Overview

Integrating published and freely available genome-wide association studies (GWAS) summary statistics from multiple sources (published GWAS, the NHGRI-EBI GWAS Catalog, or UKB-based GWAS), we created an online repository for polygenic risk scores (PRS) for common cancer traits. Our framework condenses these summary statistics into PRS using linkage disequilibrium pruning and p-value thresholding (fixed or data-adaptively optimized thresholds) or penalized, genome-wide effect size weighting. We evaluate them in the cancer-enriched cohort of the Michigan Genomics Initiative (MGI), a longitudinal biorepository effort at Michigan Medicine, and in the population-based UK Biobank Study (UKB). For each PRS construct, measures on performance, calibration, and discrimination are provided. Beyond the cancer PRS evaluation in MGI and UKB, the PRSweb platform features construct downloads, risk evaluation in the top percentiles, and phenome-wide PRS association studies (PRS-PheWAS) for a subset of PRS that are predictive for the primary cancer.
For more information, see our latest article in The American Journal of Human Genetics here and the “Method” tab on top of this page."





Sign indicates " No predictive PRS found; weak association between PRS and trait of interest".
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Breast cancer [female] with MGI and odds ratio (top 1% versus rest)

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Association Overall Performance Discrimination/AAUC Odds Ratio
Top 1% vs Rest
GWAS

Source 		Phenotype
Description 		Method # SNPs P-value Pseudo-R2 Brier score AAUC 95%CI Odds Ratio 95 % CI PRS
PheWAS		 Download PRS
UKB GWAS (PHESANT) Cancer code, self-reported: br.. PRS-CS 1111495 1.3e-18 0.0167 0.138 0.576 0.56, 0.592 1.6 0.981,2.62 link --
UKB GWAS (PHESANT) Cancer code, self-reported: br.. P&T 68 3.2e-21 0.0188 0.138 0.58 0.563, 0.597 1.54 0.924,2.56 link --
UKB GWAS (PHESANT) Cancer code, self-reported: br.. Lassosum 30041 7.8e-22 0.0196 0.138 0.586 0.57, 0.603 1.59 0.962,2.62 link --
UKB GWAS (FINNGEN) Malignant neoplasm of breast PRS-CS 1111495 3.7e-21 0.0193 0.138 0.581 0.564, 0.597 2.17 1.38,3.41 link --
UKB GWAS (FINNGEN) Malignant neoplasm of breast P&T 120 1.1e-28 0.0257 0.137 0.595 0.578, 0.611 2.31 1.47,3.61 link --
UKB GWAS (FINNGEN) Malignant neoplasm of breast Lassosum 2267 3.4e-32 0.03 0.137 0.6 0.584, 0.616 2.37 1.54,3.65 link --
UKB GWAS (ICD10) Diagnoses - main ICD10: C50 Ma.. PRS-CS 1111495 7.1e-20 0.0183 0.138 0.578 0.56, 0.596 2.03 1.29,3.2 link --
UKB GWAS (ICD10) Diagnoses - main ICD10: C50 Ma.. P&T 42 1.5e-23 0.0212 0.138 0.584 0.568, 0.601 1.43 0.853,2.41 link --
UKB GWAS (ICD10) Diagnoses - main ICD10: C50 Ma.. Lassosum 4047 3e-28 0.0264 0.137 0.595 0.579, 0.61 2.05 1.3,3.24 link --
UKB GWAS (ICD10) Diagnoses - main ICD10: D05 Ca.. P&T 25 0.00014 0.00286 0.139 0.52 0.504, 0.538 1.39 0.817,2.36 link --
GWAS Catalog (2019-05-03) Breast cancer;Breast cancer (e.. P&T 62 5.2e-37 0.0346 0.136 0.607 0.589, 0.623 3.06 2.04,4.6 link --
Michailidou K et al. 2018 Breast cancer [female]; ER neg.. PRS-CS 1119140 5e-19 0.0179 0.138 0.578 0.56, 0.594 1.8 1.13,2.88 link --
Michailidou K et al. 2018 Breast cancer [female]; ER neg.. P&T 217 1e-18 0.0173 0.138 0.576 0.559, 0.593 1.84 1.14,2.97 link --
Michailidou K et al. 2018 Breast cancer [female]; ER neg.. Lassosum 18866 2.4e-17 0.0152 0.138 0.571 0.555, 0.588 1.87 1.16,3.01 link --
Michailidou K et al. 2018 Breast cancer [female]; ER pos.. PRS-CS 1119140 4.7e-59 0.0603 0.134 0.643 0.627, 0.658 3.71 2.52,5.47 link --
Michailidou K et al. 2018 Breast cancer [female]; ER pos.. P&T 1142 8.1e-45 0.0438 0.136 0.621 0.605, 0.638 2.7 1.77,4.1 link --
Michailidou K et al. 2018 Breast cancer [female]; ER pos.. Lassosum 61635 5.1e-54 0.0546 0.135 0.634 0.618, 0.65 4.03 2.78,5.85 link --
Michailidou K et al. 2018 Breast cancer [female], Overal.. PRS-CS 1119140 1e-65 0.0661 0.133 0.651 0.635, 0.666 3.22 2.15,4.81 link --
Michailidou K et al. 2018 Breast cancer [female], Overal.. P&T 3038 2.2e-53 0.0532 0.135 0.635 0.618, 0.651 2.84 1.88,4.28 link --
Michailidou K et al. 2018 Breast cancer [female], Overal.. Lassosum 118388 1.2e-58 0.0592 0.134 0.641 0.625, 0.656 2.48 1.63,3.77 link --
UKB GWAS (PheCode) Breast cancer [female] PRS-CS 1119237 2.1e-26 0.0248 0.137 0.59 0.573, 0.607 1.79 1.12,2.86 link --
UKB GWAS (PheCode) Breast cancer [female] P&T 84 2.8e-33 0.0307 0.137 0.605 0.588, 0.621 2.09 1.31,3.32 link --
UKB GWAS (PheCode) Breast cancer [female] Lassosum 6977 2.4e-36 0.034 0.137 0.609 0.592, 0.624 1.94 1.21,3.11 link --
Michailidou K et al. 2018 Breast cancer [female]; ER neg.. PRS-CS 1115376 4.2e-06 0.00453 0.139 0.539 0.52, 0.556 1.51 0.907,2.51 link --
Michailidou K et al. 2018 Breast cancer [female]; ER neg.. P&T 9 6.5e-11 0.00934 0.139 0.548 0.53, 0.564 1.88 1.18,2.99 link --
Michailidou K et al. 2018 Breast cancer [female]; ER neg.. Lassosum 270 1.6e-11 0.00979 0.139 0.546 0.529, 0.562 2.11 1.34,3.33 link --
Michailidou K et al. 2018 Breast cancer [female]; ER pos.. PRS-CS 1115436 4.2e-39 0.0383 0.136 0.613 0.595, 0.63 3.75 2.55,5.51 link --
Michailidou K et al. 2018 Breast cancer [female]; ER pos.. P&T 310 1.2e-30 0.0281 0.137 0.597 0.58, 0.612 2.98 1.98,4.47 link --
Michailidou K et al. 2018 Breast cancer [female]; ER pos.. Lassosum 98026 2.7e-38 0.037 0.136 0.61 0.594, 0.626 2.29 1.47,3.59 link --
Michailidou K et al. 2018 Breast cancer [female], Overal.. PRS-CS 1115484 1.3e-45 0.0443 0.135 0.622 0.605, 0.638 3.43 2.32,5.05 link --
Michailidou K et al. 2018 Breast cancer [female], Overal.. P&T 363 8e-38 0.0353 0.136 0.609 0.592, 0.626 3.44 2.31,5.13 link --
Michailidou K et al. 2018 Breast cancer [female], Overal.. Lassosum 18356 2.7e-47 0.0464 0.136 0.624 0.607, 0.641 2.49 1.61,3.84 link --