A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk.

Authors:
Yingchang Lu
Yingchang Lu
Wageningen University and Research Center
Netherlands
Alicia Beeghly-Fadiel
Lang Wu
Lang Wu
University of British Columbia
Canada
Xingyi Guo
Xingyi Guo
Albert Einstein College of Medicine
Bingshan Li
Bingshan Li
Baylor College of Medicine
United States
Joellen M Schildkraut
Joellen M Schildkraut
University of Virginia
Charlottesville | United States
Hae Kyung Im
Hae Kyung Im
University of Chicago
United States
Yian A Chen
Yian A Chen
Medical University of South Carolina
United States
Jennifer B Permuth Brett M Reid Jamie K Teer Kirsten B Moysich Irene L Andrulis Hoda Anton-Culver Banu K Arun Elisa V Bandera Rosa B Barkardottir Daniel R Barnes Javier Benitez Line Bjorge James Brenton Ralf Butzow Trinidad Caldes Maria A Caligo Ian Campbell Jenny Chang-Claude Kathleen B M Claes Fergus J Couch Daniel W Cramer Mary B Daly Anna deFazio Joe Dennis Orland Diez Susan M Domchek Thilo Dörk Douglas F Easton Diana M Eccles Peter A Fasching Renée T Fortner George Fountzilas Eitan Friedman Patricia A Ganz Judy Garber Graham G Giles Andrew K Godwin David E Goldgar Marc T Goodman Mark H Greene Jacek Gronwald Ute Hamann Florian Heitz Michelle A T Hildebrandt Claus K Høgdall Antoinette Hollestelle Peter J Hulick David G Huntsman Evgeny N Imyanitov Claudine Isaacs Anna Jakubowska Paul James Beth Y Karlan Linda E Kelemen Lambertus A Kiemeney Susanne K Kjaer Ava Kwong Nhu D Le Goska Leslie Fabienne Lesueur Douglas A Levine Amalia Mattiello Taymaa May Lesley McGuffog Iain A McNeish Melissa A Merritt Francesmary Modugno Marco Montagna Susan L Neuhausen Heli Nevanlinna Finn C Nielsen Liene Nikitina-Zake Robert L Nussbaum Kenneth Offit Edith Olah Olufunmilayo I Olopade Sara H Olson Håkan Olsson Ana Osorio Sue K Park Michael T Parsons Petra H M Peeters Tanja Pejovic Paolo Peterlongo Catherine M Phelan Miquel Angel Pujana Susan J Ramus Gad Rennert Harvey Risch Gustavo C Rodriguez Cristina Rodríguez-Antona Isabelle Romieu Matti A Rookus Mary Anne Rossing Iwona K Rzepecka Dale P Sandler Rita K Schmutzler Veronica W Setiawan Priyanka Sharma Weiva Sieh Jacques Simard Christian F Singer Honglin Song Melissa C Southey Amanda B Spurdle Rebecca Sutphen Anthony J Swerdlow Manuel R Teixeira Soo H Teo Mads Thomassen Marc Tischkowitz Amanda E Toland Antonia Trichopoulou Nadine Tung Shelley S Tworoger Elizabeth J van Rensburg Adriaan Vanderstichele Ana Vega Digna Velez Edwards Penelope M Webb Jeffrey N Weitzel Nicolas Wentzensen Emily White Alicja Wolk Anna H Wu Drakoulis Yannoukakos Kristin K Zorn Simon A Gayther Antonis C Antoniou Andrew Berchuck Ellen L Goode Georgia Chenevix-Trench Thomas A Sellers Paul D P Pharoah Wei Zheng Jirong Long

Cancer Res 2018 Sep 27;78(18):5419-5430. Epub 2018 Jul 27.

Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee.

Large-scale genome-wide association studies (GWAS) have identified approximately 35 loci associated with epithelial ovarian cancer (EOC) risk. The majority of GWAS-identified disease susceptibility variants are located in noncoding regions, and causal genes underlying these associations remain largely unknown. Here, we performed a transcriptome-wide association study to search for novel genetic loci and plausible causal genes at known GWAS loci. We used RNA sequencing data (68 normal ovarian tissue samples from 68 individuals and 6,124 cross-tissue samples from 369 individuals) and high-density genotyping data from European descendants of the Genotype-Tissue Expression (GTEx V6) project to build ovarian and cross-tissue models of genetically regulated expression using elastic net methods. We evaluated 17,121 genes for their -predicted gene expression in relation to EOC risk using summary statistics data from GWAS of 97,898 women, including 29,396 EOC cases. With a Bonferroni-corrected significance level of < 2.2 × 10, we identified 35 genes, including at 11q14.2 (Z = 5.08, = 3.83 × 10, the cross-tissue model; 1 Mb away from any GWAS-identified EOC risk variant), a potential novel locus for EOC risk. All other 34 significantly associated genes were located within 1 Mb of known GWAS-identified loci, including 23 genes at 6 loci not previously linked to EOC risk. Upon conditioning on nearby known EOC GWAS-identified variants, the associations for 31 genes disappeared and three genes remained ( < 1.47 × 10). These data identify one novel locus ) and 34 genes at 13 known EOC risk loci associated with EOC risk, providing new insights into EOC carcinogenesis. Transcriptomic analysis of a large cohort confirms earlier GWAS loci and reveals FZD4 as a novel locus associated with EOC risk. .

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Source
http://dx.doi.org/10.1158/0008-5472.CAN-18-0951DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6139053PMC

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September 2018
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