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Abstract
Coronary artery disease (or coronary heart disease), is the leading cause of mortality in many of the developing as well as the developed countries of the world. Cholesterol-enriched plaques in the heart's blood vessels combined with inflammation lead to the lesion expansion, narrowing of blood vessels, reduced blood flow, and may subsequently cause lesion rupture and a heart attack. Even though several environmental risk factors have been established, such as high LDL-cholesterol, diabetes, and high blood pressure, the underlying genetic composition may substantially modify the disease risk; hence, genome composition and gene-environment interactions may be critical for disease progression. Ongoing scientific efforts have seen substantial advancements related to the fields of genetics and genomics, with the major breakthroughs yet to come. As genomics is the most rapidly advancing field in the life sciences, it is important to present a comprehensive overview of current efforts. Here, we present a summary of various genetic and genomics assays and approaches applied to coronary artery disease research.
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Affiliation(s)
- Milos Pjanic
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA
| | - Clint L Miller
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA
| | - Robert Wirka
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA
| | - Juyong B Kim
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA
| | - Daniel M DiRenzo
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA.
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102
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Incorporating Functional Annotations for Fine-Mapping Causal Variants in a Bayesian Framework Using Summary Statistics. Genetics 2016; 204:933-958. [PMID: 27655946 DOI: 10.1534/genetics.116.188953] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 09/07/2016] [Indexed: 12/21/2022] Open
Abstract
Functional annotations have been shown to improve both the discovery power and fine-mapping accuracy in genome-wide association studies. However, the optimal strategy to incorporate the large number of existing annotations is still not clear. In this study, we propose a Bayesian framework to incorporate functional annotations in a systematic manner. We compute the maximum a posteriori solution and use cross validation to find the optimal penalty parameters. By extending our previous fine-mapping method CAVIARBF into this framework, we require only summary statistics as input. We also derived an exact calculation of Bayes factors using summary statistics for quantitative traits, which is necessary when a large proportion of trait variance is explained by the variants of interest, such as in fine mapping expression quantitative trait loci (eQTL). We compared the proposed method with PAINTOR using different strategies to combine annotations. Simulation results show that the proposed method achieves the best accuracy in identifying causal variants among the different strategies and methods compared. We also find that for annotations with moderate effects from a large annotation pool, screening annotations individually and then combining the top annotations can produce overly optimistic results. We applied these methods on two real data sets: a meta-analysis result of lipid traits and a cis-eQTL study of normal prostate tissues. For the eQTL data, incorporating annotations significantly increased the number of potential causal variants with high probabilities.
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103
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Lawrenson K, Kar S, McCue K, Kuchenbaeker K, Michailidou K, Tyrer J, Beesley J, Ramus SJ, Li Q, Delgado MK, Lee JM, Aittomäki K, Andrulis IL, Anton-Culver H, Arndt V, Arun BK, Arver B, Bandera EV, Barile M, Barkardottir RB, Barrowdale D, Beckmann MW, Benitez J, Berchuck A, Bisogna M, Bjorge L, Blomqvist C, Blot W, Bogdanova N, Bojesen A, Bojesen SE, Bolla MK, Bonanni B, Børresen-Dale AL, Brauch H, Brennan P, Brenner H, Bruinsma F, Brunet J, Buhari SA, Burwinkel B, Butzow R, Buys SS, Cai Q, Caldes T, Campbell I, Canniotto R, Chang-Claude J, Chiquette J, Choi JY, Claes KBM, Cook LS, Cox A, Cramer DW, Cross SS, Cybulski C, Czene K, Daly MB, Damiola F, Dansonka-Mieszkowska A, Darabi H, Dennis J, Devilee P, Diez O, Doherty JA, Domchek SM, Dorfling CM, Dörk T, Dumont M, Ehrencrona H, Ejlertsen B, Ellis S, Engel C, Lee E, Evans DG, Fasching PA, Feliubadalo L, Figueroa J, Flesch-Janys D, Fletcher O, Flyger H, Foretova L, Fostira F, Foulkes WD, Fridley BL, Friedman E, Frost D, Gambino G, Ganz PA, Garber J, García-Closas M, Gentry-Maharaj A, Ghoussaini M, Giles GG, Glasspool R, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Goode EL, Goodman MT, Greene MH, Gronwald J, Guénel P, Haiman CA, Hall P, Hallberg E, Hamann U, Hansen TVO, Harrington PA, Hartman M, Hassan N, Healey S, Heitz F, Herzog J, Høgdall E, Høgdall CK, Hogervorst FBL, Hollestelle A, Hopper JL, Hulick PJ, Huzarski T, Imyanitov EN, Isaacs C, Ito H, Jakubowska A, Janavicius R, Jensen A, John EM, Johnson N, Kabisch M, Kang D, Kapuscinski M, Karlan BY, Khan S, Kiemeney LA, Kjaer SK, Knight JA, Konstantopoulou I, Kosma VM, Kristensen V, Kupryjanczyk J, Kwong A, de la Hoya M, Laitman Y, Lambrechts D, Le N, De Leeneer K, Lester J, Levine DA, Li J, Lindblom A, Long J, Lophatananon A, Loud JT, Lu K, Lubinski J, Mannermaa A, Manoukian S, Le Marchand L, Margolin S, Marme F, Massuger LFAG, Matsuo K, Mazoyer S, McGuffog L, McLean C, McNeish I, Meindl A, Menon U, Mensenkamp AR, Milne RL, Montagna M, Moysich KB, Muir K, Mulligan AM, Nathanson KL, Ness RB, Neuhausen SL, Nevanlinna H, Nord S, Nussbaum RL, Odunsi K, Offit K, Olah E, Olopade OI, Olson JE, Olswold C, O'Malley D, Orlow I, Orr N, Osorio A, Park SK, Pearce CL, Pejovic T, Peterlongo P, Pfeiler G, Phelan CM, Poole EM, Pylkäs K, Radice P, Rantala J, Rashid MU, Rennert G, Rhenius V, Rhiem K, Risch HA, Rodriguez G, Rossing MA, Rudolph A, Salvesen HB, Sangrajrang S, Sawyer EJ, Schildkraut JM, Schmidt MK, Schmutzler RK, Sellers TA, Seynaeve C, Shah M, Shen CY, Shu XO, Sieh W, Singer CF, Sinilnikova OM, Slager S, Song H, Soucy P, Southey MC, Stenmark-Askmalm M, Stoppa-Lyonnet D, Sutter C, Swerdlow A, Tchatchou S, Teixeira MR, Teo SH, Terry KL, Terry MB, Thomassen M, Tibiletti MG, Tihomirova L, Tognazzo S, Toland AE, Tomlinson I, Torres D, Truong T, Tseng CC, Tung N, Tworoger SS, Vachon C, van den Ouweland AMW, van Doorn HC, van Rensburg EJ, Van't Veer LJ, Vanderstichele A, Vergote I, Vijai J, Wang Q, Wang-Gohrke S, Weitzel JN, Wentzensen N, Whittemore AS, Wildiers H, Winqvist R, Wu AH, Yannoukakos D, Yoon SY, Yu JC, Zheng W, Zheng Y, Khanna KK, Simard J, Monteiro AN, French JD, Couch FJ, Freedman ML, Easton DF, Dunning AM, Pharoah PD, Edwards SL, Chenevix-Trench G, Antoniou AC, Gayther SA. Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus. Nat Commun 2016; 7:12675. [PMID: 27601076 PMCID: PMC5023955 DOI: 10.1038/ncomms12675] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 07/20/2016] [Indexed: 02/02/2023] Open
Abstract
A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10(-20)), ER-negative BC (P=1.1 × 10(-13)), BRCA1-associated BC (P=7.7 × 10(-16)) and triple negative BC (P-diff=2 × 10(-5)). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10(-3)) and ABHD8 (P<2 × 10(-3)). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3'-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk.
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Affiliation(s)
- Kate Lawrenson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Siddhartha Kar
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Karen McCue
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Karoline Kuchenbaeker
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Kyriaki Michailidou
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jonathan Tyrer
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jonathan Beesley
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Susan J. Ramus
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Qiyuan Li
- Medical College, Xiamen University, Xiamen 361102, China
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Melissa K. Delgado
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Janet M. Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki 00029 HUS, Finland
| | - Irene L. Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute, School of Medicine, University of California Irvine, Irvine, California 92697, USA
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Banu K. Arun
- University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Brita Arver
- Department of Oncology, Karolinska University Hospital, Stockholm 171 77, Sweden
| | - Elisa V. Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Monica Barile
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan 20141, Italy
| | - Rosa B. Barkardottir
- Department of Pathology, Landspitali University Hospital and BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik 600169-2039, Iceland
| | - Daniel Barrowdale
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Matthias W. Beckmann
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen 91054, Germany
| | - Javier Benitez
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid E-28029, Spain
- Centro de Investigación en Red de Enfermedades Raras, Valencia 28029, Spain
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Maria Bisogna
- Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York 10065, USA
| | - Line Bjorge
- Department of Gynecology and Obstetrics, Haukeland University Hospital, 5021 Bergen, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki FIN-00029, Finland
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
- International Epidemiology Institute, Rockville, Maryland 20850, USA
| | - Natalia Bogdanova
- Gynaecology Research Unit, Hannover Medical School, Hannover D-30625, Germany
| | - Anders Bojesen
- Department of Clinical Genetics, Vejle Hospital, Vejle 7100, Denmark
| | - Stig E. Bojesen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev 2730, Denmark
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, Herlev 2730, Denmark
| | - Manjeet K. Bolla
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan 20141, Italy
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo N-0310, Norway
- K.G. Jebsen Center for Breast Cancer Research, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo N-0310, Norway
| | - Hiltrud Brauch
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart D-70376, Germany
- University of Tübingen, Tübingen 72074, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon 69008, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ), Heidelberg 69121, Germany
| | - Fiona Bruinsma
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
| | - Joan Brunet
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBGI (Institut d'Investigació Biomèdica de Girona), Catalan Institute of Oncology, Girona 08908, Spain
| | - Shaik Ahmad Buhari
- Department of Surgery, National University Health System, Singapore 119077, Singapore
| | - Barbara Burwinkel
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg 69120, Germany
| | - Ralf Butzow
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki 00029 HUS, Finland
- Department of Pathology, Helsinki University Central Hospital, Helsinki 00029, Finland
| | - Saundra S. Buys
- Department of Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
| | - Trinidad Caldes
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC (El Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid 28040, Spain
| | - Ian Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria 3002, Australia
| | - Rikki Canniotto
- Cancer Pathology & Prevention, Division of Cancer Prevention and Population Sciences, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo 14263, New York, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69121, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Jocelyne Chiquette
- Unité de recherche en santé des populations, Centre des maladies du sein Deschênes-Fabia, Centre de recherche FRSQ du Centre hospitalier affilié universitaire de Québec, Québec City, Québec G1J 1Z4, Canada
| | - Ji-Yeob Choi
- Cancer Research Institute, Seoul National University, Seoul 08826, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | | | - Linda S. Cook
- Division of Epidemiology and Biostatistics, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Angela Cox
- Sheffield Cancer Research, Department of Oncology, University of Sheffield, Sheffield S10 2TN, UK
| | - Daniel W. Cramer
- Harvard HT Chan School of Public Health, Boston, Massachusetts 02115, USA
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Simon S. Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Cezary Cybulski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-115, Poland
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Mary B. Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| | - Francesca Damiola
- INSERM U1052, CNRS UMR5286, Université Lyon, Centre de Recherche en Cancérologie de Lyon, Lyon 69373, France
| | - Agnieszka Dansonka-Mieszkowska
- Department of Pathology and Laboratory Diagnostics the Maria Sklodowska Curie Memorial Cancer Center and Institute of Oncology, Warsaw 44-101, Poland
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Joe Dennis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden 2333, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333, The Netherlands
| | - Orland Diez
- Oncogenetics Group, University Hospital Vall d'Hebron, Vall d'Hebron Institute of Oncology (VHIO) and Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Jennifer A. Doherty
- Department of Community and Family Medicine, Section of Biostatistics & Epidemiology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03755, USA
| | - Susan M. Domchek
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | | | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover D-30625, Germany
| | - Martine Dumont
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, Québec G1V 4G2, Canada
| | - Hans Ehrencrona
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 751 05, Sweden
- Department of Clinical Genetics, Lund University Hospital, Lund 221 00, Sweden
| | - Bent Ejlertsen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, 2100 Copenhagen, Denmark
| | - Steve Ellis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04107 Leipzig, Germany
| | - Eunjung Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - D. Gareth Evans
- Genomic Medicine, Manchester Academic Health Sciences Centre, Institute of Human Development, Manchester University, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9PL, UK
| | - Peter A. Fasching
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen 91054, Germany
- University of California at Los Angeles, David Geffen School of Medicine, Department of Medicine, Division of Hematology and Oncology, Los Angeles California 90095, USA
| | - Lidia Feliubadalo
- Molecular Diagnostic Unit, Hereditary Cancer Program, IDIBELL (Bellvitge Biomedical Research Institute),Catalan Institute of Oncology, Barcelona 08908, Spain
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland 20892, USA
| | - Dieter Flesch-Janys
- Institute for Medical Biometrics and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
- Department of Cancer Epidemiology, Clinical Cancer Registry, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London SW7 3RP, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
| | - Lenka Foretova
- Masaryk Memorial Cancer Institute and Medical Faculty MU, 625 00 Brno, Czech Republic
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, (INRASTES) Institute of Nuclear and Radiological Sciences and Technology, National Centre for Scientific Research ‘Demokritos', Aghia Paraskevi Attikis, Athens 153 10, Greece
| | - William D. Foulkes
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montreal, Montreal, Quebec H2W 1S6, Canada
| | - Brooke L. Fridley
- Biostatistics and Informatics Shared Resource, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Eitan Friedman
- Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Debra Frost
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Gaetana Gambino
- Section of Genetic Oncology, Department of Laboratory Medicine, University and University Hospital of Pisa, Pisa 56126, Italy
| | - Patricia A. Ganz
- UCLA Schools of Medicine and Public Health, Division of Cancer Prevention & Control Research, Jonsson Comprehensive Cancer Center, Los Angeles, California 90024, USA
| | - Judy Garber
- Cancer Risk and Prevention Clinic, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland 20892, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | | | - Maya Ghoussaini
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Rosalind Glasspool
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, Glasgow G12 0YN, UK
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Mark S. Goldberg
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montreal, Québec H3A 1A1, Canada
- Department of Medicine, McGill University, Montreal, Québec H3A 1A1, Canada
| | - David E. Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
| | - Anna González-Neira
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid E-28029, Spain
| | - Ellen L. Goode
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55902, USA
| | - Marc T. Goodman
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
- Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Mark H. Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland 20892, USA
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, 70-204 Szczecin, Poland
| | - Pascal Guénel
- Environmental Epidemiology of Cancer, Center for Research in Epidemiology and Population Health, INSERM, 94805 Villejuif, France
- University Paris-Sud, 91405 Villejuif, France
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55902, USA
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Thomas V. O. Hansen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, 2100 Copenhagen, Denmark
| | - Patricia A. Harrington
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Mikael Hartman
- Department of Surgery, National University Health System, Singapore 119077, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore Singapore 119077, Singapore
| | - Norhashimah Hassan
- Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, 50603 Kuala Lumpur, Malaysia
- Cancer Research Initiatives Foundation, Subang Jaya, 47500 Selangor, Malaysia
| | - Sue Healey
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, 45136 Essen, Germany
- Department of Gynecology and Gynecologic Oncology, Dr Horst Schmidt Kliniken Wiesbaden, 65199 Wiesbaden, Germany
| | - Josef Herzog
- Clinical Cancer Genetics, for the City of Hope Clinical Cancer Genetics Community Research Network, Duarte California 91010, USA
| | - Estrid Høgdall
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, 2730 Copenhagen, Denmark
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | - Claus K. Høgdall
- Department of Gynecology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Antoinette Hollestelle
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, 3015 Rotterdam, The Netherlands
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Peter J. Hulick
- Center for Medical Genetics, NorthShore University Health System, Evanston, Illinois, 60201, USA
| | - Tomasz Huzarski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-115, Poland
| | | | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington District of Columbia 20057, USA
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Aichi 464-8681, Japan
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-115, Poland
| | - Ramunas Janavicius
- State Research Institute Centre for Innovative Medicine, LT-01102 Vilnius, Lithuania
| | - Allan Jensen
- Department of Gynecology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Esther M. John
- Department of Epidemiology, Cancer Prevention Institute of California, Fremont, California 94538, USA
| | - Nichola Johnson
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London SW7 3RP, UK
| | - Maria Kabisch
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Daehee Kang
- Cancer Research Institute, Seoul National University, Seoul 08826, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 08826, Korea
| | - Miroslav Kapuscinski
- Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Beth Y. Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Sofia Khan
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki 00029 HUS, Finland
| | - Lambertus A. Kiemeney
- Radboud University Medical Centre, Radboud Institute for Health Sciences, 6500 Nijmegen, The Netherlands
| | - Susanne Kruger Kjaer
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
- Department of Gynecology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Julia A. Knight
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario M5T 3M7, Canada
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, (INRASTES) Institute of Nuclear and Radiological Sciences and Technology, National Centre for Scientific Research ‘Demokritos', Aghia Paraskevi Attikis, Athens 153 10, Greece
| | - Veli-Matti Kosma
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, 70210 Kuopio, Finland
- Cancer Center, Kuopio University Hospital, 70210 Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, 70210 Kuopio, Finland
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo N-0310, Norway
- K.G. Jebsen Center for Breast Cancer Research, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo N-0310, Norway
- Department of Clinical Molecular Biology, Oslo University Hospital, University of Oslo, 1478 Oslo, Norway
| | - Jolanta Kupryjanczyk
- Department of Pathology and Laboratory Diagnostics the Maria Sklodowska Curie Memorial Cancer Center and Institute of Oncology, Warsaw 44-101, Poland
| | - Ava Kwong
- The Hong Kong Hereditary Breast Cancer Family Registry, Cancer Genetics Center, Hong Kong Sanatorium and Hospital, Hong Kong, China
- Department of Surgery, The University of Hong Kong, Hong Kong, China
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC (El Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid 28040, Spain
| | - Yael Laitman
- Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Diether Lambrechts
- Vesalius Research Center, VIB, 3000 Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, 3000 Leuven, Belgium
| | - Nhu Le
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University, Ghent 9000, Belgium
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Douglas A. Levine
- Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York 10065, USA
| | - Jingmei Li
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
| | - Artitaya Lophatananon
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry CV4 7AL, UK
| | - Jennifer T. Loud
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland 20892, USA
| | - Karen Lu
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-115, Poland
| | - Arto Mannermaa
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, 70210 Kuopio, Finland
- Cancer Center, Kuopio University Hospital, 70210 Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, 70210 Kuopio, Finland
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT), 20133 Milan, Italy
| | | | - Sara Margolin
- Department of Oncology - Pathology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Frederik Marme
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg 69120, Germany
- National Center for Tumour Diseases, University of Heidelberg, 69117 Heidelberg, Germany
| | - Leon F. A. G. Massuger
- Department of Gynaecology, Radboud University Medical Centre, 6500 Nijmegen, The Netherlands
| | - Keitaro Matsuo
- Department of Preventive Medicine, Kyushu University Faculty of Medical Sciences, Fukuoka 812-8582, Japan
| | - Sylvie Mazoyer
- INSERM U1052, CNRS UMR5286, Université Lyon, Centre de Recherche en Cancérologie de Lyon, Lyon 69373, France
| | - Lesley McGuffog
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Catriona McLean
- Anatomical Pathology, The Alfred Hospital, Melbourne, Victoria 3004, Australia
| | - Iain McNeish
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Beatson Institute for Cancer Research, Glasgow G61 1BD, UK
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, 81675 Munich, Germany
| | - Usha Menon
- Women's Cancer, UCL EGA Institute for Women's Health, London WC1E 6AU, UK
| | - Arjen R. Mensenkamp
- Department of Human Genetics, Radboud University Medical Centre, 6500 Nijmegen, The Netherlands
| | - Roger L. Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Instituto Oncologico Veneto IOV, IRCCS, 35128 Padua, Italy
| | - Kirsten B. Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry CV4 7AL, UK
- Institute of Population Health, University of Manchester, Manchester M13 9PL, UK
| | - Anna Marie Mulligan
- Laboratory Medicine Program, University Health Network, Toronto, Ontario M5G 1L7, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Katherine L. Nathanson
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Roberta B. Ness
- The University of Texas School of Public Health, Houston, Texas 77030, USA
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki 00029 HUS, Finland
| | - Silje Nord
- K.G. Jebsen Center for Breast Cancer Research, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo N-0310, Norway
| | - Robert L. Nussbaum
- Department of Medicine and Genetics, University of California, San Francisco, California 94143, USA
| | - Kunle Odunsi
- Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York 10065, USA
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, 1122 Budapest, Hungary
| | - Olufunmilayo I. Olopade
- Center for Clinical Cancer Genetics and Global Health, University of Chicago Medical Center, Chicago, Illinois 60637, USA
| | - Janet E. Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55902, USA
| | - Curtis Olswold
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55902, USA
| | - David O'Malley
- The Ohio State University and the James Cancer Center, Columbus, Ohio 43210, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York 10017, USA
| | - Nick Orr
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Ana Osorio
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Centre (CNIO), 28019 Madrid, Spain
- Biomedical Network on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Sue Kyung Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 08826, Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul, 03080 Korea
| | - Celeste L. Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Tanja Pejovic
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon 97239, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Paolo Peterlongo
- IFOM, The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, 16 20139 Milan, Italy
| | - Georg Pfeiler
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Catherine M. Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida 33606, USA
| | - Elizabeth M. Poole
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumour Biology, Northern Finland Laboratory Centre NordLab, FI-90014 Oulu, Finland
- Laboratory of Cancer Genetics and Tumour Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, FI-90014 Oulu, Finland
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT), 20133 Milan, Italy
| | - Johanna Rantala
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Muhammad Usman Rashid
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore 54000, Pakistan
| | - Gad Rennert
- Clalit National Israeli Cancer Control Center and Department of Community Medicine and Epidemiology, Carmel Medical Center and B. Rappaport Faculty of Medicine, Haifa 34362, Israel
| | - Valerie Rhenius
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Kerstin Rhiem
- Centre of Familial Breast and Ovarian Cancer, Department of Gynaecology and Obstetrics and Centre for Integrated Oncology (CIO), Center for Molecular Medicine Cologne (CMMC), University Hospital of Cologne, 50931 Cologne, Germany
| | - Harvey A. Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut 06510, USA
| | - Gus Rodriguez
- Division of Gynecologic Oncology, NorthShore University HealthSystem, Evanston, Illinois 60201, USA
| | - Mary Anne Rossing
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
- Department of Epidemiology, University of Washington, Seattle, Washington 98109, USA
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69121, Germany
| | - Helga B. Salvesen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, 5021 Bergen, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway
| | | | - Elinor J. Sawyer
- Research Oncology, Guy's Hospital, King's College London, London SE1 9RT, UK
| | - Joellen M. Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
- Cancer Control and Population Sciences, Duke Cancer Institute, Durham, North Carolina 27710, USA
| | - Marjanka K. Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, The Netherlands
| | - Rita K. Schmutzler
- Division of Molecular Gyneco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, 50676 Cologne, Germany
- Center for Integrated Oncology, University Hospital of Cologne, 50676 Cologne, Germany
- Center for Molecular Medicine, University Hospital of Cologne, 50676 Cologne, Germany
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, 50676 Cologne, Germany
| | - Thomas A. Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida 33606, USA
| | - Caroline Seynaeve
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, 3015 Rotterdam, The Netherlands
| | - Mitul Shah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Chen-Yang Shen
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- School of Public Health, China Medical University, Taichung 404, Taiwan
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
| | - Weiva Sieh
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford California 94305, USA
| | - Christian F. Singer
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Olga M. Sinilnikova
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon – Centre Léon Bérard, Lyon 69008, France
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon 69003, France
| | - Susan Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55902, USA
| | - Honglin Song
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, Québec G1V 4G2, Canada
| | - Melissa C. Southey
- Department of Pathology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Marie Stenmark-Askmalm
- Department of Clinical Genetics, Lund University Hospital, Lund 221 00, Sweden
- Division of Clinical Genetics, Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Dominique Stoppa-Lyonnet
- Institut Curie, Department of Tumour Biology, Paris, France; Institut Curie, INSERM U830, 75248 Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, 75270 Paris, France
| | - Christian Sutter
- Institute of Human Genetics, Department of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Anthony Swerdlow
- Division of Breast Cancer Research, The Institute of Cancer Research, London SW7 3RP, UK
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Sandrine Tchatchou
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Manuel R. Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto 4200-072, Portugal
- Biomedical Sciences Institute (ICBAS), Porto University, Porto 4099-002, Portugal
| | - Soo H. Teo
- Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, 50603 Kuala Lumpur, Malaysia
- Cancer Research Initiatives Foundation, Subang Jaya, 47500 Selangor, Malaysia
| | - Kathryn L. Terry
- Harvard HT Chan School of Public Health, Boston, Massachusetts 02115, USA
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York 10027, USA
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark
| | - Maria Grazia Tibiletti
- UO Anatomia Patologica, Ospedale di Circolo-Università dell'Insubria, 21100 Varese, Italy
| | - Laima Tihomirova
- Latvian Biomedical Research and Study Centre, Riga LV-1067, Latvia
| | - Silvia Tognazzo
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV - IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico), 64 - 35128 Padua, Italy
| | - Amanda Ewart Toland
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 7BN, UK
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Cra. 7 #40-62 Bogota, Colombia
| | - Thérèse Truong
- Environmental Epidemiology of Cancer, Center for Research in Epidemiology and Population Health, INSERM, 94805 Villejuif, France
- University Paris-Sud, 91405 Villejuif, France
| | - Chiu-chen Tseng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Shelley S. Tworoger
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Celine Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55902, USA
| | | | - Helena C. van Doorn
- Department of Gynecology, Family Cancer Clinic, Erasmus MC Cancer Institute, 3015 CE Rotterdam, The Netherlands
| | | | - Laura J. Van't Veer
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, The Netherlands
| | - Adriaan Vanderstichele
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Ignace Vergote
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York 10065, USA
| | - Qin Wang
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | | | - Jeffrey N. Weitzel
- Clinical Cancer Genetics, for the City of Hope Clinical Cancer Genetics Community Research Network, Duarte California 91010, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda Maryland 20892, USA
| | - Alice S. Whittemore
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford California 94305, USA
| | - Hans Wildiers
- Multidisciplinary Breast Center, Department of General Medical Oncology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumour Biology, Northern Finland Laboratory Centre NordLab, FI-90014 Oulu, Finland
- Laboratory of Cancer Genetics and Tumour Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, FI-90014 Oulu, Finland
| | - Anna H. Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research ‘Demokritos', Athens 153 10, Greece
| | - Sook-Yee Yoon
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, 47500 Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, 59100 Kuala Lumpur, Malaysia
| | - Jyh-Cherng Yu
- Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, 114 Taiwan
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
| | - Ying Zheng
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, Québec G1V 4G2, Canada
| | - Alvaro N. Monteiro
- Cancer Epidemiology Program, Division of Population Sciences, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
| | - Juliet D. French
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Fergus J. Couch
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55902, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Matthew L. Freedman
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Douglas F. Easton
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Alison M. Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Paul D. Pharoah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Stacey L. Edwards
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | | | - Antonis C. Antoniou
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Simon A. Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
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Abstract
Prostate cancer is the most commonly diagnosed cancer among men in the United States as well as most Western countries. A significant proportion of men report having a positive family history of prostate cancer in a first-degree relative (father, brother, son), which is important in that family history is one of the only established risk factors for the disease and plays a role in decision-making for prostate cancer screening. Familial aggregation of prostate cancer is considered a surrogate marker of genetic susceptibility to developing the disease, but shared environment cannot be excluded as an explanation for clustering of cases among family members. Prostate cancer is both a clinically and genetically heterogeneous disease with inherited factors predicted to account for 40%-50% of cases, comprised of both rare highly to moderately penetrant gene variants, as well as common genetic variants of low penetrance. Most notably, HOXB13 and BRCA2 mutations have been consistently shown to increase prostate cancer risk, and are more commonly observed among patients diagnosed with early-onset disease. A recurrent mutation in HOXB13 has been shown to predispose to hereditary prostate cancer (HPC), and BRCA2 mutations to hereditary breast and ovarian cancer (HBOC). Genome-wide association studies (GWAS) have also identified approximately 100 loci that associate with modest (odds ratios <2.0) increases in prostate cancer risk, only some of which have been replicated in subsequent studies. Despite these efforts, genetic testing in prostate cancer lags behind other common tumors like breast and colorectal cancer. To date, National Comprehensive Cancer Network (NCCN) guidelines have highly selective criteria for BRCA1/2 testing for men with prostate cancer based on personal history and/or specific family cancer history. Tumor sequencing is also leading to the identification of germline mutations in prostate cancer patients, informing the scope of inheritance. Advances in genetic testing for inherited and familial prostate cancer (FPC) are needed to inform personalized cancer risk screening and treatment approaches.
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Affiliation(s)
- Veda N Giri
- Cancer Risk Assessment and Clinical Cancer Genetics Program, Division of Population Science, Department of Medical Oncology, Center of Excellence for Cancer Risk, Prevention, and Control Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA.
| | - Jennifer L Beebe-Dimmer
- Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine Department of Oncology, Detroit, MI
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Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer. Nat Genet 2016; 48:1142-50. [PMID: 27526323 DOI: 10.1038/ng.3637] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 07/06/2016] [Indexed: 12/16/2022]
Abstract
Long noncoding RNAs (lncRNAs) represent an attractive class of candidates to mediate cancer risk. Through integrative analysis of the lncRNA transcriptome with genomic data and SNP data from prostate cancer genome-wide association studies (GWAS), we identified 45 candidate lncRNAs associated with risk to prostate cancer. We further evaluated the mechanism underlying the top hit, PCAT1, and found that a risk-associated variant at rs7463708 increases binding of ONECUT2, a novel androgen receptor (AR)-interacting transcription factor, at a distal enhancer that loops to the PCAT1 promoter, resulting in upregulation of PCAT1 upon prolonged androgen treatment. In addition, PCAT1 interacts with AR and LSD1 and is required for their recruitment to the enhancers of GNMT and DHCR24, two androgen late-response genes implicated in prostate cancer development and progression. PCAT1 promotes prostate cancer cell proliferation and tumor growth in vitro and in vivo. These findings suggest that modulating lncRNA expression is an important mechanism for risk-associated SNPs in promoting prostate transformation.
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Lee M, Crawford NPS. Defining the Influence of Germline Variation on Metastasis Using Systems Genetics Approaches. Adv Cancer Res 2016; 132:73-109. [PMID: 27613130 DOI: 10.1016/bs.acr.2016.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cancer is estimated to be responsible for 8 million deaths worldwide and over half a million deaths every year in the United States. The majority of cancer-related deaths in solid tumors is directly associated with the effects of metastasis. While the influence of germline factors on cancer risk and development has long been recognized, the contribution of hereditary variation to tumor progression and metastasis has only gained acceptance more recently. A variety of approaches have been used to define how hereditary variation influences tumor progression and metastasis. One approach that garnered much early attention was epidemiological studies of cohorts of cancer patients, which demonstrated that specific loci within the human genome are associated with a differential propensity for aggressive tumor development. However, a powerful, and somewhat underutilized approach has been the use of systems genetics approaches in transgenic mouse models of human cancer. Such approaches are typically multifaceted, and involve integration of multiple lines of evidence derived, for example, from genetic and transcriptomic screens of genetically diverse mouse models of cancer, coupled with bioinformatics analysis of human cancer datasets, and functional analysis of candidate genes. These methodologies have allowed for the identification of multiple hereditary metastasis susceptibility genes, with wide-ranging cellular functions including regulation of gene transcription, cell proliferation, and cell-cell adhesion. In this chapter, we review how each of these approaches have facilitated the identification of these hereditary metastasis modifiers, the molecular functions of these metastasis-associated genes, and the implications of these findings upon patient survival.
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Affiliation(s)
- M Lee
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, MD, United States
| | - N P S Crawford
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, MD, United States.
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107
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Stueve TR, Marconett CN, Zhou B, Borok Z, Laird-Offringa IA. The importance of detailed epigenomic profiling of different cell types within organs. Epigenomics 2016; 8:817-29. [PMID: 27305639 PMCID: PMC5066118 DOI: 10.2217/epi-2016-0005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The human body consists of hundreds of kinds of cells specified from a single genome overlaid with cell type-specific epigenetic information. Comprehensively profiling the body's distinct epigenetic landscapes will allow researchers to verify cell types used in regenerative medicine and to determine the epigenetic effects of disease, environmental exposures and genetic variation. Key marks/factors that should be investigated include regions of nucleosome-free DNA accessible to regulatory factors, histone marks defining active enhancers and promoters, DNA methylation levels, regulatory RNAs, and factors controlling the three-dimensional conformation of the genome. Here we use the lung to illustrate the importance of investigating an organ's purified cell epigenomes, and outline the challenges and promise of realizing a comprehensive catalog of primary cell epigenomes.
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Affiliation(s)
- Theresa Ryan Stueve
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Department of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Crystal N Marconett
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Beiyun Zhou
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Division of Pulmonary & Critical Care Medicine, Department of Medicine, Will Rogers Institute Pulmonary Research Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Zea Borok
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Department of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Division of Pulmonary & Critical Care Medicine, Department of Medicine, Will Rogers Institute Pulmonary Research Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Ite A Laird-Offringa
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Department of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
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108
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Groner AC, Cato L, de Tribolet-Hardy J, Bernasocchi T, Janouskova H, Melchers D, Houtman R, Cato ACB, Tschopp P, Gu L, Corsinotti A, Zhong Q, Fankhauser C, Fritz C, Poyet C, Wagner U, Guo T, Aebersold R, Garraway LA, Wild PJ, Theurillat JP, Brown M. TRIM24 Is an Oncogenic Transcriptional Activator in Prostate Cancer. Cancer Cell 2016; 29:846-858. [PMID: 27238081 PMCID: PMC5124371 DOI: 10.1016/j.ccell.2016.04.012] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 12/15/2015] [Accepted: 04/27/2016] [Indexed: 01/22/2023]
Abstract
Androgen receptor (AR) signaling is a key driver of prostate cancer (PC). While androgen-deprivation therapy is transiently effective in advanced disease, tumors often progress to a lethal castration-resistant state (CRPC). We show that recurrent PC-driver mutations in speckle-type POZ protein (SPOP) stabilize the TRIM24 protein, which promotes proliferation under low androgen conditions. TRIM24 augments AR signaling, and AR and TRIM24 co-activated genes are significantly upregulated in CRPC. Expression of TRIM24 protein increases from primary PC to CRPC, and both TRIM24 protein levels and the AR/TRIM24 gene signature predict disease recurrence. Analyses in CRPC cells reveal that the TRIM24 bromodomain and the AR-interacting motif are essential to support proliferation. These data provide a rationale for therapeutic TRIM24 targeting in SPOP mutant and CRPC patients.
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Affiliation(s)
- Anna C Groner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Laura Cato
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonas de Tribolet-Hardy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Hana Janouskova
- Institute of Oncology Research, Bellinzona 6500, Switzerland
| | | | - René Houtman
- PamGene International, Den Bosch 521HH, the Netherlands
| | - Andrew C B Cato
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Patrick Tschopp
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Lei Gu
- Division of Newborn Medicine, Children's Hospital Boston and Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Andrea Corsinotti
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH16 4UU, UK; Laboratory Animal Resource Center, Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Qing Zhong
- Institute of Surgical Pathology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Christian Fankhauser
- Institute of Surgical Pathology, University Hospital Zurich, Zurich 8091, Switzerland; Department of Urology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Christine Fritz
- Institute of Surgical Pathology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Cédric Poyet
- Department of Urology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Ulrich Wagner
- Institute of Surgical Pathology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich 8093, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich 8093, Switzerland; Faculty of Science, University of Zurich, Zurich 8057, Switzerland
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Peter J Wild
- Institute of Surgical Pathology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Jean-Philippe Theurillat
- Institute of Oncology Research, Bellinzona 6500, Switzerland; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne 1011, Switzerland.
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
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109
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Ahmed M, Dorling L, Kerns S, Fachal L, Elliott R, Partliament M, Rosenstein BS, Vega A, Gómez-Caamaño A, Barnett G, Dearnaley DP, Hall E, Sydes M, Burnet N, Pharoah PDP, Eeles R, West CML. Common genetic variation associated with increased susceptibility to prostate cancer does not increase risk of radiotherapy toxicity. Br J Cancer 2016; 114:1165-74. [PMID: 27070714 PMCID: PMC4865979 DOI: 10.1038/bjc.2016.94] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/04/2016] [Accepted: 03/08/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Numerous germline single-nucleotide polymorphisms increase susceptibility to prostate cancer, some lying near genes involved in cellular radiation response. This study investigated whether prostate cancer patients with a high genetic risk have increased toxicity following radiotherapy. METHODS The study included 1560 prostate cancer patients from four radiotherapy cohorts: RAPPER (n=533), RADIOGEN (n=597), GenePARE (n=290) and CCI (n=150). Data from genome-wide association studies were imputed with the 1000 Genomes reference panel. Individuals were genetically similar with a European ancestry based on principal component analysis. Genetic risks were quantified using polygenic risk scores. Regression models tested associations between risk scores and 2-year toxicity (overall, urinary frequency, decreased stream, rectal bleeding). Results were combined across studies using standard inverse-variance fixed effects meta-analysis methods. RESULTS A total of 75 variants were genotyped/imputed successfully. Neither non-weighted nor weighted polygenic risk scores were associated with late radiation toxicity in individual studies (P>0.11) or after meta-analysis (P>0.24). No individual variant was associated with 2-year toxicity. CONCLUSION Patients with a high polygenic susceptibility for prostate cancer have no increased risk for developing late radiotherapy toxicity. These findings suggest that patients with a genetic predisposition for prostate cancer, inferred by common variants, can be safely treated using current standard radiotherapy regimens.
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Affiliation(s)
- Mahbubl Ahmed
- The Institute of Cancer Research, Royal Marsden NHS Foundation Trust, 123 Old Brompton Road, London SW7 3RP, UK
| | - Leila Dorling
- Centre for Cancer Genetic Epidemiology, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Sarah Kerns
- Department of Radiation Oncology, University of Rochester Medical Centre, Saunders Research Building, 265 Crittenden Boulevard, Rochester, NY 14620, USA
| | - Laura Fachal
- Centre for Cancer Genetic Epidemiology, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
- Genomic Medicine Group, CIBERER, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Rebecca Elliott
- Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital NHS Foundation Trust, Manchester M20 4BX, UK
| | | | - Barry S Rosenstein
- Department of Radiation Oncology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, IDIS, CIBERER, Santiago de Compostela 15706, Spain
| | - Antonio Gómez-Caamaño
- Department of Radiation Oncology, USC University Hospital Complex, SERGAS, Santiago de Compostela, Spain
| | - Gill Barnett
- Centre for Cancer Genetic Epidemiology, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - David P Dearnaley
- The Institute of Cancer Research, Royal Marsden NHS Foundation Trust, 123 Old Brompton Road, London SW7 3RP, UK
| | - Emma Hall
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London SM2 5NG, UK
| | - Matt Sydes
- Clinical Trials Unit (CTU), Medical Research Council, London WC2B 6NH, UK
| | - Neil Burnet
- Department of Oncology, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ UK
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Ros Eeles
- The Institute of Cancer Research, Royal Marsden NHS Foundation Trust, 123 Old Brompton Road, London SW7 3RP, UK
| | - Catharine M L West
- Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital NHS Foundation Trust, Manchester M20 4BX, UK
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110
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Gusev A, Shi H, Kichaev G, Pomerantz M, Li F, Long HW, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Zheng W, Pettaway CA, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Chokkalingam AP, John EM, Murphy AB, Signorello LB, Carpten J, Leske MC, Wu SY, Hennis AJM, Neslund-Dudas C, Hsing AW, Chu L, Goodman PJ, Klein EA, Witte JS, Casey G, Kaggwa S, Cook MB, Stram DO, Blot WJ, Eeles RA, Easton D, Kote-Jarai ZS, Al Olama AA, Benlloch S, Muir K, Giles GG, Southey MC, Fitzgerald LM, Gronberg H, Wiklund F, Aly M, Henderson BE, Schleutker J, Wahlfors T, Tammela TLJ, Nordestgaard BG, Key TJ, Travis RC, Neal DE, Donovan JL, Hamdy FC, Pharoah P, Pashayan N, Khaw KT, Stanford JL, Thibodeau SN, McDonnell SK, Schaid DJ, Maier C, Vogel W, Luedeke M, Herkommer K, Kibel AS, Cybulski C, Wokolorczyk D, Kluzniak W, Cannon-Albright L, Teerlink C, Brenner H, Dieffenbach AK, Arndt V, Park JY, Sellers TA, Lin HY, Slavov C, Kaneva R, Mitev V, Batra J, Spurdle A, Clements JA, Teixeira MR, Pandha H, Michael A, Paulo P, Maia S, Kierzek A, Conti DV, Albanes D, Berg C, Berndt SI, Campa D, Crawford ED, Diver WR, Gapstur SM, Gaziano JM, Giovannucci E, Hoover R, Hunter DJ, Johansson M, Kraft P, Le Marchand L, Lindström S, Navarro C, Overvad K, Riboli E, Siddiq A, Stevens VL, Trichopoulos D, Vineis P, Yeager M, Trynka G, Raychaudhuri S, Schumacher FR, Price AL, Freedman ML, Haiman CA, Pasaniuc B. Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation. Nat Commun 2016; 7:10979. [PMID: 27052111 PMCID: PMC4829663 DOI: 10.1038/ncomms10979] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 02/03/2016] [Indexed: 12/22/2022] Open
Abstract
Although genome-wide association studies have identified over 100 risk loci that explain ∼33% of familial risk for prostate cancer (PrCa), their functional effects on risk remain largely unknown. Here we use genotype data from 59,089 men of European and African American ancestries combined with cell-type-specific epigenetic data to build a genomic atlas of single-nucleotide polymorphism (SNP) heritability in PrCa. We find significant differences in heritability between variants in prostate-relevant epigenetic marks defined in normal versus tumour tissue as well as between tissue and cell lines. The majority of SNP heritability lies in regions marked by H3k27 acetylation in prostate adenoc7arcinoma cell line (LNCaP) or by DNaseI hypersensitive sites in cancer cell lines. We find a high degree of similarity between European and African American ancestries suggesting a similar genetic architecture from common variation underlying PrCa risk. Our findings showcase the power of integrating functional annotation with genetic data to understand the genetic basis of PrCa.
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Affiliation(s)
- Alexander Gusev
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Huwenbo Shi
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Gleb Kichaev
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Mark Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Fugen Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Henry W. Long
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02115, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Sue A. Ingles
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Rick A. Kittles
- University of Arizona College of Medicine and University of Arizona Cancer Center, Tucson, Arizona 85721, USA
| | - Sara S. Strom
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Benjamin A. Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, Michigan 48202, USA
| | - Barbara Nemesure
- Department of Preventive Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - William B. Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, Maryland 21205, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Curtis A. Pettaway
- Department of Urology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Edward D. Yeboah
- Korle Bu Teaching Hospital, Accra, Ghana
- University of Ghana Medical School, Accra, Ghana
| | - Yao Tettey
- Korle Bu Teaching Hospital, Accra, Ghana
- University of Ghana Medical School, Accra, Ghana
| | - Richard B. Biritwum
- Korle Bu Teaching Hospital, Accra, Ghana
- University of Ghana Medical School, Accra, Ghana
| | - Andrew A. Adjei
- Korle Bu Teaching Hospital, Accra, Ghana
- University of Ghana Medical School, Accra, Ghana
| | - Evelyn Tay
- Korle Bu Teaching Hospital, Accra, Ghana
- University of Ghana Medical School, Accra, Ghana
| | | | | | | | - Esther M. John
- Cancer Prevention Institute of California, Fremont, California 94538, USA
- Stanford University School of Medicine and Stanford Cancer Institute, Palo Alto, California 94305, USA
| | - Adam B. Murphy
- Department of Urology, Northwestern University, Chicago, Illinois 60611, USA
| | - Lisa B. Signorello
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- International Epidemiology Institute, Rockville, Maryland 20850, USA
| | - John Carpten
- The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - M. Cristina Leske
- Department of Preventive Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Suh-Yuh Wu
- Department of Preventive Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Anslem J. M. Hennis
- Department of Preventive Medicine, Stony Brook University, Stony Brook, New York 11794, USA
- Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies, Bridgetown, Barbados
| | | | - Ann W. Hsing
- Cancer Prevention Institute of California, Fremont, California 94538, USA
- Stanford University School of Medicine and Stanford Cancer Institute, Palo Alto, California 94305, USA
| | - Lisa Chu
- Cancer Prevention Institute of California, Fremont, California 94538, USA
- Stanford University School of Medicine and Stanford Cancer Institute, Palo Alto, California 94305, USA
| | - Phyllis J. Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Eric A. Klein
- Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - John S. Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California 94118, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California 94118, USA
| | - Graham Casey
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Sam Kaggwa
- Department of Surgery, Makerere University College of Health Sciences, Kampala 94118, Uganda
| | - Michael B. Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Daniel O. Stram
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - William J. Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- International Epidemiology Institute, Rockville, Maryland 20850, USA
| | - Rosalind A. Eeles
- The Institute of Cancer Research, Sutton SM2 5NG, UK
- Royal Marsden National Health Service (NHS) Foundation Trust, London and Sutton, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | | | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Sara Benlloch
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester M13 9PL, UK
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Graham G. Giles
- Cancer Epidemiology Centre, The Cancer Council Victoria, 615 St Kilda Road, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria 3004, Australia
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Grattan Street, Parkville, Victoria 3010, Australia
| | - Liesel M. Fitzgerald
- Cancer Epidemiology Centre, The Cancer Council Victoria, 615 St Kilda Road, Melbourne, Victoria 3004, Australia
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm 171 77, Sweden
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm 171 77, Sweden
| | - Markus Aly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm 171 77, Sweden
- Department of Clinical Sciences at Danderyds Hospital, Stockholm 171 77, Sweden
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90007, USA
| | - Johanna Schleutker
- Department of Medical Biochemistry and Genetics Institute of Biomedicine Kiinamyllynkatu 10, University of Turku, Turku FI-20014, Finland
- BioMediTech, University of Tampere and FimLab Laboratories, Tampere 33200, Finland
| | - Tiina Wahlfors
- BioMediTech, University of Tampere and FimLab Laboratories, Tampere 33200, Finland
| | - Teuvo L. J. Tammela
- Department of Urology, Tampere University Hospital and Medical School, University of Tampere, Tampere 33200, Finland
| | - Børge G. Nordestgaard
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev Ringvej 75, Herlev DK-2730, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1165, Densmark
| | - Tim J. Key
- Cancer Epidemiology, Nuffield Department of Population Health; University of Oxford, Oxford OX3 7LF, UK
| | - Ruth C. Travis
- Cancer Epidemiology, Nuffield Department of Population Health; University of Oxford, Oxford OX3 7LF, UK
| | - David E. Neal
- University of Cambridge, Department of Oncology, Addenbrooke's Hospital, Box 279, Hills Road, Cambridge CB2 0QQ
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Jenny L. Donovan
- School of Social and Community Medicine, University of Bristol, Canynge Hall, 39 Whatley Road, Bristol BS8 2PS, UK
| | - Freddie C. Hamdy
- Department of Public Health, Section for Epidemiology, Aarhus University, Aarhus OX1 3PN, Denmark
- Faculty of Medical Science, University of Oxford, John Radcliffe Hospital, Oxford OX1 3PN, UK
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
- University College London, Department of Applied Health Research, 1-19 Torrington Place, London WC1E 7HB, UK
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge CB1 8RN, UK
| | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington 98109, USA
| | | | | | | | - Christiane Maier
- Institute of Human Genetics, University Hospital Ulm, 89081 Ulm, Germany
| | - Walther Vogel
- Institute of Human Genetics, University Hospital Ulm, 89081 Ulm, Germany
| | - Manuel Luedeke
- Department of Urology, University Hospital Ulm, 89081 Ulm, Germany
| | - Kathleen Herkommer
- Department of Urology, Klinikum rechts der Isar der Technischen Universitaet Muenchen, 81675 Munich, Germany
| | - Adam S. Kibel
- Division of Urologic Surgery, Brigham and Womens Hospital, Dana-Farber Cancer Institute, 75 Francis Street, Boston, Massachusetts 02115, USA
| | - 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
| | - Wojciech Kluzniak
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Lisa Cannon-Albright
- Division of Genetic Epidemiology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah 84132, USA
| | - Craig Teerlink
- Division of Genetic Epidemiology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah 84132, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
| | - Aida K. Dieffenbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Jong Y. Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, Florida 33612, USA
| | - Thomas A. Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, Florida 33612, USA
| | - Hui-Yi Lin
- Biostatistics Program, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, Florida 33612, USA
| | - Chavdar Slavov
- Department of Urology and Alexandrovska University Hospital, Medical University, Sofia 1431, Bulgaria
| | - Radka Kaneva
- Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University, Sofia, 2 Zdrave Str., Sofia 1431, Bulgaria
| | - Vanio Mitev
- Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University, Sofia, 2 Zdrave Str., Sofia 1431, Bulgaria
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Amanda Spurdle
- Molecular Cancer Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland 4000, Australia
| | - Judith A. Clements
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Manuel R. Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto 4200, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto 4200, Portugal
| | - Hardev Pandha
- The University of Surrey, Guildford, Surrey GU2 7XH, UK
| | | | - Paula Paulo
- Department of Genetics, Portuguese Oncology Institute, Porto 4200, Portugal
| | - Sofia Maia
- Department of Genetics, Portuguese Oncology Institute, Porto 4200, Portugal
| | | | - David V. Conti
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033, USA
| | - Demetrius Albanes
- Nutritional Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland 20892, USA
| | - Christine Berg
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins Medicine, Baltimore, Maryland 21287, USA
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Daniele Campa
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - E. David Crawford
- Urologic Oncology, University of Colorado at Denver Health Sciences Center, Denver, Colorado 80230, USA
| | - W. Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - Susan M. Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - J. Michael Gaziano
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
- Division of Aging, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Edward Giovannucci
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Robert Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - David J. Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Mattias Johansson
- International Agency for Research on Cancer, Lyon 69008, France
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå 907 36, Sweden
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii 96813, USA
| | - Sara Lindström
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Carmen Navarro
- Department of Epidemiology, Regional Health Authority, Murcia 30009, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 28029, Spain
| | - Kim Overvad
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins Medicine, Baltimore, Maryland 21287, USA
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Afshan Siddiq
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Victoria L. Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - Dimitrios Trichopoulos
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Bureau of Epidemiologic Research, Academy of Athens, Athens 106 79, Greece
- Hellenic Health Foundation, Athens 106 79, Greece
| | - Paolo Vineis
- HuGeF Foundation, Torino 10126, Italy
- School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Gosia Trynka
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Soumya Raychaudhuri
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Institute of Inflammation and Repair, University of Manchester, Manchester M13 9PT, UK
| | - Frederick R. Schumacher
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033, USA
| | - Alkes L. Price
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Matthew L. Freedman
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02115, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Christopher A. Haiman
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California 90095, USA
- Departments of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
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111
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Hashemi M, Moradi N, Ziaee SAM, Narouie B, Soltani MH, Rezaei M, Shahkar G, Taheri M. Association between single nucleotide polymorphism in miR-499, miR-196a2, miR-146a and miR-149 and prostate cancer risk in a sample of Iranian population. J Adv Res 2016; 7:491-8. [PMID: 27222754 DOI: 10.1016/j.jare.2016.03.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/23/2016] [Accepted: 03/24/2016] [Indexed: 01/29/2023] Open
Abstract
MicroRNAs (miRNAs) play an important role in regulating gene expression at the post-transcriptional level and are involved in numerous physiological processes. Accumulating evidence suggests that single-nucleotide polymorphisms (SNPs) in human miRNA genes may affect miRNA biogenesis pathway and influence the susceptibility to several diseases such as cancer. The present study aimed to evaluate the impact of miR-499 rs3746444, miR-196a2 rs11614913, miR-149 rs2292832, and miR-146a rs2910164 polymorphisms on prostate cancer (PCa) risk in a sample of Iranian population. This case-control study was done on 169 patients with pathologically confirmed PCa and 182 benign prostatic hyperplasia (BPH). The genotyping assays were done using T-ARMS-PCR or PCR-RFLP methods. The findings indicated that CC genotype of miR-499 rs3746444 polymorphism increased the risk of PCa (OR = 1.76, 95% CI = 1.12-2.79, P = 0.019) compared to TT genotype. No statistically significant association was found between miR-196a2 rs11614913, miR-149 rs2292832, and miR-146a rs2910164 polymorphisms and PCa risk. In summary, the findings indicated that miR-499 rs3746444 polymorphism increased the risk of PCa in an Iranian population. Further studies with larger sample sizes and different ethnicities are necessary to verify the findings of the present study.
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Affiliation(s)
- Mohammad Hashemi
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran; Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Nazanin Moradi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Seyed Amir Mohsen Ziaee
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Behzad Narouie
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Hosein Soltani
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezaei
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ghazaleh Shahkar
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohsen Taheri
- Genetics of Non Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
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112
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Whitington T, Gao P, Song W, Ross-Adams H, Lamb AD, Yang Y, Svezia I, Klevebring D, Mills IG, Karlsson R, Halim S, Dunning MJ, Egevad L, Warren AY, Neal DE, Grönberg H, Lindberg J, Wei GH, Wiklund F. Gene regulatory mechanisms underpinning prostate cancer susceptibility. Nat Genet 2016; 48:387-97. [PMID: 26950096 DOI: 10.1038/ng.3523] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 02/08/2016] [Indexed: 12/29/2022]
Abstract
Molecular characterization of genome-wide association study (GWAS) loci can uncover key genes and biological mechanisms underpinning complex traits and diseases. Here we present deep, high-throughput characterization of gene regulatory mechanisms underlying prostate cancer risk loci. Our methodology integrates data from 295 prostate cancer chromatin immunoprecipitation and sequencing experiments with genotype and gene expression data from 602 prostate tumor samples. The analysis identifies new gene regulatory mechanisms affected by risk locus SNPs, including widespread disruption of ternary androgen receptor (AR)-FOXA1 and AR-HOXB13 complexes and competitive binding mechanisms. We identify 57 expression quantitative trait loci at 35 risk loci, which we validate through analysis of allele-specific expression. We further validate predicted regulatory SNPs and target genes in prostate cancer cell line models. Finally, our integrated analysis can be accessed through an interactive visualization tool. This analysis elucidates how genome sequence variation affects disease predisposition via gene regulatory mechanisms and identifies relevant genes for downstream biomarker and drug development.
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Affiliation(s)
- Thomas Whitington
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ping Gao
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Wei Song
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Helen Ross-Adams
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Alastair D Lamb
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Yuehong Yang
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ilaria Svezia
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Daniel Klevebring
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ian G Mills
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.,Department of Molecular Oncology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway.,Prostate Cancer UK/Movember Centre of Excellence for Prostate Cancer Research, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Silvia Halim
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Cancer Research UK Beatson Institute, Glasgow, UK
| | - Mark J Dunning
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Lars Egevad
- Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden.,Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Anne Y Warren
- Department of Pathology, Addenbrooke's Hospital, Cambridge, UK
| | - David E Neal
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Gong-Hong Wei
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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113
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Cai M, Kim S, Wang K, Farnham PJ, Coetzee GA, Lu W. 4C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus. Sci Rep 2016; 6:22462. [PMID: 26934861 PMCID: PMC4776156 DOI: 10.1038/srep22462] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/15/2016] [Indexed: 02/07/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified >100 independent susceptibility loci for prostate cancer, including the hot spot at 8q24. However, how genetic variants at this locus confer disease risk hasn’t been fully characterized. Using circularized chromosome conformation capture (4C) coupled with next-generation sequencing and an enhancer at 8q24 as “bait”, we identified genome-wide partners interacting with this enhancer in cell lines LNCaP and C4-2B. These 4C-identified regions are distributed in open nuclear compartments, featuring active histone marks (H3K4me1, H3K4me2 and H3K27Ac). Transcription factors NKX3-1, FOXA1 and AR (androgen receptor) tend to occupy these 4C regions. We identified genes located at the interacting regions, and found them linked to positive regulation of mesenchymal cell proliferation in LNCaP and C4-2B, and several pathways (TGF beta signaling pathway in LNCaP and p53 pathway in C4-2B). Common genes (e.g. MYC and POU5F1B) were identified in both prostate cancer cell lines. However, each cell line also had exclusive genes (e.g. ELAC2 and PTEN in LNCaP and BRCA2 and ZFHX3 in C4-2B). In addition, BCL-2 identified in C4-2B might contribute to the progression of androgen-refractory prostate cancer. Overall, our work reveals key genes and pathways involved in prostate cancer onset and progression.
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Affiliation(s)
- Mingyang Cai
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA.,Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA.,Division of Biostatistics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Sewoon Kim
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Kai Wang
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA.,Division of Biostatistics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA.,Department of Psychiatry, University of Southern California, Los Angeles, CA 90033, USA
| | - Peggy J Farnham
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.,Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Gerhard A Coetzee
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA.,Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Wange Lu
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
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114
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Goodarzi MO. Genetics of Common Endocrine Disease: The Present and the Future. J Clin Endocrinol Metab 2016; 101:787-94. [PMID: 26908105 PMCID: PMC4803177 DOI: 10.1210/jc.2015-3640] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/05/2015] [Indexed: 01/01/2023]
Abstract
CONTEXT In honor of the 75th issue of the Journal of Clinical Endocrinology and Metabolism, the author was invited to present his perspectives on genetics in human endocrinology. This paper reviews what the field has achieved in the genetics of common endocrine disease, and offers predictions on where the field will move in the future and its impact on endocrine clinical practice. EVIDENCE ACQUISITION The October 2015 data release of the National Human Genome Research Institute-European Bioinformatics Institute (NHGRI-EBI) Catalog of Published Genome-wide Association Studies was queried regarding endocrinologic diseases and traits. PubMed searches were focused on genetic prediction of disease, genetic findings and drug targets, functional interrogation of genetic loci, use of genetics to subtype disease, missing heritability, systems genomics, and higher order chromatin structures as regulators of gene function. EVIDENCE SYNTHESIS Nearly a quarter of genome wide association study findings concern endocrinologic diseases and traits. While these findings have not yet dramatically altered clinical care, genetics will have a major impact by providing the drug targets of tomorrow, facilitated by experimental and bioinformatic advances that will shorten the time from gene discovery to drug development. Use of genetic findings to subtype common endocrine disease will allow more precise prevention and treatment efforts. Future advances will allow us to move away from the common view of DNA as a string of letters, allowing exploration of higher order structure that likely explains much "missing heritability." CONCLUSIONS The future will see a greater role of genetics at the bedside, with genetic epidemiologic discoveries leading not only to new treatments of endocrine disease, but also helping us prescribe the right drug to the right patients by allowing subclassification of common heterogeneous endocrine conditions. Future technological breakthroughs will reveal the heritable mysteries hidden in chromatin structure, leading to a more complete characterization of heritability that will propel our ability to translate genetic findings into new preventions and treatments.
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Affiliation(s)
- Mark O Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048
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115
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Genomic approach to understand association between single nucleotide polymorphisms and risk of Korean serous ovarian cancer at stage IIIc. Mol Cell Toxicol 2016. [DOI: 10.1007/s13273-016-0004-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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116
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Ahmed M, Eeles R. Germline genetic profiling in prostate cancer: latest developments and potential clinical applications. Future Sci OA 2016; 2:FSO87. [PMID: 28031937 PMCID: PMC5137984 DOI: 10.4155/fso.15.87] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 11/10/2015] [Indexed: 12/16/2022] Open
Abstract
Familial and twin studies have demonstrated a significant inherited component to prostate cancer predisposition. Genome wide association studies have shown that there are 100 single nucleotide polymorphisms which have been associated with the development of prostate cancer. This review aims to discuss the scientific methods used to identify these susceptibility loci. It will also examine the current clinical utility of these loci, which include the development of risk models as well as predicting treatment efficacy and toxicity. In order to refine the clinical utility of the susceptibility loci, international consortia have been developed to combine statistical power as well as skills and knowledge to further develop models that could be used to predict risk and treatment outcomes.
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Affiliation(s)
- Mahbubl Ahmed
- The Institute of Cancer Research, London SM2 5NG, UK
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117
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Luo Z, Lin C. Enhancer, epigenetics, and human disease. Curr Opin Genet Dev 2016; 36:27-33. [DOI: 10.1016/j.gde.2016.03.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/24/2016] [Indexed: 02/09/2023]
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118
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Hazelett DJ, Conti DV, Han Y, Al Olama AA, Easton D, Eeles RA, Kote-Jarai Z, Haiman CA, Coetzee GA. Reducing GWAS Complexity. Cell Cycle 2016; 15:22-4. [PMID: 26771711 PMCID: PMC4825730 DOI: 10.1080/15384101.2015.1120928] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/12/2015] [Indexed: 10/22/2022] Open
Abstract
Genome-wide association studies (GWAS) have revealed numerous genomic 'hits' associated with complex phenotypes. In most cases these hits, along with surrogate genetic variation as measure by numerous single nucleotide polymorphisms (SNPs) that are in linkage disequilibrium, are not in coding genes making assignment of functionality or causality intractable. Here we propose that fine-mapping along with the matching of risk SNPs at chromatin biofeatures lessen this complexity by reducing the number of candidate functional/causal SNPs. For example, we show here that only on average 2 SNPs per prostate cancer risk locus are likely candidates for functionality/causality; we further propose that this manageable number should be taken forward in mechanistic studies. The candidate SNPs can be looked up for each prostate cancer risk region in 2 recent publications in 2015 (1,2) from our groups.
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Affiliation(s)
- Dennis J. Hazelett
- Bioinformatics and Computational Biology Research Center, Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - David V. Conti
- Departments of Preventive Medicine and Urology, USC/Norris Cancer Center, USA
| | - Ying Han
- Departments of Preventive Medicine and Urology, USC/Norris Cancer Center, USA
| | - Ali Amin Al Olama
- Division of Genetics & Epidemiology, Centre of Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Doug Easton
- Division of Genetics & Epidemiology, Centre of Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Rosalind A. Eeles
- The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Zsofia Kote-Jarai
- The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | | | - Gerhard A. Coetzee
- Departments of Preventive Medicine and Urology, USC/Norris Cancer Center, USA
- The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
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119
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Mancuso N, Rohland N, Rand KA, Tandon A, Allen A, Quinque D, Mallick S, Li H, Stram A, Sheng X, Kote-Jarai Z, Easton DF, Eeles RA, Le Marchand L, Lubwama A, Stram D, Watya S, Conti DV, Henderson B, Haiman CA, Pasaniuc B, Reich D. The contribution of rare variation to prostate cancer heritability. Nat Genet 2016; 48:30-5. [PMID: 26569126 PMCID: PMC7534691 DOI: 10.1038/ng.3446] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/20/2015] [Indexed: 12/13/2022]
Abstract
We report targeted sequencing of 63 known prostate cancer risk regions in a multi-ancestry study of 9,237 men and use the data to explore the contribution of low-frequency variation to disease risk. We show that SNPs with minor allele frequencies (MAFs) of 0.1-1% explain a substantial fraction of prostate cancer risk in men of African ancestry. We estimate that these SNPs account for 0.12 (standard error (s.e.) = 0.05) of variance in risk (∼42% of the variance contributed by SNPs with MAF of 0.1-50%). This contribution is much larger than the fraction of neutral variation due to SNPs in this class, implying that natural selection has driven down the frequency of many prostate cancer risk alleles; we estimate the coupling between selection and allelic effects at 0.48 (95% confidence interval [0.19, 0.78]) under the Eyre-Walker model. Our results indicate that rare variants make a disproportionate contribution to genetic risk for prostate cancer and suggest the possibility that rare variants may also have an outsize effect on other common traits.
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Affiliation(s)
- Nicholas Mancuso
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Kristin A Rand
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Arti Tandon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Alexander Allen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Dominique Quinque
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Heng Li
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Alex Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Xin Sheng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | | | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK
- Royal Marsden National Health Service (NHS) Foundation Trust, London and Sutton, UK
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Alex Lubwama
- School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - Daniel Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Stephen Watya
- School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Brian Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
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120
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Tak YG, Farnham PJ. Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome. Epigenetics Chromatin 2015; 8:57. [PMID: 26719772 PMCID: PMC4696349 DOI: 10.1186/s13072-015-0050-4] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/09/2015] [Indexed: 12/13/2022] Open
Abstract
Considerable progress towards an understanding of complex diseases has been made in recent years due to the development of high-throughput genotyping technologies. Using microarrays that contain millions of single-nucleotide polymorphisms (SNPs), Genome Wide Association Studies (GWASs) have identified SNPs that are associated with many complex diseases or traits. For example, as of February 2015, 2111 association studies have identified 15,396 SNPs for various diseases and traits, with the number of identified SNP-disease/trait associations increasing rapidly in recent years. However, it has been difficult for researchers to understand disease risk from GWAS results. This is because most GWAS-identified SNPs are located in non-coding regions of the genome. It is important to consider that the GWAS-identified SNPs serve only as representatives for all SNPs in the same haplotype block, and it is equally likely that other SNPs in high linkage disequilibrium (LD) with the array-identified SNPs are causal for the disease. Because it was hoped that disease-associated coding variants would be identified if the true casual SNPs were known, investigators have expanded their analyses using LD calculation and fine-mapping. However, such analyses also identified risk-associated SNPs located in non-coding regions. Thus, the GWAS field has been left with the conundrum as to how a single-nucleotide change in a non-coding region could confer increased risk for a specific disease. One possible answer to this puzzle is that the variant SNPs cause changes in gene expression levels rather than causing changes in protein function. This review provides a description of (1) advances in genomic and epigenomic approaches that incorporate functional annotation of regulatory elements to prioritize the disease risk-associated SNPs that are located in non-coding regions of the genome for follow-up studies, (2) various computational tools that aid in identifying gene expression changes caused by the non-coding disease-associated SNPs, and (3) experimental approaches to identify target genes of, and study the biological phenotypes conferred by, non-coding disease-associated SNPs.
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Affiliation(s)
- Yu Gyoung Tak
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
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Abstract
This protocol provides a rapid, streamlined and scalable strategy to systematically scan genomic regions for the presence of transcriptional regulatory regions that are active in a specific cell type. It creates genomic tiles spanning a region of interest that are subsequently cloned by recombination into a luciferase reporter vector containing the simian virus 40 promoter. Tiling clones are transfected into specific cell types to test for the presence of transcriptional regulatory regions. The protocol includes testing of different single-nucleotide polymorphism (SNP) alleles to determine their effect on regulatory activity. This procedure provides a systematic framework for identifying candidate functional SNPs within a locus during functional analysis of genome-wide association studies. This protocol adapts and combines previous well-established molecular biology methods to provide a streamlined strategy, based on automated primer design and recombinational cloning, allowing one to rapidly go from a genomic locus to a set of candidate functional SNPs in 8 weeks.
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122
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Thibodeau SN, French AJ, McDonnell SK, Cheville J, Middha S, Tillmans L, Riska S, Baheti S, Larson MC, Fogarty Z, Zhang Y, Larson N, Nair A, O'Brien D, Wang L, Schaid DJ. Identification of candidate genes for prostate cancer-risk SNPs utilizing a normal prostate tissue eQTL data set. Nat Commun 2015; 6:8653. [PMID: 26611117 PMCID: PMC4663677 DOI: 10.1038/ncomms9653] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/17/2015] [Indexed: 01/23/2023] Open
Abstract
Multiple studies have identified loci associated with the risk of developing prostate cancer but the associated genes are not well studied. Here we create a normal prostate tissue-specific eQTL data set and apply this data set to previously identified prostate cancer (PrCa)-risk SNPs in an effort to identify candidate target genes. The eQTL data set is constructed by the genotyping and RNA sequencing of 471 samples. We focus on 146 PrCa-risk SNPs, including all SNPs in linkage disequilibrium with each risk SNP, resulting in 100 unique risk intervals. We analyse cis-acting associations where the transcript is located within 2 Mb (±1 Mb) of the risk SNP interval. Of all SNP–gene combinations tested, 41.7% of SNPs demonstrate a significant eQTL signal after adjustment for sample histology and 14 expression principal component covariates. Of the 100 PrCa-risk intervals, 51 have a significant eQTL signal and these are associated with 88 genes. This study provides a rich resource to study biological mechanisms underlying genetic risk to PrCa. Single nucleotide polymorphisms—SNPs—have been identified for prostate cancer but whether these SNPs alter the expression of genes is largely unknown. In this study, the authors search for genes located within 2 Mb of the SNPs and identify SNPs that influence gene expression, so called expression quantitative trait loci.
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Affiliation(s)
- S N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - A J French
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - S K McDonnell
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - J Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - S Middha
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - L Tillmans
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - S Riska
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - S Baheti
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - M C Larson
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - Z Fogarty
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - Y Zhang
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, 660W Redwood Street, Baltimore, Maryland 21201, USA
| | - N Larson
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - A Nair
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - D O'Brien
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - L Wang
- Department of Pathology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
| | - D J Schaid
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
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123
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Lawrenson K, Iversen ES, Tyrer J, Weber RP, Concannon P, Hazelett DJ, Li Q, Marks JR, Berchuck A, Lee JM, Aben KKH, Anton-Culver H, Antonenkova N, Bandera EV, Bean Y, Beckmann MW, Bisogna M, Bjorge L, Bogdanova N, Brinton LA, Brooks-Wilson A, Bruinsma F, Butzow R, Campbell IG, Carty K, Chang-Claude J, Chenevix-Trench G, Chen A, Chen Z, Cook LS, Cramer DW, Cunningham JM, Cybulski C, Plisiecka-Halasa J, Dennis J, Dicks E, Doherty JA, Dörk T, du Bois A, Eccles D, Easton DT, Edwards RP, Eilber U, Ekici AB, Fasching PA, Fridley BL, Gao YT, Gentry-Maharaj A, Giles GG, Glasspool R, Goode EL, Goodman MT, Gronwald J, Harter P, Hasmad HN, Hein A, Heitz F, Hildebrandt MAT, Hillemanns P, Hogdall E, Hogdall C, Hosono S, Jakubowska A, Paul J, Jensen A, Karlan BY, Kjaer SK, Kelemen LE, Kellar M, Kelley JL, Kiemeney LA, Krakstad C, Lambrechts D, Lambrechts S, Le ND, Lee AW, Cannioto R, Leminen A, Lester J, Levine DA, Liang D, Lissowska J, Lu K, Lubinski J, Lundvall L, Massuger LFAG, Matsuo K, McGuire V, McLaughlin JR, Nevanlinna H, McNeish I, Menon U, Modugno F, Moysich KB, Narod SA, Nedergaard L, Ness RB, Noor Azmi MA, Odunsi K, Olson SH, Orlow I, Orsulic S, Pearce CL, Pejovic T, Pelttari LM, Permuth-Wey J, Phelan CM, Pike MC, Poole EM, Ramus SJ, Risch HA, Rosen B, Rossing MA, Rothstein JH, Rudolph A, Runnebaum IB, Rzepecka IK, Salvesen HB, Budzilowska A, Sellers TA, Shu XO, Shvetsov YB, Siddiqui N, Sieh W, Song H, Southey MC, Sucheston L, Tangen IL, Teo SH, Terry KL, Thompson PJ, Timorek A, Tworoger SS, Van Nieuwenhuysen E, Vergote I, Vierkant RA, Wang-Gohrke S, Walsh C, Wentzensen N, Whittemore AS, Wicklund KG, Wilkens LR, Woo YL, Wu X, Wu AH, Yang H, Zheng W, Ziogas A, Coetzee GA, Freedman ML, Monteiro ANA, Moes-Sosnowska J, Kupryjanczyk J, Pharoah PD, Gayther SA, Schildkraut JM. Common variants at the CHEK2 gene locus and risk of epithelial ovarian cancer. Carcinogenesis 2015; 36:1341-53. [PMID: 26424751 PMCID: PMC4635670 DOI: 10.1093/carcin/bgv138] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 09/14/2015] [Accepted: 09/16/2015] [Indexed: 12/15/2022] Open
Abstract
Genome-wide association studies have identified 20 genomic regions associated with risk of epithelial ovarian cancer (EOC), but many additional risk variants may exist. Here, we evaluated associations between common genetic variants [single nucleotide polymorphisms (SNPs) and indels] in DNA repair genes and EOC risk. We genotyped 2896 common variants at 143 gene loci in DNA samples from 15 397 patients with invasive EOC and controls. We found evidence of associations with EOC risk for variants at FANCA, EXO1, E2F4, E2F2, CREB5 and CHEK2 genes (P ≤ 0.001). The strongest risk association was for CHEK2 SNP rs17507066 with serous EOC (P = 4.74 x 10(-7)). Additional genotyping and imputation of genotypes from the 1000 genomes project identified a slightly more significant association for CHEK2 SNP rs6005807 (r (2) with rs17507066 = 0.84, odds ratio (OR) 1.17, 95% CI 1.11-1.24, P = 1.1×10(-7)). We identified 293 variants in the region with likelihood ratios of less than 1:100 for representing the causal variant. Functional annotation identified 25 candidate SNPs that alter transcription factor binding sites within regulatory elements active in EOC precursor tissues. In The Cancer Genome Atlas dataset, CHEK2 gene expression was significantly higher in primary EOCs compared to normal fallopian tube tissues (P = 3.72×10(-8)). We also identified an association between genotypes of the candidate causal SNP rs12166475 (r (2) = 0.99 with rs6005807) and CHEK2 expression (P = 2.70×10(-8)). These data suggest that common variants at 22q12.1 are associated with risk of serous EOC and CHEK2 as a plausible target susceptibility gene.
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Affiliation(s)
- Kate Lawrenson
- Present address: Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA and
| | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
| | - Jonathan Tyrer
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research laboratory, Cambridge CB2 1TN, UK
| | - Rachel Palmieri Weber
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Patrick Concannon
- Genetics Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Dennis J Hazelett
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Qiyuan Li
- Medical School, Xiamen University, Xiamen 361000, China
| | - Jeffrey R Marks
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Katja K H Aben
- Department for Health Evidence, Nijmegen 6500 HB, The Netherlands, Comprehensive Cancer Center, Utrecht 3542 EG, The Netherlands
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - Natalia Antonenkova
- Byelorussian Institute for Oncology and Medical Radiology Aleksandrov N.N., Minsk 223052, Belarus
| | - Elisa V Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Yukie Bean
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR 97239, USA, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen 91054, Germany
| | - Maria Bisogna
- Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Line Bjorge
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen 5021, Norway, Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, Bergen 5020, Norway
| | - Natalia Bogdanova
- Gynaecology Research Unit, Hannover Medical School, Hannover 30625, Germany
| | - Louise A Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20852, USA
| | - Angela Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada, Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Fiona Bruinsma
- Cancer Epidemiology Centre, Cancer Council of Victoria, Melbourne Victoria 3004, Australia
| | - Ralf Butzow
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki 00029, Finland, Department of Pathology, Helsinki University Central Hospital, Helsinki 00029, Finland
| | - Ian G Campbell
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria 8006, Australia, Department of Pathology, University of Melbourne, Parkville, Victoria 3002, Australia, Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3002, Australia
| | - Karen Carty
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, Glasgow G12 0YN, UK
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69009, Germany
| | - Georgia Chenevix-Trench
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane Queensland 4029, Australia
| | - Ann Chen
- Department of Biostatistics, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Zhihua Chen
- Department of Biostatistics, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Linda S Cook
- Division of Epidemiology and Biostatistics, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA
| | - Daniel W Cramer
- Harvard School of Public Health, Boston, MA 02115, USA, Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Cezary Cybulski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-115, Poland
| | - Joanna Plisiecka-Halasa
- Department of Cancer Epidemiology and Prevention, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02-781, Poland
| | - Joe Dennis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Ed Dicks
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jennifer A Doherty
- Department of Community and Family Medicine, Section of Biostatistics and Epidemiology, The Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover 30625, Germany
| | - Andreas du Bois
- Genetics Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32611, USA, Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Kliniken Wiesbaden, Wiesbaden 65199, Germany
| | - Diana Eccles
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton SO16 5YA, UK
| | - Douglas T Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Robert P Edwards
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton SO16 5YA, UK, Ovarian Cancer Center of Excellence, University of Pittsburgh, Pittsburgh, PA 15222, USA
| | - Ursula Eilber
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69009, Germany
| | - Arif B Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen 91054, Germany
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen 91054, Germany, Department of Medicine, Division of Hematology and Oncology, University of California at Los Angeles, David Geffen School of Medicine, Los Angeles CA 90095, USA
| | - Brooke L Fridley
- Biostatistics and Informatics Shared Resource, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Yu-Tang Gao
- Shanghai Cancer Institute, Shanghai 200032, China
| | - Aleksandra Gentry-Maharaj
- Department of Women's Cancer, Institute for Women's Health, University College London, London W1T 7DN, UK
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council of Victoria, Melbourne Victoria 3004, Australia, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria 3010, Australia
| | - Rosalind Glasspool
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, Glasgow G12 0YN, UK
| | - Ellen L Goode
- Department of Health Science Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Marc T Goodman
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA, Department of Biomedical Sciences, Community and Population Health Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-115, Poland
| | - Philipp Harter
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, Essen 45136, Germany, Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Kliniken Wiesbaden, Wiesbaden 65199, Germany
| | - Hanis Nazihah Hasmad
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya 47500, Malaysia
| | - Alexander Hein
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen 91054, Germany
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, Essen 45136, Germany, Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Kliniken Wiesbaden, Wiesbaden 65199, Germany
| | - Michelle A T Hildebrandt
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peter Hillemanns
- Departments of Obstetrics and Gynaecology, Hannover Medical School, Hannover 30625, Germany
| | - Estrid Hogdall
- Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen DK-2100, Denmark, Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Claus Hogdall
- Gyn Clinic, Rigshospitalet, University of Copenhagen DK-2100, Denmark
| | - Satoyo Hosono
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Aichi 464-8681, Japan
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-115, Poland
| | - James Paul
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, Glasgow G12 0YN, UK
| | - Allan Jensen
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Susanne Kruger Kjaer
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark, Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Linda E Kelemen
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Melissa Kellar
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR 97239, USA, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Joseph L Kelley
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA 15222, USA
| | - Lambertus A Kiemeney
- Department for Health Evidence and Department of Urology, Radboud University Medical Centre, Nijmegen 6500 HB, The Netherlands
| | - Camilla Krakstad
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen 5021, Norway, Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, Bergen 5020, Norway
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven 3000, Belgium, Laboratory for Translational Genetics, Department of Oncology, University of Leuven 3000, Belgium
| | - Sandrina Lambrechts
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, 3000, Belgium
| | - Nhu D Le
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | | | - Rikki Cannioto
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Arto Leminen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki 00029, Finland
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Douglas A Levine
- Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Dong Liang
- College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02-781, Poland
| | - Karen Lu
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-115, Poland
| | - Lene Lundvall
- Gyn Clinic, Rigshospitalet, University of Copenhagen DK-2100, Denmark
| | - Leon F A G Massuger
- Department of Gynaecology, Radboud University Medical Centre, Nijmegen 6500 HB, The Netherlands
| | - Keitaro Matsuo
- Department of Preventive Medicine, Kyushu University Faculty of Medical Sciences, Fukuoka 812-8582, Japan
| | - Valerie McGuire
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John R McLaughlin
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki 00029, Finland
| | - Iain McNeish
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Beatson Institute for Cancer Research, Glasgow G61 1QH, UK
| | - Usha Menon
- Department of Women's Cancer, Institute for Women's Health, University College London, London W1T 7DN, UK
| | - Francesmary Modugno
- Ovarian Cancer Center of Excellence, University of Pittsburgh, Pittsburgh, PA 15222, USA, Women's Cancer Research Program, Magee-Women's Research Institute and University of Pittsburgh Cancer Institute, Pittsburgh, PA 15222, USA, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA 15222, USA, Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15222, USA
| | - Kirsten B Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Steven A Narod
- Women's College Research Institute, Toronto, Ontario M5G 1N8, Canada
| | - Lotte Nedergaard
- Department of Pathology, Rigshospitalet, University of Copenhagen DK-2100, Denmark
| | - Roberta B Ness
- The University of Texas School of Public Health, Houston, TX 77225, USA
| | - Mat Adenan Noor Azmi
- Department of Obstetrics and Gynaecology, University Malaya Medical Centre, University Malaya, Kuala Lumpur 50603, Malaysia
| | - Kunle Odunsi
- Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Sandra Orsulic
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Celeste L Pearce
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Tanja Pejovic
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR 97239, USA, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Liisa M Pelttari
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki 00029, Finland
| | - Jennifer Permuth-Wey
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Catherine M Phelan
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Malcolm C Pike
- Department of Statistical Science, Duke University, Durham, NC 27708, USA, Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Elizabeth M Poole
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA, Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | | | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06520, USA
| | - Barry Rosen
- Department of Gynecologic-Oncology, Princess Margaret Hospital, and Department of Obstetrics and Gynecology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5G 1X6, Canada
| | - Mary Anne Rossing
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Department of Epidemiology, University of Washington, Seattle, WA 98109, USA
| | - Joseph H Rothstein
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69009, Germany
| | - Ingo B Runnebaum
- Department of Gynecology, Jena University Hospital - Friedrich Schiller University, Jena D-07743, Germany
| | - Iwona K Rzepecka
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-115, Poland
| | - Helga B Salvesen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen 5021, Norway, Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, Bergen 5020, Norway
| | - Agnieszka Budzilowska
- Department of Cancer Epidemiology and Prevention, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02-781, Poland
| | - Thomas A Sellers
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Yurii B Shvetsov
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Hawaii 96826, USA
| | - Nadeem Siddiqui
- Department of Gynaecological Oncology, Glasgow Royal Infirmary, Glasgow G4 0SF, UK
| | - Weiva Sieh
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Honglin Song
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research laboratory, Cambridge CB2 1TN, UK
| | - Melissa C Southey
- Department of Pathology, University of Melbourne, Parkville, Victoria 3002, Australia
| | - Lara Sucheston
- College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA
| | - Ingvild L Tangen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen 5021, Norway, Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, Bergen 5020, Norway
| | - Soo-Hwang Teo
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, Kuala Lumpur 50603, Malaysia
| | - Kathryn L Terry
- Harvard School of Public Health, Boston, MA 02115, USA, Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Pamela J Thompson
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA, Department of Biomedical Sciences, Community and Population Health Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Agnieszka Timorek
- Department of Obstetrics, Gynecology and Oncology, IInd Faculty of Medicine, Warsaw Medical University and Brodnowski Hospital, Warsaw 03-242, Poland
| | - Shelley S Tworoger
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA, Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Els Van Nieuwenhuysen
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, 3000, Belgium
| | - Ignace Vergote
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, 3000, Belgium
| | - Robert A Vierkant
- Department of Health Science Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Shan Wang-Gohrke
- Department of Obstetrics and Gynecology, University of Ulm, Ulm 89075, Germany
| | - Christine Walsh
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20852, USA
| | - Alice S Whittemore
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kristine G Wicklund
- Department of Epidemiology, University of Washington, Seattle, WA 98109, USA
| | - Lynne R Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Hawaii 96826, USA
| | - Yin-Ling Woo
- Department of Obstetrics and Gynaecology, University Malaya Medical Centre, University Malaya, Kuala Lumpur 50603, Malaysia, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, Kuala Lumpur 50603, Malaysia
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Hannah Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20852, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Argyrios Ziogas
- Comprehensive Cancer Center, Utrecht 3542 EG, The Netherlands
| | - Gerhard A Coetzee
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Matthew L Freedman
- Department of Medical Oncology, 02115, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, Division of Population Sciences, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA and
| | - Joanna Moes-Sosnowska
- Department of Cancer Epidemiology and Prevention, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02-781, Poland
| | - Jolanta Kupryjanczyk
- Department of Cancer Epidemiology and Prevention, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02-781, Poland
| | - Paul D Pharoah
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research laboratory, Cambridge CB2 1TN, UK
| | - Simon A Gayther
- Present address: Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Joellen M Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC 27710, USA, Cancer Control and Population Sciences, Duke Cancer Institute, Durham, NC 27710, USA,
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Yao L, Berman BP, Farnham PJ. Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol 2015; 50:550-73. [PMID: 26446758 PMCID: PMC4666684 DOI: 10.3109/10409238.2015.1087961] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Enhancers are short regulatory sequences bound by sequence-specific transcription factors and play a major role in the spatiotemporal specificity of gene expression patterns in development and disease. While it is now possible to identify enhancer regions genomewide in both cultured cells and primary tissues using epigenomic approaches, it has been more challenging to develop methods to understand the function of individual enhancers because enhancers are located far from the gene(s) that they regulate. However, it is essential to identify target genes of enhancers not only so that we can understand the role of enhancers in disease but also because this information will assist in the development of future therapeutic options. After reviewing models of enhancer function, we discuss recent methods for identifying target genes of enhancers. First, we describe chromatin structure-based approaches for directly mapping interactions between enhancers and promoters. Second, we describe the use of correlation-based approaches to link enhancer state with the activity of nearby promoters and/or gene expression. Third, we describe how to test the function of specific enhancers experimentally by perturbing enhancer–target relationships using high-throughput reporter assays and genome editing. Finally, we conclude by discussing as yet unanswered questions concerning how enhancers function, how target genes can be identified, and how to distinguish direct from indirect changes in gene expression mediated by individual enhancers.
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Affiliation(s)
- Lijing Yao
- a Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles , CA , USA and
| | - Benjamin P Berman
- b Department of Biomedical Sciences , Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Peggy J Farnham
- a Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles , CA , USA and
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125
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Han Y, Hazelett DJ, Wiklund F, Schumacher FR, Stram DO, Berndt SI, Wang Z, Rand KA, Hoover RN, Machiela MJ, Yeager M, Burdette L, Chung CC, Hutchinson A, Yu K, Xu J, Travis RC, Key TJ, Siddiq A, Canzian F, Takahashi A, Kubo M, Stanford JL, Kolb S, Gapstur SM, Diver WR, Stevens VL, Strom SS, Pettaway CA, Al Olama AA, Kote-Jarai Z, Eeles RA, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Chokkalingam AP, Isaacs WB, Chen C, Lindstrom S, Le Marchand L, Giovannucci EL, Pomerantz M, Long H, Li F, Ma J, Stampfer M, John EM, Ingles SA, Kittles RA, Murphy AB, Blot WJ, Signorello LB, Zheng W, Albanes D, Virtamo J, Weinstein S, Nemesure B, Carpten J, Leske MC, Wu SY, Hennis AJM, Rybicki BA, Neslund-Dudas C, Hsing AW, Chu L, Goodman PJ, Klein EA, Zheng SL, Witte JS, Casey G, Riboli E, Li Q, Freedman ML, Hunter DJ, Gronberg H, Cook MB, Nakagawa H, Kraft P, Chanock SJ, Easton DF, Henderson BE, Coetzee GA, Conti DV, Haiman CA. Integration of multiethnic fine-mapping and genomic annotation to prioritize candidate functional SNPs at prostate cancer susceptibility regions. Hum Mol Genet 2015; 24:5603-18. [PMID: 26162851 PMCID: PMC4572069 DOI: 10.1093/hmg/ddv269] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/07/2015] [Indexed: 01/27/2023] Open
Abstract
Interpretation of biological mechanisms underlying genetic risk associations for prostate cancer is complicated by the relatively large number of risk variants (n = 100) and the thousands of surrogate SNPs in linkage disequilibrium. Here, we combined three distinct approaches: multiethnic fine-mapping, putative functional annotation (based upon epigenetic data and genome-encoded features), and expression quantitative trait loci (eQTL) analyses, in an attempt to reduce this complexity. We examined 67 risk regions using genotyping and imputation-based fine-mapping in populations of European (cases/controls: 8600/6946), African (cases/controls: 5327/5136), Japanese (cases/controls: 2563/4391) and Latino (cases/controls: 1034/1046) ancestry. Markers at 55 regions passed a region-specific significance threshold (P-value cutoff range: 3.9 × 10(-4)-5.6 × 10(-3)) and in 30 regions we identified markers that were more significantly associated with risk than the previously reported variants in the multiethnic sample. Novel secondary signals (P < 5.0 × 10(-6)) were also detected in two regions (rs13062436/3q21 and rs17181170/3p12). Among 666 variants in the 55 regions with P-values within one order of magnitude of the most-associated marker, 193 variants (29%) in 48 regions overlapped with epigenetic or other putative functional marks. In 11 of the 55 regions, cis-eQTLs were detected with nearby genes. For 12 of the 55 regions (22%), the most significant region-specific, prostate-cancer associated variant represented the strongest candidate functional variant based on our annotations; the number of regions increased to 20 (36%) and 27 (49%) when examining the 2 and 3 most significantly associated variants in each region, respectively. These results have prioritized subsets of candidate variants for downstream functional evaluation.
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Affiliation(s)
- Ying Han
- Department of Preventive Medicine, Keck School of Medicine
| | | | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Fredrick R Schumacher
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc., Frederick, MD, USA
| | - Kristin A Rand
- Department of Preventive Medicine, Keck School of Medicine
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Merideth Yeager
- Cancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc., Frederick, MD, USA
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc., Frederick, MD, USA
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc., Frederick, MD, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Timothy J Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Afshan Siddiq
- Department of Genomics of Common Disease, School of Public Health
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center, Heidelberg, Germany
| | | | | | - 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
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Victoria L Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | | | - Curtis A Pettaway
- Department of Urology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK, Royal Marsden National Health Services (NHS) Foundation Trust, London and Sutton, UK
| | - Edward D Yeboah
- Korle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana
| | - Yao Tettey
- Korle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana
| | - Richard B Biritwum
- Korle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana
| | - Andrew A Adjei
- Korle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana
| | - Evelyn Tay
- Korle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana
| | | | | | | | - William B Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - Constance Chen
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology
| | - Sara Lindstrom
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | | | - Henry Long
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Fugen Li
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jing Ma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Esther M John
- Cancer Prevention Institute of California, Fremont, CA, USA, Division of Epidemiology, Department of Health Research and Policy, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Rick A Kittles
- University of Arizona College of Medicine and University of Arizona Cancer Center, Tucson, AZ, USA
| | - Adam B Murphy
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - William J Blot
- International Epidemiology Institute, Rockville, MD, USA, Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Barbara Nemesure
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - John Carpten
- The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - M Cristina Leske
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Suh-Yuh Wu
- Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, 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
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | | | - Ann W Hsing
- Cancer Prevention Institute of California, Fremont, CA, USA, Division of Epidemiology, Department of Health Research and Policy, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisa Chu
- Cancer Prevention Institute of California, Fremont, CA, USA, Division of Epidemiology, Department of Health Research and Policy, and 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
| | - Eric A Klein
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - S Lilly Zheng
- Center for Cancer Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California, San Francisco, CA, USA and
| | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
| | - Qiyuan Li
- Medical College, Xiamen University, Xiamen 361102, China
| | | | - David J Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Michael B Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hidewaki Nakagawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Gerhard A Coetzee
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center,
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126
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Amin Al Olama A, Dadaev T, Hazelett DJ, Li Q, Leongamornlert D, Saunders EJ, Stephens S, Cieza-Borrella C, Whitmore I, Benlloch Garcia S, Giles GG, Southey MC, Fitzgerald L, Gronberg H, Wiklund F, Aly M, Henderson BE, Schumacher F, Haiman CA, Schleutker J, Wahlfors T, Tammela TL, Nordestgaard BG, Key TJ, Travis RC, Neal DE, Donovan JL, Hamdy FC, Pharoah P, Pashayan N, Khaw KT, Stanford JL, Thibodeau SN, Mcdonnell SK, Schaid DJ, Maier C, Vogel W, Luedeke M, Herkommer K, Kibel AS, Cybulski C, Wokołorczyk D, Kluzniak W, Cannon-Albright L, Brenner H, Butterbach K, Arndt V, Park JY, Sellers T, Lin HY, Slavov C, Kaneva R, Mitev V, Batra J, Clements JA, Spurdle A, Teixeira MR, Paulo P, Maia S, Pandha H, Michael A, Kierzek A, Govindasami K, Guy M, Lophatonanon A, Muir K, Viñuela A, Brown AA, Freedman M, Conti DV, Easton D, Coetzee GA, Eeles RA, Kote-Jarai Z. Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans. Hum Mol Genet 2015; 24:5589-602. [PMID: 26025378 PMCID: PMC4572072 DOI: 10.1093/hmg/ddv203] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 02/02/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same region.
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Affiliation(s)
- Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory
| | - Tokhir Dadaev
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Dennis J Hazelett
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA, Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Qiuyan Li
- Medical College, Xiamen University, Xiamen, China
| | - Daniel Leongamornlert
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Edward J Saunders
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Sarah Stephens
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Clara Cieza-Borrella
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Ian Whitmore
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Sara Benlloch Garcia
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory
| | - Graham G Giles
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, VIC, Australia, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, Australia
| | | | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Markus Aly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden, Department of Clinical Sciences, Danderyds Hospital, Stockholm, Sweden
| | - Brian E Henderson
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Johanna Schleutker
- Department of Medical Biochemistry and Genetics Institute of Biomedicine, University of Turku, Turku, Finland, BioMediTech, University of Tampere and FimLab Laboratories, Tampere, Finland
| | - Tiina Wahlfors
- BioMediTech, University of Tampere and FimLab Laboratories, Tampere, Finland
| | - Teuvo L Tammela
- Department of Urology, Tampere University Hospital and Medical School, University of Tampere, Tampere, Finland
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tim J Key
- Cancer Epidemiology, Nuffield Department of Population Health
| | - Ruth C Travis
- Cancer Epidemiology, Nuffield Department of Population Health
| | - David E Neal
- Department of Oncology, Addenbrooke's Hospital, Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Jenny L Donovan
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK, Faculty of Medical Science, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Strangeways Laboratory
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Strangeways Laboratory, Department of Applied Health Research, University College London, London, UK
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, UK
| | - 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
| | | | | | | | | | - Walther Vogel
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Manuel Luedeke
- Department of Urology, University Hospital Ulm, Ulm, Germany
| | - Kathleen Herkommer
- Department of Urology, Klinikum rechts der Isar der Technischen Universitaet Muenchen, Munich, Germany
| | - Adam S Kibel
- Division of Urologic Surgery, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston, USA
| | - 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
| | - Wojciech Kluzniak
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Lisa Cannon-Albright
- Division of Genetic Epidemiology, Department of 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
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Katja Butterbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Thomas Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Hui-Yi Lin
- Biostatistics Program, Moffitt Cancer Center, Tampa, FL, USA
| | - Chavdar Slavov
- Department of Urology and Alexandrovska University Hospital, Medical University, Sofia, Bulgaria
| | - Radka Kaneva
- Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University, Sofia, Bulgaria
| | - Vanio Mitev
- Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University, Sofia, Bulgaria
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, Australia
| | - Judith A Clements
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, Australia
| | - Amanda Spurdle
- Molecular Cancer Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Australia
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal, Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Paula Paulo
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Sofia Maia
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | | | | | | | - Koveela Govindasami
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Michelle Guy
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Artitaya Lophatonanon
- Institute of Population Health, University of Manchester, Manchester, UK, Warwick Medical School, University of Warwick, Coventry, UK
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, UK, Warwick Medical School, University of Warwick, Coventry, UK
| | - Ana Viñuela
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Andrew A Brown
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway, Department of Genetic Medicine and Development, University of Geneva, Switzerland and
| | | | - David V Conti
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA, Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory
| | - Gerhard A Coetzee
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA, Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK,
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127
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Lawrenson K, Li Q, Kar S, Seo JH, Tyrer J, Spindler TJ, Lee J, Chen Y, Karst A, Drapkin R, Aben KKH, Anton-Culver H, Antonenkova N, Baker H, Bandera EV, Bean Y, Beckmann MW, Berchuck A, Bisogna M, Bjorge L, Bogdanova N, Brinton LA, Brooks-Wilson A, Bruinsma F, Butzow R, Campbell IG, Carty K, Chang-Claude J, Chenevix-Trench G, Chen A, Chen Z, Cook LS, Cramer DW, Cunningham JM, Cybulski C, Dansonka-Mieszkowska A, Dennis J, Dicks E, Doherty JA, Dörk T, du Bois A, Dürst M, Eccles D, Easton DT, Edwards RP, Eilber U, Ekici AB, Fasching PA, Fridley BL, Gao YT, Gentry-Maharaj A, Giles GG, Glasspool R, Goode EL, Goodman MT, Grownwald J, Harrington P, Harter P, Hasmad HN, Hein A, Heitz F, Hildebrandt MAT, Hillemanns P, Hogdall E, Hogdall C, Hosono S, Iversen ES, Jakubowska A, James P, Jensen A, Ji BT, Karlan BY, Kruger Kjaer S, Kelemen LE, Kellar M, Kelley JL, Kiemeney LA, Krakstad C, Kupryjanczyk J, Lambrechts D, Lambrechts S, Le ND, Lee AW, Lele S, Leminen A, Lester J, Levine DA, Liang D, Lissowska J, Lu K, Lubinski J, Lundvall L, Massuger LFAG, Matsuo K, McGuire V, McLaughlin JR, Nevanlinna H, McNeish I, Menon U, Modugno F, Moysich KB, Narod SA, Nedergaard L, Ness RB, Azmi MAN, Odunsi K, Olson SH, Orlow I, Orsulic S, Weber RP, Pearce CL, Pejovic T, Pelttari LM, Permuth-Wey J, Phelan CM, Pike MC, Poole EM, Ramus SJ, Risch HA, Rosen B, Rossing MA, Rothstein JH, Rudolph A, Runnebaum IB, Rzepecka IK, Salvesen HB, Schildkraut JM, Schwaab I, Sellers TA, Shu XO, Shvetsov YB, Siddiqui N, Sieh W, Song H, Southey MC, Sucheston L, Tangen IL, Teo SH, Terry KL, Thompson PJ, Timorek A, Tsai YY, Tworoger SS, van Altena AM, Van Nieuwenhuysen E, Vergote I, Vierkant RA, Wang-Gohrke S, Walsh C, Wentzensen N, Whittemore AS, Wicklund KG, Wilkens LR, Woo YL, Wu X, Wu AH, Yang H, Zheng W, Ziogas A, Monteiro A, Pharoah PD, Gayther SA, Freedman ML. Cis-eQTL analysis and functional validation of candidate susceptibility genes for high-grade serous ovarian cancer. Nat Commun 2015; 6:8234. [PMID: 26391404 PMCID: PMC4580986 DOI: 10.1038/ncomms9234] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/31/2015] [Indexed: 12/23/2022] Open
Abstract
Genome-wide association studies have reported 11 regions conferring risk of high-grade serous epithelial ovarian cancer (HGSOC). Expression quantitative trait locus (eQTL) analyses can identify candidate susceptibility genes at risk loci. Here we evaluate cis-eQTL associations at 47 regions associated with HGSOC risk (P≤10(-5)). For three cis-eQTL associations (P<1.4 × 10(-3), FDR<0.05) at 1p36 (CDC42), 1p34 (CDCA8) and 2q31 (HOXD9), we evaluate the functional role of each candidate by perturbing expression of each gene in HGSOC precursor cells. Overexpression of HOXD9 increases anchorage-independent growth, shortens population-doubling time and reduces contact inhibition. Chromosome conformation capture identifies an interaction between rs2857532 and the HOXD9 promoter, suggesting this SNP is a leading causal variant. Transcriptomic profiling after HOXD9 overexpression reveals enrichment of HGSOC risk variants within HOXD9 target genes (P=6 × 10(-10) for risk variants (P<10(-4)) within 10 kb of a HOXD9 target gene in ovarian cells), suggesting a broader role for this network in genetic susceptibility to HGSOC.
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Affiliation(s)
- Kate Lawrenson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Qiyuan Li
- Medical College, Xiamen University, Xiamen 361102, China
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Siddhartha Kar
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Ji-Heui Seo
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Jonathan Tyrer
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Tassja J. Spindler
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Janet Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Yibu Chen
- Bioinformatics Service, Norris Medical Library, University of Southern California, Los Angeles, California 90033, USA
| | - Alison Karst
- Departments of Pathology and Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Ronny Drapkin
- Departments of Pathology and Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Katja K. H. Aben
- Department for Health Evidence, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands
- Comprehensive Cancer Center, The Netherlands, PO Box 19079, 3501 DB Utrecht, The Netherlands
| | - Hoda Anton-Culver
- Department of Epidemiology, Director of Genetic Epidemiology Research Institute, School of Medicine, University of California Irvine, Irvine, California 92697, USA
| | - Natalia Antonenkova
- Byelorussian Institute for Oncology and Medical Radiology Aleksandrov N.N., 223040 Minsk, Belarus
| | - Helen Baker
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Elisa V. Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Yukie Bean
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon 97239, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Matthias W. Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Maria Bisogna
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Line Bjorge
- Department of Gynecology and Obstetrics, Haukeland University Hospital, N-5058 Bergen, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway
| | - Natalia Bogdanova
- Gynaecology Research Unit, Hannover Medical School, 30625 Hannover, Germany
| | - Louise A. Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda Maryland, 20892, USA
| | - Angela Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada V5Z 1L3
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Fiona Bruinsma
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
| | - Ralf Butzow
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, 00100 Helsinki, Finland
- Department of Pathology, Helsinki University Central Hospital, FI-00014 Helsinki, Finland
| | - Ian G. Campbell
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria 3002, Australia
- Department of Pathology, University of Melbourne, Parkville, Victoria 3010, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Karen Carty
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, Glasgow G12 0YN, UK
| | - Jenny Chang-Claude
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, 69120 Heidelberg, Germany
| | - Georgia Chenevix-Trench
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Anne Chen
- Department of Biostatistics, Moffitt Cancer Center, Tampa, Florida 33612, USA
| | - Zhihua Chen
- Department of Biostatistics, Moffitt Cancer Center, Tampa, Florida 33612, USA
| | - Linda S. Cook
- Division of Epidemiology and Biostatistics, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Daniel W. Cramer
- Harvard School of Public Health, Boston, Massachusetts 02215, USA
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Julie M. Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Cezary Cybulski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | | | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Ed Dicks
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Jennifer A. Doherty
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, 30625 Hannover, Germany
| | - Andreas du Bois
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, 45136 Essen, Germany
- Department of Gynecology and Gynecologic Oncology, Dr Horst Schmidt Kliniken Wiesbaden, 65199 Wiesbaden, Germany
| | - Matthias Dürst
- Department of Gynecology, Jena University Hospital—Friedrich Schiller University, 07737 Jena, Germany
| | - Diana Eccles
- Faculty of Medicine, University of Southampton, Southampton SO16 5YA, UK
| | - Douglas T. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Robert P. Edwards
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
- Ovarian Cancer Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania, 15213, USA
| | - Ursula Eilber
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, 69120 Heidelberg, Germany
| | - Arif B. Ekici
- University Hospital Erlangen, Institute of Human Genetics, Friedrich-Alexander-University Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Peter A. Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Brooke L. Fridley
- Biostatistics and Informatics Shared Resource, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
| | - Yu-Tang Gao
- Shanghai Cancer Institute, Shanghai 200030, China
| | - Aleksandra Gentry-Maharaj
- Department of Women's Cancer, Institute for Women's Health, University College London, London W1T 7DN, UK
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Rosalind Glasspool
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, Glasgow G12 0YN, UK
| | - Ellen L. Goode
- Department of Health Science Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Marc T. Goodman
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
- Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Jacek Grownwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Patricia Harrington
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Philipp Harter
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, 45136 Essen, Germany
- Department of Gynecology and Gynecologic Oncology, Dr Horst Schmidt Kliniken Wiesbaden, 65199 Wiesbaden, Germany
| | - Hanis Nazihah Hasmad
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, 47500 Subang Jaya, Malaysia
| | - Alexander Hein
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, 45136 Essen, Germany
- Department of Gynecology and Gynecologic Oncology, Dr Horst Schmidt Kliniken Wiesbaden, 65199 Wiesbaden, Germany
| | - Michelle A. T. Hildebrandt
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Peter Hillemanns
- Departments of Obstetrics and Gynaecology, Hannover Medical School, 30625 Hannover, Germany
| | - Estrid Hogdall
- Institute of Cancer Epidemiology, Danish Cancer Society, DK-2100 Copenhagen, Denmark
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, 1165 Copenhagen, Denmark
| | - Claus Hogdall
- Gyn Clinic, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Satoyo Hosono
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya 464-0021, Japan
| | - Edwin S. Iversen
- Department of Statistical Science, Duke University, Durham, North Carolina 27708, USA
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Paul James
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, Glasgow G12 0YN, UK
| | - Allan Jensen
- Department of Gynecology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda Maryland, 20892, USA
| | - Beth Y. Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Susanne Kruger Kjaer
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
- Department of Gynaecology, The Juliane Marie Centre, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Linda E. Kelemen
- Department of Public Health Sciences, College of Medicine, Medical University of South Carolina, Charleston, South Carolina 29435, USA
| | - Melissa Kellar
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon 97239, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Joseph L. Kelley
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Lambertus A. Kiemeney
- Radboud University Medical Mentre, Radboud Institute for Health Sciences, 6500 HB Nijmegen, The Netherlands
| | - Camilla Krakstad
- Department of Gynecology and Obstetrics, Haukeland University Hospital, N-5058 Bergen, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway
| | - Jolanta Kupryjanczyk
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Diether Lambrechts
- Vesalius Research Center, VIB, 3000 Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, B-3000 Leuven, Belgium
| | - Sandrina Lambrechts
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Nhu D. Le
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia, Canada V5Z 1L3
| | - Alice W. Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Shashi Lele
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Arto Leminen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, 00100 Helsinki, Finland
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Douglas A. Levine
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Dong Liang
- College of Pharmacy and Health Sciences, Texas Southern University, Houston, Texas 77004, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Karen Lu
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Lene Lundvall
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, 1165 Copenhagen, Denmark
| | - Leon F. A. G. Massuger
- Department of Gynaecology, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Keitaro Matsuo
- Department of Preventive Medicine, Kyushu University Faculty of Medical Sciences, 819-0395 Fukuoka, Japan
| | - Valerie McGuire
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford California 94305, USA
| | - John R. McLaughlin
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, 00100 Helsinki, Finland
| | - Ian McNeish
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, Beatson Institute for Cancer Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Usha Menon
- Department of Women's Cancer, Institute for Women's Health, University College London, London W1T 7DN, UK
| | - Francesmary Modugno
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
- Ovarian Cancer Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania, 15213, USA
- Women's Cancer Research Program, Magee-Women's Research Institute and University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania 15213, USA
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania 15261, USA
| | - Kirsten B. Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Steven A. Narod
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10017, USA
| | - Lotte Nedergaard
- Department of Pathology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Roberta B. Ness
- The University of Texas School of Public Health, Houston, Texas 77030, USA
| | - Mat Adenan Noor Azmi
- Department of Obstetrics and Gynaecology, University Malaya Medical Centre, University Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kunle Odunsi
- Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Sara H. Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10017, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10017, USA
| | - Sandra Orsulic
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Rachel Palmieri Weber
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Celeste L. Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Tanja Pejovic
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon 97239, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Liisa M. Pelttari
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, 00100 Helsinki, Finland
| | - Jennifer Permuth-Wey
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida 33612, USA
| | - Catherine M. Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida 33612, USA
| | - Malcolm C. Pike
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Elizabeth M. Poole
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02215, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA
| | - Susan J. Ramus
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Harvey A. Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut 06510, USA
| | - Barry Rosen
- Department of Gynecologic-Oncology, Princess Margaret Hospital, and Department of Obstetrics and Gynecology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada M5S 2J7
| | - Mary Anne Rossing
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
- Department of Epidemiology, University of Washington, Seattle, Washington 98195, USA
| | - Joseph H. Rothstein
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford California 94305, USA
| | - Anja Rudolph
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, 69120 Heidelberg, Germany
| | - Ingo B. Runnebaum
- Department of Gynecology, Jena University Hospital—Friedrich Schiller University, 07737 Jena, Germany
| | - Iwona K. Rzepecka
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Helga B. Salvesen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, N-5058 Bergen, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway
| | - Joellen M. Schildkraut
- Cancer Control and Population Sciences, Duke Cancer Institute, Durham, North Carolina 27710, USA
- Institut für Humangenetik Wiesbaden, 65187 Wiesbaden, Germany
| | - Ira Schwaab
- Institut für Humangenetik Wiesbaden, 65187 Wiesbaden, Germany
| | - Thomas A. Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida 33612, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Yurii B. Shvetsov
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, 96813, USA
| | - Nadeem Siddiqui
- Department of Gynaecological Oncology, Glasgow Royal Infirmary, Glasgow G4 0SF, UK
| | - Weiva Sieh
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford California 94305, USA
| | - Honglin Song
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Melissa C. Southey
- Department of Pathology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Lara Sucheston
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Ingvild L. Tangen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, N-5058 Bergen, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway
| | - Soo-Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, 47500 Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kathryn L. Terry
- Division of Epidemiology and Biostatistics, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico 87131, USA
- Harvard School of Public Health, Boston, Massachusetts 02215, USA
| | - Pamela J. Thompson
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
- Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Agnieszka Timorek
- Department of Obstetrics, Gynecology and Oncology, IInd Faculty of Medicine, Warsaw Medical University and Brodnowski Hospital, Warsaw, Poland
| | - Ya-Yu Tsai
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida 33612, USA
| | - Shelley S. Tworoger
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02215, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA
| | - Anne M. van Altena
- Department of Gynaecology, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Els Van Nieuwenhuysen
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Ignace Vergote
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Robert A. Vierkant
- Department of Health Science Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Shan Wang-Gohrke
- Department of Obstetrics and Gynecology, University of Ulm, 89075 Ulm, Germany
| | - Christine Walsh
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda Maryland, 20892, USA
| | - Alice S. Whittemore
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford California 94305, USA
| | - Kristine G. Wicklund
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Lynne R. Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, 96813, USA
| | - Yin-Ling Woo
- Department of Obstetrics and Gynaecology, University Malaya Medical Centre, University Malaya, 50603 Kuala Lumpur, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, 50603 Kuala Lumpur, Malaysia
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Anna H. Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Hannah Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda Maryland, 20892, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Argyrios Ziogas
- Department of Epidemiology, Director of Genetic Epidemiology Research Institute, School of Medicine, University of California Irvine, Irvine, California 92697, USA
| | - Alvaro Monteiro
- Cancer Epidemiology Program, Division of Population Sciences, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
| | - Paul D. Pharoah
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Simon A. Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Matthew L. Freedman
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
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Chen H, Yu H, Wang J, Zhang Z, Gao Z, Chen Z, Lu Y, Liu W, Jiang D, Zheng SL, Wei GH, Issacs WB, Feng J, Xu J. Systematic enrichment analysis of potentially functional regions for 103 prostate cancer risk-associated loci. Prostate 2015; 75:1264-76. [PMID: 26015065 DOI: 10.1002/pros.23008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 12/31/2022]
Abstract
BACKGROUND More than 100 prostate cancer (PCa) risk-associated single nucleotide polymorphisms (SNPs) have been identified by genome wide association studies (GWAS). However, the molecular mechanisms are unclear for most of these SNPs. METHODS All reported PCa risk-associated SNPs reaching the genome-wide significance level of P < 1 × 10(-7) (index SNPs), as well as SNPs in linkage disequilibrium (LD, r(2) ≥ 0.5) with them were cataloged. Genomic regions with potentially functional impact were also identified, including UCSC annotated coding regions (exon and snoRNA/miRNA) and regulatory regions, as well as binding regions for transcription factors (TFs), histone modifications (HMs), DNase I hypersensitivity (DHSs), and RNA Polymerase IIA (POLR2A) defined by ChIP-Seq in prostate cell lines and tissues. Enrichment analysis was performed to test whether PCa risk-associated SNPs are located in these functional regions more than expected. RESULTS A total of 103 PCa risk-associated index SNPs and 7,244 SNPs in LD with these index SNPs were cataloged. Genomic regions with potentially functional impact, grouped in 30 different categories of functionalities, were identified. Enrichment analysis indicated that genomic regions in the following 15 categories were enriched for the PCa risk-associated SNPs: exons, CpG regions, 6 TFs (AR, ERG, FOXA1, HOXB13, CTCF, and NR3C1), 5 HMs (H3K4me1, H3K4me2, H3K4me3, H3K27AC, and H3T11P), DHSs and POLR2A. In contrast, significantly fewer PCa risk SNPs were mapped to binding regions for H3K27me3, a repressive chromatin marker. CONCLUSIONS The PCa risk-associated SNPs discovered to date may affect PCa risk through multiple different mechanisms, especially by affecting binding regions of TFs/HMs.
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Affiliation(s)
- Haitao Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston Salem, North Carolina
- Center for Genomic Translational Medicine and Prevention, Fudan School of Public Health, Fudan University, Shanghai, P.R. China
| | - Hongjie Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Jianqing Wang
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Zheng Zhang
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston Salem, North Carolina
| | - Zhengrong Gao
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston Salem, North Carolina
| | - Zhuo Chen
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston Salem, North Carolina
| | - Yulan Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Wennuan Liu
- Program for Personalized Cancer Care and Department of Surgery, North Shore University Health System, Evanston, Illinois
| | - Deke Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
- Program for Personalized Cancer Care and Department of Surgery, North Shore University Health System, Evanston, Illinois
| | - S Lilly Zheng
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston Salem, North Carolina
- Program for Personalized Cancer Care and Department of Surgery, North Shore University Health System, Evanston, Illinois
| | - Gong-Hong Wei
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - William B Issacs
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Junjie Feng
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston Salem, North Carolina
| | - Jianfeng Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston Salem, North Carolina
- Center for Genomic Translational Medicine and Prevention, Fudan School of Public Health, Fudan University, Shanghai, P.R. China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, P.R. China
- Program for Personalized Cancer Care and Department of Surgery, North Shore University Health System, Evanston, Illinois
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129
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Analysis of Prostate Cancer Susceptibility Variants in South African Men: Replicating Associations on Chromosomes 8q24 and 10q11. Prostate Cancer 2015; 2015:465184. [PMID: 26347821 PMCID: PMC4549549 DOI: 10.1155/2015/465184] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/02/2015] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies (GWAS) have implicated single nucleotide polymorphisms (SNPs) on chromosomes 2p15, 6q25, 7p15.2, 7q21, 8q24, 10q11, 10q26, 11q13, 17q12, 17q24, 19q13, and Xp11, with prostate cancer (PCa) susceptibility and/or tumour aggressiveness, in populations of African, European, and Asian ancestry. The objective of this study was to confirm these associations in South African Mixed Ancestry and White men. We evaluated 17 prioritised GWAS SNPs in South African cases (331 Mixed Ancestry and 155 White) and controls (178 Mixed Ancestry and 145 White). The replicated SNP associations for the different South African ethnic groups were rs7008482 (8q24) (p = 2.45 × 10−5), rs6983267 (8q24) (p = 4.48 × 10−7), and rs10993994 (10q11) (p = 1.40 × 10−3) in Mixed Ancestry men and rs10993994 (p = 1.56 × 10−9) in White men. No significant associations were observed for the analyses stratified by disease aggressiveness in the individual and the combined population group analysis. The present study demonstrates that a number of known PCa susceptibility variants may contribute to disease susceptibility in South African men. Larger genetic investigations extended to other South African population groups are warranted to confirm the role of these and other SNPs in disease susceptibility.
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130
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Coetzee SG, Coetzee GA, Hazelett DJ. motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites. Bioinformatics 2015; 31:3847-9. [PMID: 26272984 PMCID: PMC4653394 DOI: 10.1093/bioinformatics/btv470] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/06/2015] [Indexed: 11/13/2022] Open
Abstract
Summary: Functional annotation represents a key step toward the understanding and interpretation of germline and somatic variation as revealed by genome-wide association studies (GWAS) and The Cancer Genome Atlas (TCGA), respectively. GWAS have revealed numerous genetic risk variants residing in non-coding DNA associated with complex diseases. For sequences that lie within enhancers or promoters of transcription, it is not straightforward to assess the effects of variants on likely transcription factor binding sites. Consequently we introduce motifbreakR, which allows the biologist to judge whether the sequence surrounding a polymorphism or mutation is a good match, and how much information is gained or lost in one allele of the polymorphism or mutation relative to the other. MotifbreakR is flexible, giving a choice of algorithms for interrogation of genomes with motifs from many public sources that users can choose from. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within bioconductor. Availability and implementation:https://github.com/Simon-Coetzee/MotifBreakR, www.bioconductor.org. Contact:dennis.hazelett@cshs.org
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Affiliation(s)
- Simon G Coetzee
- Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA and
| | - Gerhard A Coetzee
- Department of Urology and Preventive Medicine, USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Dennis J Hazelett
- Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA and
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131
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Kazemian M, Ren M, Lin JX, Liao W, Spolski R, Leonard WJ. Comprehensive assembly of novel transcripts from unmapped human RNA-Seq data and their association with cancer. Mol Syst Biol 2015; 11:826. [PMID: 26253570 PMCID: PMC4562499 DOI: 10.15252/msb.156172] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Crucial parts of the genome including genes encoding microRNAs and noncoding RNAs went unnoticed for years, and even now, despite extensive annotation and assembly of the human genome, RNA-sequencing continues to yield millions of unmappable and thus uncharacterized reads. Here, we examined > 300 billion reads from 536 normal donors and 1,873 patients encompassing 21 cancer types, identified ∼300 million such uncharacterized reads, and using a distinctive approach de novo assembled 2,550 novel human transcripts, which mainly represent long noncoding RNAs. Of these, 230 exhibited relatively specific expression or non-expression in certain cancer types, making them potential markers for those cancers, whereas 183 exhibited tissue specificity. Moreover, we used lentiviral-mediated expression of three selected transcripts that had higher expression in normal than in cancer patients and found that each inhibited the growth of HepG2 cells. Our analysis provides a comprehensive and unbiased resource of unmapped human transcripts and reveals their associations with specific cancers, providing potentially important new genes for therapeutic targeting.
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Affiliation(s)
- Majid Kazemian
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute National Institutes of Health, Bethesda, MD, USA
| | - Min Ren
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute National Institutes of Health, Bethesda, MD, USA
| | - Jian-Xin Lin
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute National Institutes of Health, Bethesda, MD, USA
| | - Wei Liao
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute National Institutes of Health, Bethesda, MD, USA
| | - Rosanne Spolski
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute National Institutes of Health, Bethesda, MD, USA
| | - Warren J Leonard
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute National Institutes of Health, Bethesda, MD, USA
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132
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Kichaev G, Pasaniuc B. Leveraging Functional-Annotation Data in Trans-ethnic Fine-Mapping Studies. Am J Hum Genet 2015; 97:260-71. [PMID: 26189819 DOI: 10.1016/j.ajhg.2015.06.007] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 06/09/2015] [Indexed: 01/10/2023] Open
Abstract
Localization of causal variants underlying known risk loci is one of the main research challenges following genome-wide association studies. Risk loci are typically dissected through fine-mapping experiments in trans-ethnic cohorts for leveraging the variability in the local genetic structure across populations. More recent works have shown that genomic functional annotations (i.e., localization of tissue-specific regulatory marks) can be integrated for increasing fine-mapping performance within single-population studies. Here, we introduce methods that integrate the strength of association between genotype and phenotype, the variability in the genetic backgrounds across populations, and the genomic map of tissue-specific functional elements to increase trans-ethnic fine-mapping accuracy. Through extensive simulations and empirical data, we have demonstrated that our approach increases fine-mapping resolution over existing methods. We analyzed empirical data from a large-scale trans-ethnic rheumatoid arthritis (RA) study and showed that the functional genetic architecture of RA is consistent across European and Asian ancestries. In these data, we used our proposed methods to reduce the average size of the 90% credible set from 29 variants per locus for standard non-integrative approaches to 22 variants.
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Affiliation(s)
- Gleb Kichaev
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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133
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Grimmer MR, Farnham PJ. Can genome engineering be used to target cancer-associated enhancers? Epigenomics 2015; 6:493-501. [PMID: 25431942 DOI: 10.2217/epi.14.30] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Transcriptional misregulation is involved in the development of many diseases, especially neoplastic transformation. Distal regulatory elements, such as enhancers, play a major role in specifying cell-specific transcription patterns in both normal and diseased tissues, suggesting that enhancers may be prime targets for therapeutic intervention. By focusing on modulating gene regulation mediated by cell type-specific enhancers, there is hope that normal epigenetic patterning in an affected tissue could be restored with fewer side effects than observed with treatments employing relatively nonspecific inhibitors such as epigenetic drugs. New methods employing genomic nucleases and site-specific epigenetic regulators targeted to specific genomic regions, using either artificial DNA-binding proteins or RNA-DNA interactions, may allow precise genome engineering at enhancers. However, this field is still in its infancy and further refinements that increase specificity and efficiency are clearly required.
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Affiliation(s)
- Matthew R Grimmer
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9601, USA
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134
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Coetzee SG, Shen HC, Hazelett DJ, Lawrenson K, Kuchenbaecker K, Tyrer J, Rhie SK, Levanon K, Karst A, Drapkin R, Ramus SJ, Couch FJ, Offit K, Chenevix-Trench G, Monteiro ANA, Antoniou A, Freedman M, Coetzee GA, Pharoah PDP, Noushmehr H, Gayther SA. Cell-type-specific enrichment of risk-associated regulatory elements at ovarian cancer susceptibility loci. Hum Mol Genet 2015; 24:3595-607. [PMID: 25804953 PMCID: PMC4459387 DOI: 10.1093/hmg/ddv101] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/16/2015] [Indexed: 02/07/2023] Open
Abstract
Understanding the regulatory landscape of the human genome is a central question in complex trait genetics. Most single-nucleotide polymorphisms (SNPs) associated with cancer risk lie in non-protein-coding regions, implicating regulatory DNA elements as functional targets of susceptibility variants. Here, we describe genome-wide annotation of regions of open chromatin and histone modification in fallopian tube and ovarian surface epithelial cells (FTSECs, OSECs), the debated cellular origins of high-grade serous ovarian cancers (HGSOCs) and in endometriosis epithelial cells (EECs), the likely precursor of clear cell ovarian carcinomas (CCOCs). The regulatory architecture of these cell types was compared with normal human mammary epithelial cells and LNCaP prostate cancer cells. We observed similar positional patterns of global enhancer signatures across the three different ovarian cancer precursor cell types, and evidence of tissue-specific regulatory signatures compared to non-gynecological cell types. We found significant enrichment for risk-associated SNPs intersecting regulatory biofeatures at 17 known HGSOC susceptibility loci in FTSECs (P = 3.8 × 10(-30)), OSECs (P = 2.4 × 10(-23)) and HMECs (P = 6.7 × 10(-15)) but not for EECs (P = 0.45) or LNCaP cells (P = 0.88). Hierarchical clustering of risk SNPs conditioned on the six different cell types indicates FTSECs and OSECs are highly related (96% of samples using multi-scale bootstrapping) suggesting both cell types may be precursors of HGSOC. These data represent the first description of regulatory catalogues of normal precursor cells for different ovarian cancer subtypes, and provide unique insights into the tissue specific regulatory variation with respect to the likely functional targets of germline genetic susceptibility variants for ovarian cancer.
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Affiliation(s)
- Simon G Coetzee
- Department of Genetics - Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto-SP CEP: 14049-900, Brazil, Center for Cell Based Therapy, Rua Tenente Catão Roxo, 2501, Monte Alegre, Ribeirão Preto, SP, CEP: 14051-140, Brazil
| | - Howard C Shen
- Department of Preventive Medicine, Keck School of Medicine and
| | - Dennis J Hazelett
- Department of Preventive Medicine, Keck School of Medicine and, Department of Urology, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Kate Lawrenson
- Department of Preventive Medicine, Keck School of Medicine and
| | - Karoline Kuchenbaecker
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Jonathan Tyrer
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Suhn K Rhie
- Department of Preventive Medicine, Keck School of Medicine and, Department of Urology, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Keren Levanon
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Alison Karst
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Ronny Drapkin
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Susan J Ramus
- Department of Preventive Medicine, Keck School of Medicine and
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kenneth Offit
- Clinical Genetics Service, Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, Queensland Institute of Medical Research, Brisbane, Australia
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, Division of Population Sciences, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Antonis Antoniou
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Matthew Freedman
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA and
| | - Gerhard A Coetzee
- Department of Preventive Medicine, Keck School of Medicine and, Department of Urology, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Paul D P Pharoah
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Houtan Noushmehr
- Department of Genetics - Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto-SP CEP: 14049-900, Brazil, Center for Cell Based Therapy, Rua Tenente Catão Roxo, 2501, Monte Alegre, Ribeirão Preto, SP, CEP: 14051-140, Brazil, Center for Integrative Systems Biology - CISBi, NAP/USP, Rua Catão Roxo, 2501, Monte Alegre, Ribeirão Preto, SP CEP: 14051-140, Brazil
| | - Simon A Gayther
- Department of Preventive Medicine, Keck School of Medicine and,
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135
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Larson NB, McDonnell S, French AJ, Fogarty Z, Cheville J, Middha S, Riska S, Baheti S, Nair AA, Wang L, Schaid DJ, Thibodeau SN. Comprehensively evaluating cis-regulatory variation in the human prostate transcriptome by using gene-level allele-specific expression. Am J Hum Genet 2015; 96:869-82. [PMID: 25983244 PMCID: PMC4457953 DOI: 10.1016/j.ajhg.2015.04.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/17/2015] [Indexed: 12/17/2022] Open
Abstract
The identification of cis-acting regulatory variation in primary tissues has the potential to elucidate the genetic basis of complex traits and further our understanding of transcriptomic diversity across cell types. Expression quantitative trait locus (eQTL) association analysis using RNA sequencing (RNA-seq) data can improve upon the detection of cis-acting regulatory variation by leveraging allele-specific expression (ASE) patterns in association analysis. Here, we present a comprehensive evaluation of cis-acting eQTLs by analyzing RNA-seq gene-expression data and genome-wide high-density genotypes from 471 samples of normal primary prostate tissue. Using statistical models that integrate ASE information, we identified extensive cis-eQTLs across the prostate transcriptome and found that approximately 70% of expressed genes corresponded to a significant eQTL at a gene-level false-discovery rate of 0.05. Overall, cis-eQTLs were heavily concentrated near the transcription start and stop sites of affected genes, and effects were negatively correlated with distance. We identified multiple instances of cis-acting co-regulation by using phased genotype data and discovered 233 SNPs as the most strongly associated eQTLs for more than one gene. We also noted significant enrichment (25/50, p = 2E-5) of previously reported prostate cancer risk SNPs in prostate eQTLs. Our results illustrate the benefit of assessing ASE data in cis-eQTL analyses by showing better reproducibility of prior eQTL findings than of eQTL mapping based on total expression alone. Altogether, our analysis provides extensive functional context of thousands of SNPs in prostate tissue, and these results will be of critical value in guiding studies examining disease of the human prostate.
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Affiliation(s)
- Nicholas B Larson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA.
| | - Shannon McDonnell
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Amy J French
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zach Fogarty
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - John Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Sumit Middha
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Shaun Riska
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Saurabh Baheti
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Asha A Nair
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Liang Wang
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Daniel J Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephen N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
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136
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Jeong S, Patel N, Edlund CK, Hartiala J, Hazelett DJ, Itakura T, Wu PC, Avery RL, Davis JL, Flynn HW, Lalwani G, Puliafito CA, Wafapoor H, Hijikata M, Keicho N, Gao X, Argüeso P, Allayee H, Coetzee GA, Pletcher MT, Conti DV, Schwartz SG, Eaton AM, Fini ME. Identification of a Novel Mucin Gene HCG22 Associated With Steroid-Induced Ocular Hypertension. Invest Ophthalmol Vis Sci 2015; 56:2737-48. [PMID: 25813999 PMCID: PMC4416661 DOI: 10.1167/iovs.14-14803] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 12/04/2014] [Indexed: 12/24/2022] Open
Abstract
PURPOSE The pathophysiology of ocular hypertension (OH) leading to primary open-angle glaucoma shares many features with a secondary form of OH caused by treatment with glucocorticoids, but also exhibits distinct differences. In this study, a pharmacogenomics approach was taken to discover candidate genes for this disorder. METHODS A genome-wide association study was performed, followed by an independent candidate gene study, using a cohort enrolled from patients treated with off-label intravitreal triamcinolone, and handling change in IOP as a quantitative trait. RESULTS An intergenic quantitative trait locus (QTL) was identified at chromosome 6p21.33 near the 5' end of HCG22 that attained the accepted statistical threshold for genome-level significance. The HCG22 transcript, encoding a novel mucin protein, was expressed in trabecular meshwork cells, and expression was stimulated by IL-1, and inhibited by triamcinolone acetate and TGF-β. Bioinformatic analysis defined the QTL as an approximately 4 kilobase (kb) linkage disequilibrium block containing 10 common single nucleotide polymorphisms (SNPs). Four of these SNPs were identified in the National Center for Biotechnology Information (NCBI) GTEx eQTL browser as modifiers of HCG22 expression. Most are predicted to disrupt or improve motifs for transcription factor binding, the most relevant being disruption of the glucocorticoid receptor binding motif. A second QTL was identified within the predicted signal peptide of the HCG22 encoded protein that could affect its secretion. Translation, O-glycosylation, and secretion of the predicted HCG22 protein was verified in cultured trabecular meshwork cells. CONCLUSIONS Identification of two independent QTLs that could affect expression of the HCG22 mucin gene product via two different mechanisms (transcription or secretion) is highly suggestive of a role in steroid-induced OH.
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Affiliation(s)
- Shinwu Jeong
- USC Institute for Genetic Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States 2USC Eye Institute/Department of Ophthalmology, Keck School of Medicine of USC, University of Southern California
| | - Nitin Patel
- USC Institute for Genetic Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States
| | - Christopher K Edlund
- Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States
| | - Jaana Hartiala
- USC Institute for Genetic Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States
| | - Dennis J Hazelett
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States
| | - Tatsuo Itakura
- USC Institute for Genetic Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States
| | - Pei-Chang Wu
- USC Institute for Genetic Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States 5Department of Ophthalmology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Robert L Avery
- California Retina Consultants, Santa Barbara, California, United States
| | - Janet L Davis
- Bascom Palmer Eye Institute and Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Harry W Flynn
- Bascom Palmer Eye Institute and Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Geeta Lalwani
- Bascom Palmer Eye Institute and Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Carmen A Puliafito
- USC Eye Institute/Department of Ophthalmology, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States 7Bascom Palmer Eye Institute and Department of Ophthalmology, University of Miami Miller School of Med
| | | | - Minako Hijikata
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Naoto Keicho
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Xiaoyi Gao
- Department of Ophthalmology and Visual Sciences, University of Illinois, Chicago, Illinois, United States
| | - Pablo Argüeso
- The Schepens Eye Research Institute, Massachusetts Eye & Ear Infirmary and Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
| | - Hooman Allayee
- USC Institute for Genetic Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States 3Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angele
| | - Gerhard A Coetzee
- Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States 4USC/Norris Comprehensive Cancer Center, Keck School of Medicine of USC, University of Southern California, Los An
| | - Mathew T Pletcher
- Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, Jupiter, Florida, United States
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States
| | - Stephen G Schwartz
- Bascom Palmer Eye Institute and Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, Florida, United States
| | | | - M Elizabeth Fini
- USC Institute for Genetic Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, United States 2USC Eye Institute/Department of Ophthalmology, Keck School of Medicine of USC, University of Southern California
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137
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Loo LWM, Fong AYW, Cheng I, Le Marchand L. In silico functional pathway annotation of 86 established prostate cancer risk variants. PLoS One 2015; 10:e0117873. [PMID: 25658610 PMCID: PMC4320069 DOI: 10.1371/journal.pone.0117873] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/23/2014] [Indexed: 11/18/2022] Open
Abstract
Heritability is one of the strongest risk factors of prostate cancer, emphasizing the importance of the genetic contribution towards prostate cancer risk. To date, 86 established prostate cancer risk variants have been identified by genome-wide association studies (GWAS). To determine if these risk variants are located near genes that interact together in biological networks or pathways contributing to prostate cancer initiation or progression, we generated gene sets based on proximity to the 86 prostate cancer risk variants. We took two approaches to generate gene lists. The first strategy included all immediate flanking genes, up- and downstream of the risk variant, regardless of distance from the index variant, and the second strategy included genes closest to the index GWAS marker and to variants in high LD (r2 ≥0.8 in Europeans) with the index variant, within a 100 kb window up- and downstream. Pathway mapping of the two gene sets supported the importance of the androgen receptor-mediated signaling in prostate cancer biology. In addition, the hedgehog and Wnt/β-catenin signaling pathways were identified in pathway mapping for the flanking gene set. We also used the HaploReg resource to examine the 86 risk loci and variants high LD (r2 ≥0.8) for functional elements. We found that there was a 12.8 fold (p = 2.9 x 10-4) enrichment for enhancer motifs in a stem cell line and a 4.4 fold (p = 1.1 x 10-3) enrichment of DNase hypersensitivity in a prostate adenocarcinoma cell line, indicating that the risk and correlated variants are enriched for transcriptional regulatory motifs. Our pathway-based functional annotation of the prostate cancer risk variants highlights the potential regulatory function that GWAS risk markers, and their highly correlated variants, exert on genes. Our study also shows that these genes may function cooperatively in key signaling pathways in prostate cancer biology.
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Affiliation(s)
- Lenora W. M. Loo
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Aaron Y. W. Fong
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Iona Cheng
- Epidemiology Research Department, Cancer Prevention Institute of California, Fremont, California, United States of America
| | - Loïc Le Marchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
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138
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Penney KL, Sinnott JA, Tyekucheva S, Gerke T, Shui IM, Kraft P, Sesso HD, Freedman ML, Loda M, Mucci LA, Stampfer MJ. Association of prostate cancer risk variants with gene expression in normal and tumor tissue. Cancer Epidemiol Biomarkers Prev 2014; 24:255-60. [PMID: 25371445 DOI: 10.1158/1055-9965.epi-14-0694-t] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Numerous germline genetic variants are associated with prostate cancer risk, but their biologic role is not well understood. One possibility is that these variants influence gene expression in prostate tissue. We therefore examined the association of prostate cancer risk variants with the expression of genes nearby and genome-wide. METHODS We generated mRNA expression data for 20,254 genes with the Affymetrix GeneChip Human Gene 1.0 ST microarray from normal prostate (N = 160) and prostate tumor (N = 264) tissue from participants of the Physicians' Health Study and Health Professionals Follow-up Study. With linear models, we tested the association of 39 risk variants with nearby genes and all genes, and the association of each variant with canonical pathways using a global test. RESULTS In addition to confirming previously reported associations, we detected several new significant (P < 0.05) associations of variants with the expression of nearby genes including C2orf43, ITGA6, MLPH, CHMP2B, BMPR1B, and MTL5. Genome-wide, five genes (MSMB, NUDT11, RBPMS2, NEFM, and KLHL33) were significantly associated after accounting for multiple comparisons for each SNP (P < 2.5 × 10(-6)). Many more genes had an FDR <10%, including SRD5A1 and PSCA, and we observed significant associations with pathways in tumor tissue. CONCLUSIONS The risk variants were associated with several genes, including promising prostate cancer candidates and lipid metabolism pathways, suggesting mechanisms for their impact on disease. These genes should be further explored in biologic and epidemiologic studies. IMPACT Determining the biologic role of these variants can lead to improved understanding of prostate cancer etiology and identify new targets for chemoprevention.
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Affiliation(s)
- Kathryn L Penney
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts. Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.
| | - Jennifer A Sinnott
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts. Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Svitlana Tyekucheva
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts. Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Travis Gerke
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Irene M Shui
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts. Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Howard D Sesso
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts. Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. The Broad Institute, Cambridge, Massachusetts
| | - Massimo Loda
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. The Broad Institute, Cambridge, Massachusetts. Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts. Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Meir J Stampfer
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts. Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts
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139
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Abstract
Gene enhancer elements are noncoding segments of DNA that play a central role in regulating transcriptional programs that control development, cell identity, and evolutionary processes. Recent studies have shown that noncoding single nucleotide polymorphisms (SNPs) that have been associated with risk for numerous common diseases through genome-wide association studies frequently lie in cell-type-specific enhancer elements. These enhancer variants probably influence transcriptional output, thereby offering a mechanistic basis to explain their association with risk for many common diseases. This review focuses on the identification and interpretation of disease-susceptibility variants that influence enhancer function. We discuss strategies for prioritizing the study of functional enhancer SNPs over those likely to be benign, review experimental and computational approaches to identifying the gene targets of enhancer variants, and highlight efforts to quantify the impact of enhancer variants on target transcript levels and cellular phenotypes. These studies are beginning to provide insights into the mechanistic basis of many common diseases, as well as into how we might translate this knowledge for improved disease diagnosis, prevention and treatments. Finally, we highlight five major challenges often associated with interpreting enhancer variants, and discuss recent technical advances that may help to surmount these challenges.
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Affiliation(s)
- Olivia Corradin
- />Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44122 USA
| | - Peter C Scacheri
- />Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44122 USA
- />Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106 USA
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140
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Al Olama AA, Kote-Jarai Z, Berndt SI, Conti DV, Schumacher F, Han Y, Benlloch S, Hazelett DJ, Wang Z, Saunders E, Leongamornlert D, Lindstrom S, Jugurnauth-Little S, Dadaev T, Tymrakiewicz M, Stram DO, Rand K, Wan P, Stram A, Sheng X, Pooler LC, Park K, Xia L, Tyrer J, Kolonel LN, Le Marchand L, Hoover RN, Machiela MJ, Yeager M, Burdette L, Chung CC, Hutchinson A, Yu K, Goh C, Ahmed M, Govindasami K, Guy M, Tammela TLJ, Auvinen A, Wahlfors T, Schleutker J, Visakorpi T, Leinonen KA, Xu J, Aly M, Donovan J, Travis RC, Key TJ, Siddiq A, Canzian F, Khaw KT, Takahashi A, Kubo M, Pharoah P, Pashayan N, Weischer M, Nordestgaard BG, Nielsen SF, Klarskov P, Røder MA, Iversen P, Thibodeau SN, McDonnell SK, Schaid DJ, Stanford JL, Kolb S, Holt S, Knudsen B, Coll AH, Gapstur SM, Diver WR, Stevens VL, Maier C, Luedeke M, Herkommer K, Rinckleb AE, Strom SS, Pettaway C, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Chokkalingam AP, Cannon-Albright L, Cybulski C, Wokołorczyk D, Kluźniak W, Park J, Sellers T, Lin HY, Isaacs WB, Partin AW, Brenner H, Dieffenbach AK, Stegmaier C, Chen C, Giovannucci EL, Ma J, Stampfer M, Penney KL, Mucci L, John EM, Ingles SA, Kittles RA, Murphy AB, Pandha H, Michael A, Kierzek AM, Blot W, Signorello LB, Zheng W, Albanes D, Virtamo J, Weinstein S, Nemesure B, Carpten J, Leske C, Wu SY, Hennis A, Kibel AS, Rybicki BA, Neslund-Dudas C, Hsing AW, Chu L, Goodman PJ, Klein EA, Zheng SL, Batra J, Clements J, Spurdle A, Teixeira MR, Paulo P, Maia S, Slavov C, Kaneva R, Mitev V, Witte JS, Casey G, Gillanders EM, Seminara D, Riboli E, Hamdy FC, Coetzee GA, Li Q, Freedman ML, Hunter DJ, Muir K, Gronberg H, Neal DE, Southey M, Giles GG, Severi G, Cook MB, Nakagawa H, Wiklund F, Kraft P, Chanock SJ, Henderson BE, Easton DF, Eeles RA, Haiman CA. A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer. Nat Genet 2014; 46:1103-9. [PMID: 25217961 PMCID: PMC4383163 DOI: 10.1038/ng.3094] [Citation(s) in RCA: 344] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 08/19/2014] [Indexed: 02/02/2023]
Abstract
Genome-wide association studies (GWAS) have identified 76 variants associated with prostate cancer risk predominantly in populations of European ancestry. To identify additional susceptibility loci for this common cancer, we conducted a meta-analysis of > 10 million SNPs in 43,303 prostate cancer cases and 43,737 controls from studies in populations of European, African, Japanese and Latino ancestry. Twenty-three new susceptibility loci were identified at association P < 5 × 10(-8); 15 variants were identified among men of European ancestry, 7 were identified in multi-ancestry analyses and 1 was associated with early-onset prostate cancer. These 23 variants, in combination with known prostate cancer risk variants, explain 33% of the familial risk for this disease in European-ancestry populations. These findings provide new regions for investigation into the pathogenesis of prostate cancer and demonstrate the usefulness of combining ancestrally diverse populations to discover risk loci for disease.
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Affiliation(s)
- Ali Amin Al Olama
- 1] Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK. [2]
| | | | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - David V Conti
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Fredrick Schumacher
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Ying Han
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Sara Benlloch
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dennis J Hazelett
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Zhaoming Wang
- 1] Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA. [2] Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, SAIC-Frederick, Inc., Frederick, Maryland, USA
| | | | | | - Sara Lindstrom
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | | | | | | | - Daniel O Stram
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Kristin Rand
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Peggy Wan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Alex Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Xin Sheng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Loreall C Pooler
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Karen Park
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Lucy Xia
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jonathan Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Laurence N Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Merideth Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Chee Goh
- Institute of Cancer Research, London, UK
| | | | | | | | - Teuvo L J Tammela
- Department of Urology, Tampere University Hospital and Medical School, University of Tampere, Tampere, Finland
| | - Anssi Auvinen
- Department of Epidemiology, School of Health Sciences, University of Tampere, Tampere, Finland
| | - Tiina Wahlfors
- BioMediTech, University of Tampere and FimLab Laboratories, Tampere, Finland
| | - Johanna Schleutker
- 1] BioMediTech, University of Tampere and FimLab Laboratories, Tampere, Finland. [2] Department of Medical Biochemistry, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Tapio Visakorpi
- Institute of Biomedical Technology/BioMediTech, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Katri A Leinonen
- Institute of Biomedical Technology/BioMediTech, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Jianfeng Xu
- Center for Cancer Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Markus Aly
- 1] Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden. [2] Department of Clinical Sciences at Danderyds Hospital, Stockholm, Sweden
| | - Jenny Donovan
- School of Social and Community Medicine, University of Bristol, Bristol, 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
| | - Afshan Siddiq
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, UK
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, UK
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Maren Weischer
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Borge G Nordestgaard
- 1] Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark. [2] Faculty of Healthy and Medical Sciences, University of Copenhagen, Herlev, Denmark
| | - Sune F Nielsen
- 1] Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark. [2] Faculty of Healthy and Medical Sciences, University of Copenhagen, Herlev, Denmark
| | - Peter Klarskov
- Department of Urology, Herlev Hospital, Copenhagen University Hospital, Herlev, 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
| | | | | | | | - Janet L Stanford
- 1] Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA. [2] Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Sarah Holt
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Beatrice Knudsen
- Translational Pathology, Cedars-Sinai, Los Angeles, California, USA
| | | | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Victoria L Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | | | - Manuel Luedeke
- Department of Urology, University Hospital Ulm, Ulm, Germany
| | - Kathleen Herkommer
- Department of Urology, Klinikum Rechts der Isar der Technischen Universität München, Munich, Germany
| | | | - Sara S Strom
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Curtis Pettaway
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Edward D Yeboah
- 1] University of Ghana Medical School, Accra, Ghana. [2] Korle Bu Teaching Hospital, Accra, Ghana
| | - Yao Tettey
- 1] University of Ghana Medical School, Accra, Ghana. [2] Korle Bu Teaching Hospital, Accra, Ghana
| | - Richard B Biritwum
- 1] University of Ghana Medical School, Accra, Ghana. [2] Korle Bu Teaching Hospital, Accra, Ghana
| | - Andrew A Adjei
- 1] University of Ghana Medical School, Accra, Ghana. [2] Korle Bu Teaching Hospital, Accra, Ghana
| | - Evelyn Tay
- 1] University of Ghana Medical School, Accra, Ghana. [2] Korle Bu Teaching Hospital, Accra, Ghana
| | | | | | - Anand P Chokkalingam
- School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Lisa Cannon-Albright
- 1] Division of Genetic Epidemiology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA. [2] George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, USA
| | - 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
| | - Wojciech Kluźniak
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jong Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Thomas Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Hui-Yi Lin
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, USA
| | - William B Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, Maryland, USA
| | - Alan W Partin
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, Maryland, USA
| | - Hermann Brenner
- 1] Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany. [2] German Cancer Consortium, Heidelberg, Germany
| | - Aida Karina Dieffenbach
- 1] Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany. [2] German Cancer Consortium, Heidelberg, Germany
| | | | - Constance Chen
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Edward L Giovannucci
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Jing Ma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Meir Stampfer
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA. [3] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kathryn L Penney
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lorelei Mucci
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Esther M John
- 1] Cancer Prevention Institute of California, Fremont, California, USA. [2] Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Sue A Ingles
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Rick A Kittles
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Adam B Murphy
- Department of Urology, Northwestern University, Chicago, Illinois, USA
| | - Hardev Pandha
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Agnieszka Michael
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Andrzej M Kierzek
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - William Blot
- 1] International Epidemiology Institute, Rockville, Maryland, USA. [2] Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Lisa B Signorello
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Demetrius Albanes
- Nutritional Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Stephanie Weinstein
- Nutritional Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Barbara Nemesure
- Department of Preventive Medicine, Stony Brook University, Stony Brook, New York, USA
| | - John Carpten
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Cristina Leske
- Department of Preventive Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Suh-Yuh Wu
- Department of Preventive Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Anselm Hennis
- 1] Department of Preventive Medicine, Stony Brook University, Stony Brook, New York, USA. [2] Chronic Disease Research Centre, University of the West Indies, Bridgetown, Barbados
| | - Adam S Kibel
- Division of Urologic Surgery, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, Michigan, USA
| | | | - Ann W Hsing
- 1] Cancer Prevention Institute of California, Fremont, California, USA. [2] Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Lisa Chu
- 1] Cancer Prevention Institute of California, Fremont, California, USA. [2] Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Phyllis J Goodman
- Southwest Oncology Group Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Eric A Klein
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - S Lilly Zheng
- Center for Cancer Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Translational Research Institute, Brisbane, Queensland, Australia
| | - Judith Clements
- Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Translational Research Institute, Brisbane, Queensland, Australia
| | - Amanda Spurdle
- Molecular Cancer Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Manuel R Teixeira
- 1] Department of Genetics, Portuguese Oncology Institute, Porto, Portugal. [2] Biomedical Sciences Institute, University of Porto, Porto, Portugal
| | - Paula Paulo
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Sofia Maia
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Chavdar Slavov
- Department of Urology, Medical University-Sofia, Sofia, Bulgaria
| | - Radka Kaneva
- Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University-Sofia, Sofia, Bulgaria
| | - Vanio Mitev
- Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University-Sofia, Sofia, Bulgaria
| | - John S Witte
- 1] Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA. [2] Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Graham Casey
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Elizabeth M Gillanders
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland, USA
| | - Daniella Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland, USA
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Gerhard A Coetzee
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Qiyuan Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - David J Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Kenneth Muir
- 1] Institute of Population Health, University of Manchester, Manchester, UK. [2] Warwick Medical School, University of Warwick, Coventry, UK
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - David E Neal
- 1] Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK. [2] Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Melissa Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Graham G Giles
- 1] Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia. [2] Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Gianluca Severi
- 1] Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia. [2] Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia. [3] Human Genetics Foundation, Torino, Italy
| | - Michael B Cook
- 1] Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA. [2]
| | - Hidewaki Nakagawa
- 1] Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan. [2]
| | - Fredrik Wiklund
- 1] Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden. [2]
| | - Peter Kraft
- 1] Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA. [3]
| | - Stephen J Chanock
- 1] Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA. [2]
| | - Brian E Henderson
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA. [3]
| | - Douglas F Easton
- 1] Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK. [2]
| | - Rosalind A Eeles
- 1] Institute of Cancer Research, London, UK. [2] Royal Marsden National Health Service (NHS) Foundation Trust, London and Sutton, UK. [3]
| | - Christopher A Haiman
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA. [3]
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Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related deaths in the United States. Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with increased risk for CRC. A molecular understanding of the functional consequences of this genetic variation has been complicated because each GWAS SNP is a surrogate for hundreds of other SNPs, most of which are located in non-coding regions. Here we use genomic and epigenomic information to test the hypothesis that the GWAS SNPs and/or correlated SNPs are in elements that regulate gene expression, and identify 23 promoters and 28 enhancers. Using gene expression data from normal and tumour cells, we identify 66 putative target genes of the risk-associated enhancers (10 of which were also identified by promoter SNPs). Employing CRISPR nucleases, we delete one risk-associated enhancer and identify genes showing altered expression. We suggest that similar studies be performed to characterize all CRC risk-associated enhancers. Previous studies identified genetic variants associated with colorectal cancer (CRC), but the functional consequences of these genetic risk factors remain poorly understood. Here, the authors report that CRC risk variants reside in promoters and enhancers and could increase colon cancer risk through gene expression regulation.
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142
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Du M, Yuan T, Schilter KF, Dittmar RL, Mackinnon A, Huang X, Tschannen M, Worthey E, Jacob H, Xia S, Gao J, Tillmans L, Lu Y, Liu P, Thibodeau SN, Wang L. Prostate cancer risk locus at 8q24 as a regulatory hub by physical interactions with multiple genomic loci across the genome. Hum Mol Genet 2014; 24:154-66. [PMID: 25149474 DOI: 10.1093/hmg/ddu426] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Chromosome 8q24 locus contains regulatory variants that modulate genetic risk to various cancers including prostate cancer (PC). However, the biological mechanism underlying this regulation is not well understood. Here, we developed a chromosome conformation capture (3C)-based multi-target sequencing technology and systematically examined three PC risk regions at the 8q24 locus and their potential regulatory targets across human genome in six cell lines. We observed frequent physical contacts of this risk locus with multiple genomic regions, in particular, inter-chromosomal interaction with CD96 at 3q13 and intra-chromosomal interaction with MYC at 8q24. We identified at least five interaction hot spots within the predicted functional regulatory elements at the 8q24 risk locus. We also found intra-chromosomal interaction genes PVT1, FAM84B and GSDMC and inter-chromosomal interaction gene CXorf36 in most of the six cell lines. Other gene regions appeared to be cell line-specific, such as RRP12 in LNCaP, USP14 in DU-145 and SMIN3 in lymphoblastoid cell line. We further found that the 8q24 functional domains more likely interacted with genomic regions containing genes enriched in critical pathways such as Wnt signaling and promoter motifs such as E2F1 and TCF3. This result suggests that the risk locus may function as a regulatory hub by physical interactions with multiple genes important for prostate carcinogenesis. Further understanding genetic effect and biological mechanism of these chromatin interactions will shed light on the newly discovered regulatory role of the risk locus in PC etiology and progression.
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Affiliation(s)
- Meijun Du
- Department of Pathology and Cancer Center
| | | | | | | | | | | | | | | | | | - Shu Xia
- Department of Pathology and Cancer Center Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jianzhong Gao
- Beijing 3H Medical Technology Co. Ltd., Beijing 100176, China and
| | - Lori Tillmans
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yan Lu
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Pengyuan Liu
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stephen N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Liang Wang
- Department of Pathology and Cancer Center
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143
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Wang KS, Zuo L, Owusu D, Pan Y, Luo X. Prostate Cancer Related JAZF1 Gene is Associated with Schizophrenia. JOURNAL OF SCHIZOPHRENIA RESEARCH 2014; 1:1002. [PMID: 27570842 PMCID: PMC4996122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
BACKGROUND Epidemiological studies have shown that there is a reduced risk of prostate cancer among persons diagnosed with schizophrenia (SCZ). However, the mechanism of such relationship is not clear. The reduced incidence of cancer observed in SCZ patients may be related to differences in genetic background. Recently, the JAZF1 gene is found to be associated with prostate cancer and type 2 diabetes. However, no study has focused on the association of JAZF1 with the risk of SCZ. METHODS We examined genetic associations of 118 single-nucleotide polymorphisms (SNPs) within the JAZF1 gene with SCZ using one European American (EA) sample of 1,149 cases and 1,347 controls. Logistic regression analysis of SCZ as a binary trait was performed using PLINK software. RESULTS The most significant association with SCZ was observed with rs10258132 (p = 0.0011); while the next best signal was rs17156259 (p = 0.0031). The third best associated SNP was rs7791865 (p = 0.00889). In addition, haplotype analyses revealed that the A-C haplotype from rs10244184 and rs10258132 was associated with SCZ (p = 0.00093); and the G-G haplotype from rs17156238 and rs17156259 was associated with SCZ (p = 0.00455). CONCLUSION These findings provide evidence of several genetic variants in JAZF1 gene influencing the risk of SCZ and will serve as a resource for replication in other populations.
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Affiliation(s)
- Ke-Sheng Wang
- Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, Johnson City, TN, USA
| | - Lingjun Zuo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Daniel Owusu
- Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, Johnson City, TN, USA
| | - Yue Pan
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China
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144
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Intratumor DNA methylation heterogeneity reflects clonal evolution in aggressive prostate cancer. Cell Rep 2014; 8:798-806. [PMID: 25066126 DOI: 10.1016/j.celrep.2014.06.053] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/09/2014] [Accepted: 06/25/2014] [Indexed: 01/07/2023] Open
Abstract
Despite much evidence on epigenetic abnormalities in cancer, it is currently unclear to what extent epigenetic alterations can be associated with tumors' clonal genetic origins. Here, we show that the prostate intratumor heterogeneity in DNA methylation and copy-number patterns can be explained by a unified evolutionary process. By assaying multiple topographically distinct tumor sites, premalignant lesions, and lymph node metastases within five cases of prostate cancer, we demonstrate that both DNA methylation and copy-number heterogeneity consistently reflect the life history of the tumors. Furthermore, we show cases of genetic or epigenetic convergent evolution and highlight the diversity in the evolutionary origins and aberration spectrum between tumor and metastatic subclones. Importantly, DNA methylation can complement genetic data by serving as a proxy for activity at regulatory domains, as we show through identification of high epigenetic heterogeneity at androgen-receptor-bound enhancers. Epigenome variation thereby expands on the current genome-centric view on tumor heterogeneity.
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145
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Gnanapragasam VJ. Molecular markers to guide primary radical treatment selection in localized prostate cancer. Expert Rev Mol Diagn 2014; 14:871-81. [DOI: 10.1586/14737159.2014.936851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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