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Permuth JB, Pirie A, Ann Chen Y, Lin HY, Reid BM, Chen Z, Monteiro A, Dennis J, Mendoza-Fandino G, Anton-Culver H, Bandera EV, Bisogna M, Brinton L, Brooks-Wilson A, Carney ME, Chenevix-Trench G, Cook LS, Cramer DW, Cunningham JM, Cybulski C, D'Aloisio AA, Anne Doherty J, Earp M, Edwards RP, Fridley BL, Gayther SA, Gentry-Maharaj A, Goodman MT, Gronwald J, Hogdall E, Iversen ES, Jakubowska A, Jensen A, Karlan BY, Kelemen LE, Kjaer SK, Kraft P, Le ND, Levine DA, Lissowska J, Lubinski J, Matsuo K, Menon U, Modugno R, Moysich KB, Nakanishi T, Ness RB, Olson S, Orlow I, Pearce CL, Pejovic T, Poole EM, Ramus SJ, Anne Rossing M, Sandler DP, Shu XO, Song H, Taylor JA, Teo SH, Terry KL, Thompson PJ, Tworoger SS, Webb PM, Wentzensen N, Wilkens LR, Winham S, Woo YL, Wu AH, Yang H, Zheng W, Ziogas A, Phelan CM, Schildkraut JM, Berchuck A, Goode EL, Pharoah PDP, Sellers TA. Exome genotyping arrays to identify rare and low frequency variants associated with epithelial ovarian cancer risk. Hum Mol Genet 2016; 25:3600-3612. [PMID: 27378695 PMCID: PMC5179948 DOI: 10.1093/hmg/ddw196] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 06/17/2016] [Accepted: 06/20/2016] [Indexed: 12/17/2022] Open
Abstract
Rare and low frequency variants are not well covered in most germline genotyping arrays and are understudied in relation to epithelial ovarian cancer (EOC) risk. To address this gap, we used genotyping arrays targeting rarer protein-coding variation in 8,165 EOC cases and 11,619 controls from the international Ovarian Cancer Association Consortium (OCAC). Pooled association analyses were conducted at the variant and gene level for 98,543 variants directly genotyped through two exome genotyping projects. Only common variants that represent or are in strong linkage disequilibrium (LD) with previously-identified signals at established loci reached traditional thresholds for exome-wide significance (P < 5.0 × 10 - 7). One of the most significant signals (Pall histologies = 1.01 × 10 - 13;Pserous = 3.54 × 10 - 14) occurred at 3q25.31 for rs62273959, a missense variant mapping to the LEKR1 gene that is in LD (r2 = 0.90) with a previously identified 'best hit' (rs7651446) mapping to an intron of TIPARP. Suggestive associations (5.0 × 10 - 5 > P≥5.0 ×10 - 7) were detected for rare and low-frequency variants at 16 novel loci. Four rare missense variants were identified (ACTBL2 rs73757391 (5q11.2), BTD rs200337373 (3p25.1), KRT13 rs150321809 (17q21.2) and MC2R rs104894658 (18p11.21)), but only MC2R rs104894668 had a large effect size (OR = 9.66). Genes most strongly associated with EOC risk included ACTBL2 (PAML = 3.23 × 10 - 5; PSKAT-o = 9.23 × 10 - 4) and KRT13 (PAML = 1.67 × 10 - 4; PSKAT-o = 1.07 × 10 - 5), reaffirming variant-level analysis. In summary, this large study identified several rare and low-frequency variants and genes that may contribute to EOC susceptibility, albeit with possible small effects. Future studies that integrate epidemiology, sequencing, and functional assays are needed to further unravel the unexplained heritability and biology of this disease.
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Affiliation(s)
- Jennifer B Permuth
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Ailith Pirie
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Y Ann Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Hui-Yi Lin
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Brett M Reid
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Zhihua Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Alvaro Monteiro
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Joe Dennis
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | | | - Hoda Anton-Culver
- Department of Epidemiology, Director of Genetic Epidemiology Research Institute, UCI School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Elisa V Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Maria Bisogna
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Louise Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Angela Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver BC, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Michael E Carney
- Department of Obstetrics and Gynecology, John A Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
| | - Georgia Chenevix-Trench
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Linda S Cook
- Division of Epidemiology and Biostatistics, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
| | - Daniel W Cramer
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Julie M Cunningham
- Department of Laboratory of Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | | | - Jennifer Anne Doherty
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NY, USA
| | - Madalene Earp
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Robert P Edwards
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Ovarian Cancer Center of Excellence, Womens Cancer Research Program, Magee- Womens Research Institute & University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Brooke L Fridley
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA
| | - Simon A Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | | | - Marc T Goodman
- Cancer Prevention and Control, Samuel Oshin Comprehensive Cancer Institute, Cedars- Sinai Medical Center, Los Angeles, CA, USA
- Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jacek Gronwald
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Estrid Hogdall
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark and Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, NC, USA
| | - Anna Jakubowska
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Allan Jensen
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Linda E Kelemen
- Department of Public Health Sciences, Medical University of South Carolina College of Medicine, Charleston, SC, USA
| | - Suzanne K Kjaer
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Nhu D Le
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Douglas A Levine
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, The Maria Sklodowska-Curie Memorial Cancer Center, Warsaw, Poland
| | - Jan Lubinski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Keitaro Matsuo
- Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Aichi, Japan
| | - Usha Menon
- Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Rosemary Modugno
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Ovarian Cancer Center of Excellence, Womens Cancer Research Program, Magee- Womens Research Institute & University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Kirsten B Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Toru Nakanishi
- Department of Gynecologic Oncology, Aichi Cancer Center Central Hospital, Nagoya, Aichi, Japan
| | - Roberta B Ness
- The University of Texas School of Public Health, Houston, TX, USA
| | - Sara Olson
- Memorial Sloan Kettering Cancer Center, Department of Epidemiology and Biostatistics, New York,NY, USA
| | - Irene Orlow
- Memorial Sloan Kettering Cancer Center, Department of Epidemiology and Biostatistics, New York,NY, USA
| | - Celeste L Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
- Department of Epidemology,University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Tanja Pejovic
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Elizabeth M Poole
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Susan J Ramus
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Mary Anne Rossing
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Dale P Sandler
- Epidemiology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Xiao-Ou Shu
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Honglin Song
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Jack A Taylor
- Epidemiology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Soo-Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Malaysia
- University Malaya Medical Centre, University Malaya, Kuala Lumpur, Malaysia
| | - Kathryn L Terry
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Pamela J Thompson
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Shelley S Tworoger
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Penelope M Webb
- Population Health Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda MD, USA
| | - Lynne R Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Hawaii, USA
| | - Stacey Winham
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Yin-Ling Woo
- Department of Obstetrics and Gynaecology, University Malaya Medical Centre, University Malaya, Kuala Lumpur, Malaysia
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Hannah Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda MD, USA
| | - Wei Zheng
- Vanderbilt Epidemiology Center and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Argyrios Ziogas
- Department of Epidemiology, University of California Irvine, Irvine, CA, USA
| | - Catherine M Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Joellen M Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC, USA
- Cancer Control and Population Sciences, Duke Cancer Institute, Durham, NC, USA
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA, Exome genotyping arrays to identify rare and low frequency variants associated with epithelial ovarian cancer risk
| | - Ellen L Goode
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
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