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Grant Details

Grant Number: 5R01CA178535-05 Interpret this number
Primary Investigator: Gayther, Simon
Organization: Cedars-Sinai Medical Center
Project Title: The Contribution of Rare Alleles to Ovarian Cancer in the Population
Fiscal Year: 2017


DESCRIPTION (provided by applicant): Epithelial ovarian cancer (EOC) has a substantial hereditary component. Germline mutations in the high- penetrance susceptibility genes BRCA1 and BRCA2 confer EOC risks of around 50% by age 70. These genes are responsible for most families containing several cases of EOC; but the known susceptibility genes account for less than 40% of the excess familial risk of EOC indicating that other genes await discovery. We hypothesize that a substantial proportion of the excess EOC risk is due to moderately penetrant, rare or uncommon functional variants in coding DNA conferring 2 to 10 fold lifetime risks of disease. Identifying additional EOC susceptibility genes could have a major and rapid clinical impact by reducing disease associated mortality through better risk prediction-prevention strategies, and developing novel therapeutic approaches and individualized treatments. There are three phases to this project: The first is a discovery phase, in which we plan to perform exome sequencing in ~200 non-BRCA1/BRCA2 EOC families to characterize the genome wide spectrum of functional coding mutations in these families. We will also leverage sequencing data from ~400 EOC cases that have undergone germline exome sequencing through The Cancer Genome Atlas (TCGA) project, and another ~150 EOC families for whom exome sequencing is ongoing. We will then compare the frequency of candidate functional variants we find with data from a combined exome sequence analysis of ~16,000 non-cancer subjects of European origin from multiple different studies. Next, is a replication phase in which we plan to follow-up candidate genes and variants identified in phase 1, in large-scale sequencing and genotyping efforts, leveraging the epidemiological case-control collections of an international collaboration, the Ovarian Cancer Association Consortium (OCAC). We will perform candidate gene next generation sequencing for approximately 100 genes in 5,000 EOC cases and 5,000 controls to characterize the prevalence of functional deleterious mutations; and for ~20,000 non-synonymous rare variants we identify we will use a customized array to genotype these variants and an additional 260,000 rare variants from the 11,000 exome sequencing project, in 5,000 EOC cases and 5,000 controls to evaluate their disease associations. In the final phase, we will perform penetrance and survival analyses for confirmed functional variants to evaluate their clinical significance, which will indicate the immediate clinical value of the genes/variants we identify.


Exome sequencing identifies HELB as a novel susceptibility gene for non-mucinous, non-high-grade-serous epithelial ovarian cancer.
Authors: Dicks E.M. , Tyrer J.P. , Ezquina S. , Jones M. , Baierl J. , Peng P.C. , Diaz M. , Goode E. , Winham S.J. , Dörk T. , et al. .
Source: medRxiv : the preprint server for health sciences, 2024-04-03; , .
EPub date: 2024-04-03.
PMID: 38633804
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Population-based targeted sequencing of 54 candidate genes identifies PALB2 as a susceptibility gene for high-grade serous ovarian cancer.
Authors: Song H. , Dicks E.M. , Tyrer J. , Intermaggio M. , Chenevix-Trench G. , Bowtell D.D. , Traficante N. , Group A. , Brenton J. , Goranova T. , et al. .
Source: Journal of medical genetics, 2021 May; 58(5), p. 305-313.
EPub date: 2020-06-16.
PMID: 32546565
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Ovarian and Breast Cancer Risks Associated With Pathogenic Variants in RAD51C and RAD51D.
Authors: Yang X. , Song H. , Leslie G. , Engel C. , Hahnen E. , Auber B. , Horváth J. , Kast K. , Niederacher D. , Turnbull C. , et al. .
Source: Journal of the National Cancer Institute, 2020-12-14; 112(12), p. 1242-1250.
PMID: 32107557
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Rare Germline Genetic Variants and the Risks of Epithelial Ovarian Cancer.
Authors: Pavanello M. , Chan I.H. , Ariff A. , Pharoah P.D. , Gayther S.A. , Ramus S.J. .
Source: Cancers, 2020-10-19; 12(10), .
EPub date: 2020-10-19.
PMID: 33086730
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Ovarian Cancer Risk Variants Are Enriched in Histotype-Specific Enhancers and Disrupt Transcription Factor Binding Sites.
Authors: Jones M.R. , Peng P.C. , Coetzee S.G. , Tyrer J. , Reyes A.L.P. , Corona R.I. , Davis B. , Chen S. , Dezem F. , Seo J.H. , et al. .
Source: American journal of human genetics, 2020-10-01; 107(4), p. 622-635.
EPub date: 2020-09-17.
PMID: 32946763
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GENAVi: a shiny web application for gene expression normalization, analysis and visualization.
Authors: Reyes A.L.P. , Silva T.C. , Coetzee S.G. , Plummer J.T. , Davis B.D. , Chen S. , Hazelett D.J. , Lawrenson K. , Berman B.P. , Gayther S.A. , et al. .
Source: BMC genomics, 2019-10-16; 20(1), p. 745.
EPub date: 2019-10-16.
PMID: 31619158
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Germline whole exome sequencing and large-scale replication identifies FANCM as a likely high grade serous ovarian cancer susceptibility gene.
Authors: Dicks E. , Song H. , Ramus S.J. , Oudenhove E.V. , Tyrer J.P. , Intermaggio M.P. , Kar S. , Harrington P. , Bowtell D.D. , Group A.S. , et al. .
Source: Oncotarget, 2017-08-01; 8(31), p. 50930-50940.
EPub date: 2017-03-03.
PMID: 28881617
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Exome genotyping arrays to identify rare and low frequency variants associated with epithelial ovarian cancer risk.
Authors: Permuth J.B. , Pirie A. , Ann Chen Y. , Lin H.Y. , Reid B.M. , Chen Z. , Monteiro A. , Dennis J. , Mendoza-Fandino G. , AOCS Study Group , et al. .
Source: Human molecular genetics, 2016-08-15; 25(16), p. 3600-3612.
EPub date: 2016-07-04.
PMID: 27378695
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PPM1D Mosaic Truncating Variants in Ovarian Cancer Cases May Be Treatment-Related Somatic Mutations.
Authors: Pharoah P.D.P. , Song H. , Dicks E. , Intermaggio M.P. , Harrington P. , Baynes C. , Alsop K. , Australian Ovarian Cancer Study Group , Bogdanova N. , Cicek M.S. , et al. .
Source: Journal of the National Cancer Institute, 2016 Mar; 108(3), .
EPub date: 2016-01-27.
PMID: 26823519
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Investigation of Exomic Variants Associated with Overall Survival in Ovarian Cancer.
Authors: Winham S.J. , Pirie A. , Chen Y.A. , Larson M.C. , Fogarty Z.C. , Earp M.A. , Anton-Culver H. , Bandera E.V. , Cramer D. , Doherty J.A. , et al. .
Source: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 2016 Mar; 25(3), p. 446-54.
EPub date: 2016-01-08.
PMID: 26747452
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Germline Mutations in the BRIP1, BARD1, PALB2, and NBN Genes in Women With Ovarian Cancer.
Authors: Ramus S.J. , Song H. , Dicks E. , Tyrer J.P. , Rosenthal A.N. , Intermaggio M.P. , Fraser L. , Gentry-Maharaj A. , Hayward J. , Philpott S. , et al. .
Source: Journal of the National Cancer Institute, 2015 Nov; 107(11), .
EPub date: 2015-08-27.
PMID: 26315354
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Contribution of Germline Mutations in the RAD51B, RAD51C, and RAD51D Genes to Ovarian Cancer in the Population.
Authors: Song H. , Dicks E. , Ramus S.J. , Tyrer J.P. , Intermaggio M.P. , Hayward J. , Edlund C.K. , Conti D. , Harrington P. , Fraser L. , et al. .
Source: Journal of clinical oncology : official journal of the American Society of Clinical Oncology, 2015-09-10; 33(26), p. 2901-7.
EPub date: 2015-08-10.
PMID: 26261251
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Population distribution of lifetime risk of ovarian cancer in the United States.
Authors: Pearce C.L. , Stram D.O. , Ness R.B. , Stram D.A. , Roman L.D. , Templeman C. , Lee A.W. , Menon U. , Fasching P.A. , McAlpine J.N. , et al. .
Source: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 2015 Apr; 24(4), p. 671-676.
EPub date: 2015-01-26.
PMID: 25623732
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Germline mutation in BRCA1 or BRCA2 and ten-year survival for women diagnosed with epithelial ovarian cancer.
Authors: Candido-dos-Reis F.J. , Song H. , Goode E.L. , Cunningham J.M. , Fridley B.L. , Larson M.C. , Alsop K. , Dicks E. , Harrington P. , Ramus S.J. , et al. .
Source: Clinical cancer research : an official journal of the American Association for Cancer Research, 2015-02-01; 21(3), p. 652-7.
EPub date: 2014-11-14.
PMID: 25398451
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The contribution of deleterious germline mutations in BRCA1, BRCA2 and the mismatch repair genes to ovarian cancer in the population.
Authors: Song H. , Cicek M.S. , Dicks E. , Harrington P. , Ramus S.J. , Cunningham J.M. , Fridley B.L. , Tyrer J.P. , Alsop J. , Jimenez-Linan M. , et al. .
Source: Human molecular genetics, 2014-09-01; 23(17), p. 4703-9.
EPub date: 2014-04-12.
PMID: 24728189
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