62. [PMID: 24297533 PMCID: PMC3926123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The two-hit model of carcinogenesis provides a valuable framework for understanding the role of DNA repair and tumor suppressor genes in cancer development and progression. Under this model, tumor development can initiate from a single somatic mutation in individuals that inherit an inactivating germline variant. Although the two-hit model can be an overgeneralization, the tendency for the pattern of somatic mutations to differ in cancer patients that inherit predisposition alleles is a signal that can be used to identify and validate germline susceptibility variants. Here, we present the Somatic-Germline Interaction (SGI) tool, which is designed to identify statistical interaction between germline variants and somatic mutational events from next-generation sequence data. SGI interfaces with rare-variant association tests and variant classifiers to identify candidate germline susceptibility variants from case-control sequencing data. SGI then analyzes tumor-normal pair next-generation sequence data to evaluate evidence for somatic-germline interaction in each gene or pathway using two tests: the Allelic Imbalance Rank Sum (AIRS) test and the Somatic Mutation Interaction Test (SMIT). AIRS tests for preferential allelic imbalance to evaluate whether somatic mutational events tend to amplify candidate germline variants. SMIT evaluates whether somatic point mutations and small indels occur more or less frequently than expected in the presence of candidate germline variants. Both AIRS and SMIT control for heterogeneity in the mutational process resulting from regional variation in mutation rates and inter-sample variation in background mutation rates. The SGI test combines AIRS and SMIT to provide a single, unified measure of statistical interaction between somatic mutational events and germline variation. We show that the tests implemented in SGI have high power with relatively modest sample sizes in a wide variety of scenarios. We demonstrate the utility of SGI to increase the power of rare variant association studies in cancer and to validate the potential role in cancer causation of germline susceptibility variants.
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Affiliation(s)
- Hao Hu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1155 Pressler Street, Houston, TX, 77030, USA.
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44
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Hu H, Huff CD, Moore B, Flygare S, Reese MG, Yandell M. VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix. Genet Epidemiol 2013; 37:622-34. [PMID: 23836555 PMCID: PMC3791556 DOI: 10.1002/gepi.21743] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 04/09/2013] [Accepted: 05/21/2013] [Indexed: 12/03/2022]
Abstract
The need for improved algorithmic support for variant prioritization and disease-gene identification in personal genomes data is widely acknowledged. We previously presented the Variant Annotation, Analysis, and Search Tool (VAAST), which employs an aggregative variant association test that combines both amino acid substitution (AAS) and allele frequencies. Here we describe and benchmark VAAST 2.0, which uses a novel conservation-controlled AAS matrix (CASM), to incorporate information about phylogenetic conservation. We show that the CASM approach improves VAAST’s variant prioritization accuracy compared to its previous implementation, and compared to SIFT, PolyPhen-2, and MutationTaster. We also show that VAAST 2.0 outperforms KBAC, WSS, SKAT, and variable threshold (VT) using published case-control datasets for Crohn disease (NOD2), hypertriglyceridemia (LPL), and breast cancer (CHEK2). VAAST 2.0 also improves search accuracy on simulated datasets across a wide range of allele frequencies, population-attributable disease risks, and allelic heterogeneity, factors that compromise the accuracies of other aggregative variant association tests. We also demonstrate that, although most aggregative variant association tests are designed for common genetic diseases, these tests can be easily adopted as rare Mendelian disease-gene finders with a simple ranking-by-statistical-significance protocol, and the performance compares very favorably to state-of-art filtering approaches. The latter, despite their popularity, have suboptimal performance especially with the increasing case sample size.
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Affiliation(s)
- Hao Hu
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
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45
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Shapiro MD, Kronenberg Z, Li C, Domyan ET, Pan H, Campbell M, Tan H, Huff CD, Hu H, Vickrey AI, Nielsen SCA, Stringham SA, Hu H, Willerslev E, Gilbert MTP, Yandell M, Zhang G, Wang J. Genomic diversity and evolution of the head crest in the rock pigeon. Science 2013; 339:1063-7. [PMID: 23371554 DOI: 10.1126/science.1230422] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The geographic origins of breeds and the genetic basis of variation within the widely distributed and phenotypically diverse domestic rock pigeon (Columba livia) remain largely unknown. We generated a rock pigeon reference genome and additional genome sequences representing domestic and feral populations. We found evidence for the origins of major breed groups in the Middle East and contributions from a racing breed to North American feral populations. We identified the gene EphB2 as a strong candidate for the derived head crest phenotype shared by numerous breeds, an important trait in mate selection in many avian species. We also found evidence that this trait evolved just once and spread throughout the species, and that the crest originates early in development by the localized molecular reversal of feather bud polarity.
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Affiliation(s)
- Michael D Shapiro
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
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46
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Ge RL, Simonson TS, Cooksey RC, Tanna U, Qin G, Huff CD, Witherspoon DJ, Xing J, Zhengzhong B, Prchal JT, Jorde LB, McClain DA. Metabolic insight into mechanisms of high-altitude adaptation in Tibetans. Mol Genet Metab 2012; 106:244-7. [PMID: 22503288 PMCID: PMC3437309 DOI: 10.1016/j.ymgme.2012.03.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 03/09/2012] [Accepted: 03/09/2012] [Indexed: 11/26/2022]
Abstract
Recent studies have identified genes involved in high-altitude adaptation in Tibetans. Genetic variants/haplotypes within regions containing three of these genes (EPAS1, EGLN1, and PPARA) are associated with relatively decreased hemoglobin levels observed in Tibetans at high altitude, providing corroborative evidence for genetic adaptation to this extreme environment. The mechanisms that afford adaptation to high-altitude hypoxia, however, remain unclear. Considering the strong metabolic demands imposed by hypoxia, we hypothesized that a shift in fuel preference to glucose oxidation and glycolysis at the expense of fatty acid oxidation would improve adaptation to decreased oxygen availability. Correlations between serum free fatty acid and lactate concentrations in Tibetan groups living at high altitude and putatively selected haplotypes provide insight into this hypothesis. An EPAS1 haplotype that exhibits a signal of positive selection is significantly associated with increased lactate concentration, the product of anaerobic glycolysis. Furthermore, the putatively advantageous PPARA haplotype is correlated with serum free fatty acid concentrations, suggesting a possible decrease in the activity of fatty acid oxidation. Although further studies are required to assess the molecular mechanisms underlying these patterns, these associations suggest that genetic adaptation to high altitude involves alteration in energy utilization pathways.
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Affiliation(s)
- Ri-Li Ge
- Research Center for High-Altitude Medicine, Qinghai University Medical School, Xining, Qinghai 810001, People’s Republic of China
| | - Tatum S. Simonson
- University of Utah School of Medicine, Department of Human Genetics and Divisions of Endocrinology, Metabolism, and Diabetes and Division of Hematology, Salt Lake City, UT 84112, USA
| | - Robert C. Cooksey
- University of Utah School of Medicine, Department of Human Genetics and Divisions of Endocrinology, Metabolism, and Diabetes and Division of Hematology, Salt Lake City, UT 84112, USA
| | - Uran Tanna
- Research Center for High-Altitude Medicine, Qinghai University Medical School, Xining, Qinghai 810001, People’s Republic of China
| | - Ga Qin
- Research Center for High-Altitude Medicine, Qinghai University Medical School, Xining, Qinghai 810001, People’s Republic of China
| | - Chad D. Huff
- University of Utah School of Medicine, Department of Human Genetics and Divisions of Endocrinology, Metabolism, and Diabetes and Division of Hematology, Salt Lake City, UT 84112, USA
| | - David J. Witherspoon
- University of Utah School of Medicine, Department of Human Genetics and Divisions of Endocrinology, Metabolism, and Diabetes and Division of Hematology, Salt Lake City, UT 84112, USA
| | - Jinchuan Xing
- University of Utah School of Medicine, Department of Human Genetics and Divisions of Endocrinology, Metabolism, and Diabetes and Division of Hematology, Salt Lake City, UT 84112, USA
| | - Bai Zhengzhong
- Research Center for High-Altitude Medicine, Qinghai University Medical School, Xining, Qinghai 810001, People’s Republic of China
| | - Josef T. Prchal
- University of Utah School of Medicine, Department of Human Genetics and Divisions of Endocrinology, Metabolism, and Diabetes and Division of Hematology, Salt Lake City, UT 84112, USA
| | - Lynn B. Jorde
- University of Utah School of Medicine, Department of Human Genetics and Divisions of Endocrinology, Metabolism, and Diabetes and Division of Hematology, Salt Lake City, UT 84112, USA
| | - Donald A. McClain
- University of Utah School of Medicine, Department of Human Genetics and Divisions of Endocrinology, Metabolism, and Diabetes and Division of Hematology, Salt Lake City, UT 84112, USA
- Address for correspondence: Donald McClain, Division of Endocrinology, University of Utah, 30 N. 2030 E, Salt Lake City, UT 84132, Tel.: (801) 581-7755, Fax: (801) 585-0956,
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47
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Huff CD, Witherspoon DJ, Zhang Y, Gatenbee C, Denson LA, Kugathasan S, Hakonarson H, Whiting A, Davis CT, Wu W, Xing J, Watkins WS, Bamshad MJ, Bradfield JP, Bulayeva K, Simonson TS, Jorde LB, Guthery SL. Crohn's disease and genetic hitchhiking at IBD5. Mol Biol Evol 2011; 29:101-11. [PMID: 21816865 DOI: 10.1093/molbev/msr151] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Inflammatory bowel disease 5 (IBD5) is a 250 kb haplotype on chromosome 5 that is associated with an increased risk of Crohn's disease in Europeans. The OCTN1 gene is centrally located on IBD5 and encodes a transporter of the antioxidant ergothioneine (ET). The 503F variant of OCTN1 is strongly associated with IBD5 and is a gain-of-function mutation that increases absorption of ET. Although 503F has been implicated as the variant potentially responsible for Crohn's disease susceptibility at IBD5, there is little evidence beyond statistical association to support its role in disease causation. We hypothesize that 503F is a recent adaptation in Europeans that swept to relatively high frequency and that disease association at IBD5 results not from 503F itself, but from one or more nearby hitchhiking variants, in the genes IRF1 or IL5. To test for evidence of recent positive selection on the 503F allele, we employed the iHS statistic, which was significant in the European CEU HapMap population (P=0.0007) and European Human Genome Diversity Panel populations (P≤0.01). To evaluate the hypothesis of disease-variant hitchhiking, we performed haplotype association tests on high-density microarray data in a sample of 1,868 Crohn's disease cases and 5,550 controls. We found that 503F haplotypes with recombination breakpoints between OCTN1 and IRF1 or IL5 were not associated with disease (odds ratio [OR]: 1.05, P=0.21). In contrast, we observed strong disease association for 503F haplotypes with no recombination between these three genes (OR: 1.24, P=2.6×10(-8)), as expected if the sweeping haplotype harbored one or more disease-causing mutations in IRF1 or IL5. To further evaluate these disease-gene candidates, we obtained expression data from lower gastrointestinal biopsies of healthy individuals and Crohn's disease patients. We observed a 72% increase in gene expression of IRF1 among Crohn's disease patients (P=0.0006) and no significant difference in expression of OCTN1. Collectively, these data indicate that the 503F variant has increased in frequency due to recent positive selection and that disease-causing variants in linkage disequilibrium with 503F have hitchhiked to relatively high frequency, thus forming the IBD5 risk haplotype. Finally, our association results and expression data support IRF1 as a strong candidate for Crohn's disease causation.
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Affiliation(s)
- Chad D Huff
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, UT, USA.
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48
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Huff CD, Witherspoon DJ, Simonson TS, Xing J, Watkins WS, Zhang Y, Tuohy TM, Neklason DW, Burt RW, Guthery SL, Woodward SR, Jorde LB. Maximum-likelihood estimation of recent shared ancestry (ERSA). Genome Res 2011; 21:768-74. [PMID: 21324875 DOI: 10.1101/gr.115972.110] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Accurate estimation of recent shared ancestry is important for genetics, evolution, medicine, conservation biology, and forensics. Established methods estimate kinship accurately for first-degree through third-degree relatives. We demonstrate that chromosomal segments shared by two individuals due to identity by descent (IBD) provide much additional information about shared ancestry. We developed a maximum-likelihood method for the estimation of recent shared ancestry (ERSA) from the number and lengths of IBD segments derived from high-density SNP or whole-genome sequence data. We used ERSA to estimate relationships from SNP genotypes in 169 individuals from three large, well-defined human pedigrees. ERSA is accurate to within one degree of relationship for 97% of first-degree through fifth-degree relatives and 80% of sixth-degree and seventh-degree relatives. We demonstrate that ERSA's statistical power approaches the maximum theoretical limit imposed by the fact that distant relatives frequently share no DNA through a common ancestor. ERSA greatly expands the range of relationships that can be estimated from genetic data and is implemented in a freely available software package.
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Affiliation(s)
- Chad D Huff
- Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA
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49
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Simonson TS, Xing J, Barrett R, Jerah E, Loa P, Zhang Y, Watkins WS, Witherspoon DJ, Huff CD, Woodward S, Mowry B, Jorde LB. Ancestry of the Iban is predominantly Southeast Asian: genetic evidence from autosomal, mitochondrial, and Y chromosomes. PLoS One 2011; 6:e16338. [PMID: 21305013 PMCID: PMC3031551 DOI: 10.1371/journal.pone.0016338] [Citation(s) in RCA: 13] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 12/11/2010] [Indexed: 01/01/2023] Open
Abstract
Humans reached present-day Island Southeast Asia (ISEA) in one of the first major human migrations out of Africa. Population movements in the millennia following this initial settlement are thought to have greatly influenced the genetic makeup of current inhabitants, yet the extent attributed to different events is not clear. Recent studies suggest that south-to-north gene flow largely influenced present-day patterns of genetic variation in Southeast Asian populations and that late Pleistocene and early Holocene migrations from Southeast Asia are responsible for a substantial proportion of ISEA ancestry. Archaeological and linguistic evidence suggests that the ancestors of present-day inhabitants came mainly from north-to-south migrations from Taiwan and throughout ISEA approximately 4,000 years ago. We report a large-scale genetic analysis of human variation in the Iban population from the Malaysian state of Sarawak in northwestern Borneo, located in the center of ISEA. Genome-wide single-nucleotide polymorphism (SNP) markers analyzed here suggest that the Iban exhibit greatest genetic similarity to Indonesian and mainland Southeast Asian populations. The most common non-recombining Y (NRY) and mitochondrial (mt) DNA haplogroups present in the Iban are associated with populations of Southeast Asia. We conclude that migrations from Southeast Asia made a large contribution to Iban ancestry, although evidence of potential gene flow from Taiwan is also seen in uniparentally inherited marker data.
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Affiliation(s)
- Tatum S. Simonson
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Jinchuan Xing
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Robert Barrett
- Department of Psychiatry, University of Adelaide and Royal Adelaide Hospital, Adelaide, Australia
| | - Edward Jerah
- Department of Psychiatry, University of Adelaide and Royal Adelaide Hospital, Adelaide, Australia
| | - Peter Loa
- Department of Psychiatry, University of Adelaide and Royal Adelaide Hospital, Adelaide, Australia
| | - Yuhua Zhang
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - W. Scott Watkins
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - David J. Witherspoon
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Chad D. Huff
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Scott Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | - Bryan Mowry
- Queensland Centre of Mental Health Research, Brisbane, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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50
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Rope AF, Wang K, Evjenth R, Xing J, Johnston JJ, Swensen JJ, Johnson WE, Moore B, Huff CD, Bird LM, Carey JC, Opitz JM, Stevens CA, Schank C, Fain HD, Robison R, Dalley B, Chin S, South ST, Pysher TJ, Jorde LB, Hakonarson H, Lillehaug JR, Biesecker LG, Yandell M, Arnesen T, Lyon GJ. Massively parallel sequencing identifies a previously unrecognized X-linked disorder resulting in lethality in male infants owing to amino-terminal acetyltransferase deficiency. Genome Biol 2011. [PMCID: PMC3439021 DOI: 10.1186/gb-2011-12-s1-p13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Alan F Rope
- Department of Pediatrics (Medical Genetics), University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Kai Wang
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA , USA,Present address: Zilkha Neurogenetic Institute, Department of Psychiatry and Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rune Evjenth
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Jinchuan Xing
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Jennifer J Johnston
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey J Swensen
- Department of Pathology, University of Utah, Salt Lake City, UT, USA,ARUP Laboratories, Salt Lake City, Utah, USA
| | - W Evan Johnson
- Department of Statistics, Brigham Young University, Provo, Utah, USA
| | - Barry Moore
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Chad D Huff
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Lynne M Bird
- Rady Children’s Hospital and University of California, San Diego, Department of Pediatrics, San Diego, CA, USA
| | - John C Carey
- Department of Pediatrics (Medical Genetics), University of Utah School of Medicine, Salt Lake City, UT, USA
| | - John M Opitz
- Department of Pediatrics (Medical Genetics), University of Utah School of Medicine, Salt Lake City, UT, USA,Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT, USA,Department of Pathology, University of Utah, Salt Lake City, UT, USA,Department of Obstetrics and Gynecology, University of Utah, Salt Lake City, UT, USA
| | - Cathy A Stevens
- Department of Pediatrics, University of Tennessee College of Medicine, Chattanooga, TN, USA
| | - Christa Schank
- Department of Statistics, Brigham Young University, Provo, Utah, USA
| | | | - Reid Robison
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA
| | - Brian Dalley
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Steven Chin
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Sarah T South
- Department of Pediatrics (Medical Genetics), University of Utah School of Medicine, Salt Lake City, UT, USA,ARUP Laboratories, Salt Lake City, Utah, USA
| | - Theodore J Pysher
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Lynn B Jorde
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA , USA
| | - Johan R Lillehaug
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Leslie G Biesecker
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway,Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Gholson J Lyon
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA,New York University Child Study Center, New York, NY, USA,Present address: Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA , USA
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