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bioRxiv · 10.1101/2020.01.22.915751

Cancer PRSweb - an Online Repository with Polygenic Risk Scores (PRS) for Major Cancer Traits and Their Phenome-wide Exploration in Two Independent Biobanks

Fritsche, L. G.·Patil, S.·Beesley, L. J.·VandeHaar, P.·Salvatore, M.·Peng, R. B.·Taliun, D.·Zhou, X.·Mukherjee, B.
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Abstract

To facilitate scientific collaboration on polygenic risk scores (PRS) research, we created an extensive PRS online repository for 49 common cancer traits integrating freely available genome-wide association studies (GWAS) summary statistics from three sources: published GWAS, the NHGRI-EBI GWAS Catalog, and UK Biobank-based GWAS. Our framework condenses these summary statistics into PRS using various approaches such as linkage disequilibrium pruning / p-value thresholding (fixed or data-adaptively optimized thresholds) and penalized, genome-wide effect size weighting. We evaluated the PRS in two biobanks: the Michigan Genomics Initiative (MGI), a longitudinal biorepository effort at Michigan Medicine, and the population-based UK Biobank (UKB). For each PRS construct, we provide measures on predictive performance, calibration, and discrimination. Besides PRS evaluation, the Cancer-PRSweb platform features construct downloads and phenome-wide PRS association study results (PRS-PheWAS) for predictive PRS. We expect this integrated platform to accelerate PRS-related cancer research.

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Fritsche, L. G., Patil, S., Beesley, L. J., VandeHaar, P., Salvatore, M., Peng, R. B., Taliun, D., Zhou, X., Mukherjee, B.. 2020-01-23. Cancer PRSweb - an Online Repository with Polygenic Risk Scores (PRS) for Major Cancer Traits and Their Phenome-wide Exploration in Two Independent Biobanks. https://doi.org/10.1101/2020.01.22.915751

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