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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Cancer of prostate with MGI and odds ratio (top 1% versus rest)
| 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: pr.. | PRS-CS | 1111494 | 4.8e-21 | 0.0245 | 0.152 | 0.591 | 0.573, 0.609 | 2.85 | 1.76,4.62 | link | -- |
| UKB GWAS (PHESANT) | Cancer code, self-reported: pr.. | P&T | 78 | 9e-31 | 0.0379 | 0.15 | 0.608 | 0.59, 0.628 | 3.17 | 1.98,5.06 | link | -- |
| UKB GWAS (PHESANT) | Cancer code, self-reported: pr.. | Lassosum | 1401 | 3.5e-24 | 0.0281 | 0.151 | 0.595 | 0.577, 0.614 | 1.53 | 0.88,2.66 | link | -- |
| UKB GWAS (FINNGEN) | Malignant neoplasm of prostate | PRS-CS | 1111493 | 2e-36 | 0.0453 | 0.149 | 0.622 | 0.604, 0.639 | 2.66 | 1.63,4.34 | link | -- |
| UKB GWAS (FINNGEN) | Malignant neoplasm of prostate | P&T | 100 | 2.3e-45 | 0.0583 | 0.148 | 0.634 | 0.617, 0.653 | 2.96 | 1.85,4.74 | link | -- |
| UKB GWAS (FINNGEN) | Malignant neoplasm of prostate | Lassosum | 1809 | 3.2e-33 | 0.0418 | 0.15 | 0.616 | 0.597, 0.636 | 4.03 | 2.59,6.28 | link | -- |
| UKB GWAS (ICD10) | Diagnoses - main ICD10: C61 Ma.. | PRS-CS | 1111493 | 2.3e-31 | 0.039 | 0.15 | 0.612 | 0.593, 0.63 | 2.09 | 1.24,3.52 | link | -- |
| UKB GWAS (ICD10) | Diagnoses - main ICD10: C61 Ma.. | P&T | 47 | 5e-37 | 0.0456 | 0.149 | 0.619 | 0.601, 0.637 | 3.1 | 1.96,4.92 | link | -- |
| UKB GWAS (ICD10) | Diagnoses - main ICD10: C61 Ma.. | Lassosum | 905 | 1.6e-29 | 0.0358 | 0.151 | 0.607 | 0.589, 0.627 | 2.46 | 1.5,4.01 | link | -- |
| GWAS Catalog (2019-05-03) | Prostate cancer;Prostate cance.. | P&T | 122 | 7.2e-53 | 0.0675 | 0.147 | 0.646 | 0.627, 0.664 | 3.53 | 2.26,5.51 | link | -- |
| Schumacher FR et al. 2019 | Prostate cancer | PRS-CS | 1119311 | 6.9e-67 | 0.0874 | 0.145 | 0.668 | 0.651, 0.687 | 3.61 | 2.28,5.72 | link | -- |
| Schumacher FR et al. 2019 | Prostate cancer | P&T | 1301 | 1.6e-65 | 0.0837 | 0.145 | 0.67 | 0.652, 0.688 | 3.3 | 2.06,5.29 | link | -- |
| Schumacher FR et al. 2019 | Prostate cancer | Lassosum | 26418 | 3.3e-66 | 0.0861 | 0.145 | 0.665 | 0.647, 0.684 | 4.92 | 3.21,7.55 | link | -- |
| UKB GWAS (PheCode) | Cancer of prostate | PRS-CS | 1119236 | 3.8e-32 | 0.0395 | 0.15 | 0.614 | 0.595, 0.633 | 2.32 | 1.42,3.78 | link | -- |
| UKB GWAS (PheCode) | Cancer of prostate | P&T | 80 | 5.9e-40 | 0.051 | 0.149 | 0.627 | 0.608, 0.645 | 3.18 | 2.01,5.02 | link | -- |
| UKB GWAS (PheCode) | Cancer of prostate | Lassosum | 1334 | 2.5e-33 | 0.0408 | 0.15 | 0.616 | 0.598, 0.635 | 2.55 | 1.55,4.2 | link | -- |