Assessment of polygenic architecture and risk prediction based on common variants across fourteen cancers

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Abstract

Genome-wide association studies (GWAS) have led to the identification of hundreds of susceptibility loci across cancers, but the impact of further studies remains uncertain. Here we analyse summary-level data from GWAS of European ancestry across fourteen cancer sites to estimate the number of common susceptibility variants (polygenicity) and underlying effect-size distribution. All cancers show a high degree of polygenicity, involving at a minimum of thousands of loci. We project that sample sizes required to explain 80% of GWAS heritability vary from 60,000 cases for testicular to over 1,000,000 cases for lung cancer. The maximum relative risk achievable for subjects at the 99th risk percentile of underlying polygenic risk scores (PRS), compared to average risk, ranges from 12 for testicular to 2.5 for ovarian cancer. We show that PRS have potential for risk stratification for cancers of breast, colon and prostate, but less so for others because of modest heritability and lower incidence.

Metadata

Item Type:	Article
Authors/Creators:	Zhang, YD Hurson, AN Zhang, H Choudhury, PP Easton, DF Milne, RL Simard, J Hall, P Michailidou, K Dennis, J Schmidt, MK Chang-Claude, J Gharahkhani, P Whiteman, D Campbell, PT Hoffmeister, M Jenkins, M Peters, U Hsu, L Gruber, SB Casey, G Schmit, SL O’Mara, TA Spurdle, AB Thompson, DJ Tomlinson, I De Vivo, I Landi, MT Law, MH Iles, MM https://orcid.org/0000-0002-2603-6509 Demenais, F Kumar, R MacGregor, S Bishop, DT https://orcid.org/0000-0002-8752-8785 Ward, SV Bondy, ML Houlston, R Wiencke, JK Melin, B Barnholtz-Sloan, J Kinnersley, B Wrensch, MR Amos, CI Hung, RJ Brennan, P McKay, J Caporaso, NE Berndt, SI Birmann, BM Camp, NJ Kraft, P Rothman, N Slager, SL Berchuck, A Pharoah, PDP Sellers, TA Gayther, SA Pearce, CL Goode, EL Schildkraut, JM Moysich, KB Amundadottir, LT Jacobs, EJ Klein, AP Petersen, GM Risch, HA Stolzenberg-Solomon, RZ Wolpin, BM Li, D Eeles, RA Haiman, CA Kote-Jarai, Z Schumacher, FR Al Olama, AA Purdue, MP Scelo, G Dalgaard, MD Greene, MH Grotmol, T Kanetsky, PA McGlynn, KA Nathanson, KL Turnbull, C Wiklund, F Breast Cancer Association Consortium (BCAC) Barrett’s and Esophageal Adenocarcinoma Consortium (BEACON) Colon Cancer Family Registry (CCFR) Transdisciplinary Studies of Genetic Variation in Colorectal Can Endometrial Cancer Association Consortium (ECAC) Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO Melanoma Genetics Consortium (GenoMEL) Glioma International Case-Control Study (GICC) International Lung Cancer Consortium (ILCCO) Integrative Analysis of Lung Cancer Etiology and Risk (INTEGRAL) International Consortium of Investigators Working on Non-Hodgkin Ovarian Cancer Association Consortium (OCAC) Oral Cancer GWAS Pancreatic Cancer Case-Control Consortium (PanC4) Pancreatic Cancer Cohort Consortium (PanScan) Prostate Cancer Association Group to Investigate Cancer Associat Renal Cancer GWAS Testicular Cancer Consortium (TECAC) Chanock, SJ Chatterjee, N Garcia-Closas, M
Copyright, Publisher and Additional Information:	© 2020, Springer Nature. This is an open access article under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) (https://creativecommons.org/licenses/by/4.0/)
Dates:	Accepted: 4 May 2020 Published (online): 3 July 2020 Published: 3 July 2020
Institution:	The University of Leeds
Depositing User:	Symplectic Publications
Date Deposited:	03 Aug 2020 11:56
Last Modified:	21 Nov 2024 11:54
Status:	Published
Publisher:	Springer Science and Business Media LLC
Identification Number:	10.1038/s41467-020-16483-3
Open Archives Initiative ID (OAI ID):	oai:eprints.whiterose.ac.uk:157993

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Assessment of Polygenic Architecture and Risk Prediction based on Common Variants Across Fourteen Cancers. (deposited 21 Nov 2024 11:53)
- Assessment of polygenic architecture and risk prediction based on common variants across fourteen cancers. (deposited 03 Aug 2020 11:56) [Currently Displayed]

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