Assessment of Polygenic Architecture and Risk Prediction based on Common Variants Across Fourteen Cancers

Zhang, Y.; Wilcox, A. N.; Zhang, H.; Choudhury, P. P.; Easton, D. F.; Milne, R. L.; Simard, J.; Hall, P.; Michailidou, K.; Dennis, J.; Schmidt, M. K.; Chang-Claude, J.; Gharahkhani, P.; Whiteman, D.; Campbell, P. T.; Hoffmeister, M.; Jenkins, M.; Peters, U.; Hsu, L.; Gruber, S. B.; Casey, G.; Schmit, S. L.; O'Mara, T. A.; Spurdle, A. B.; Thompson, D. J.; Tomlinson, I.; Vivo, I. D.; Landi, M. T.; Law, M. H.; Iles, M. M.; Demenais, F.; Kumar, R.; MacGregor, S.; Bishop, D. T.; Ward, S. V.; Bondy, M. L.; Houlston, R.; Wiencke, J. K.; Melin, B.; Barnholtz-Sloan, J.; Kinnersley, B.; Wrensch, M. R.

doi:10.1101/723825

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bioRxiv · 10.1101/723825

Assessment of Polygenic Architecture and Risk Prediction based on Common Variants Across Fourteen Cancers

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Abstract

We analyzed summary-level data from genome-wide association studies (GWAS) of European ancestry across fourteen cancer sites to estimate the number of common susceptibility variants (polygenicity) contributing to risk, as well as the distribution of their associated effect sizes. All cancers evaluated showed polygenicity, involving at a minimum thousands of independent susceptibility variants. For some malignancies, particularly chronic lymphoid leukemia (CLL) and testicular cancer, there are a larger proportion of variants with larger effect sizes than those for other cancers. In contrast, most variants for lung and breast cancers have very small associated effect sizes. For different cancer sites, we estimate a wide range of GWAS sample sizes, required to explain 80% of GWAS heritability, varying from 60,000 cases for CLL 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, compared to average risk, ranges from 12 for testicular to 2.5 for ovarian cancer. We show that polygenic risk scores have substantial potential for risk stratification for relatively common cancers such as breast, prostate and colon, but limited potential for other cancer sites because of modest heritability and lower disease incidence.

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Zhang, Y., Wilcox, A. N., Zhang, H., Choudhury, P. P., Easton, D. F., Milne, R. L., Simard, J., Hall, P., Michailidou, K., Dennis, J., Schmidt, M. K., Chang-Claude, J., Gharahkhani, P., Whiteman, D., Campbell, P. T., Hoffmeister, M., Jenkins, M., Peters, U., Hsu, L., Gruber, S. B., Casey, G., Schmit, S. L., O'Mara, T. A., Spurdle, A. B., Thompson, D. J., Tomlinson, I., Vivo, I. D., Landi, M. T., Law, M. H., Iles, M. M., Demenais, F., Kumar, R., MacGregor, S., Bishop, D. T., Ward, S. V., Bondy, M. L., Houlston, R., Wiencke, J. K., Melin, B., Barnholtz-Sloan, J., Kinnersley, B., Wrensch, M. R.. 2019-08-09. Assessment of Polygenic Architecture and Risk Prediction based on Common Variants Across Fourteen Cancers. https://doi.org/10.1101/723825

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