Table 6.
Best Performing PRSs for the 20 Analyzed Cancer Traits in UKB
| PRS Cancer Trait (PheCode) | GWAS Source | Method Tuning Parameter | # SNPs | Brier Score | AAUC (95% CI) | Odds Ratio Continuous PRS (95% CI)a | Odds Ratio Top 1% (95% CI)b |
|---|---|---|---|---|---|---|---|
| Breast cancer [female] (174.1) | Large GWAS: Michailidou et al.11 | Lassosum: s = 0.9, λ = 0.0043 | 286,144 | 0.0807 | 0.643 (0.637,0.65) | 1.70 (1.65,1.75) | 4.02 (3.46,4.67) |
| Cancer of prostate (185) | Large GWAS: Schumacher et al.12 | Lassosum: s = 0.9, λ = 0.0055 | 178,259 | 0.0794 | 0.699 (0.690,0.710) | 2.13 (2.04,2.22) | 5.88 (4.85,7.14) |
| Colorectal cancer (153) | Large GWAS: Huyghe et al.15 | P&T: p ≤ 7.8 × 10−6 | 87 | 0.0812 | 0.617 (0.605,0.630) | 1.55 (1.48,1.62) | 4.00 (3.11,5.13) |
| Melanomas of skin (172.1) | GWAS Catalog | P&T: p ≤ 5 × 10−7 | 27 | 0.0812 | 0.619 (0.603,0.634) | 1.56 (1.48,1.66) | 3.12 (2.18,4.47) |
| Cancer of bladder (189.2) | GWAS Catalog | P&T: p ≤ 7 × 10−7 | 15 | 0.0821 | 0.571 (0.555,0.588) | 1.30 (1.23,1.38) | 2.91 (1.99,4.24) |
| Cancer of other lymphoid, histiocytic tissue (202) | GWAS Catalog | P&T: p ≤ 5 × 10−7 | 5 | 0.0822 | 0.490 (0.476,0.505) | 1.15 (1.09,1.21) | 1.97 (1.25,3.12) |
| Cancer of bronchus/lung (165.1) | GWAS Catalog | P&T: p ≤ 2.5 × 10−8 | 19 | 0.0824 | 0.552 (0.534,0.569) | 1.22 (1.15,1.30) | 1.94 (1.22,3.10) |
| Non-Hodgkins lymphoma (202.2) | GWAS Catalog | P&T: p ≤ 1 × 10−9 | 10 | 0.082 | 0.547 (0.527,0.566) | 1.24 (1.16,1.32) | 2.05 (1.24,3.40) |
| Cancer of uterus (182) | GWAS Catalog | P&T: p ≤ 1 × 10−7 | 20 | 0.082 | 0.572 (0.549,0.596) | 1.30 (1.20,1.41) | 2.60 (1.50,4.51) |
| Cancer of kidney, except pelvis (189.11) | GWAS Catalog | P&T: p ≤ 5 × 10−8 | 12 | 0.0825 | 0.517 (0.492,0.540) | 1.15 (1.06,1.25) | 2.17 (1.13,4.14) |
| Cancer of ovary (184.11) | Large GWAS: Phelan et al.9 | P&T: p ≤ 1.3 × 10−9 | 12 | 0.0824 | 0.558 (0.530,0.586) | 1.23 (1.12,1.35) | 1.55 (0.71,3.38) |
| Pancreatic cancer (157) | GWAS Catalog | P&T: p ≤ 5 × 10−9 | 10 | 0.0822 | 0.579 (0.548,0.611) | 1.34 (1.20,1.50) | 1.64 (0.655,4.12) |
| Cancer of brain and nervous system (191.1) | GWAS Catalog | P&T: p ≤ 3.2 × 10−9 | 19 | 0.0812 | 0.622 (0.590,0.653) | 1.56 (1.40,1.75) | 2.93 (1.34,6.41) |
| Multiple myeloma (204.4) | GWAS Catalog | P&T: p ≤ 2.5 × 10−8 | 21 | 0.0818 | 0.576 (0.536,0.616) | 1.32 (1.16,1.50) | 2.20 (0.854,5.66) |
| Cancer of brain (191.11) | GWAS Catalog | P&T: p ≤ 5 × 10−29 | 5 | 0.0813 | 0.606 (0.568,0.642) | 1.52 (1.34,1.71) | 4.15 (2.04,8.41) |
| Lymphoid leukemia, chronic (204.12) | GWAS Catalog | P&T: p ≤ 2.5 × 10−8 | 27 | 0.0796 | 0.672 (0.637,0.703) | 1.85 (1.62,2.11) | 2.52 (1.04,6.08) |
| Thyroid cancer (193) | GWAS Catalog | P&T: p ≤ 1 × 10−16 | 5 | 0.0804 | 0.628 (0.582,0.675) | 1.61 (1.38,1.88) | 4.41 (1.81,10.7) |
| Cancer of testis (187.2) | GWAS Catalog | P&T: p ≤ 5 × 10−6 | 44 | 0.0793 | 0.703 (0.659,0.745) | 2.11 (1.73,2.56) | 4.60 (1.75,12.1) |
| Basal cell carcinoma (172.21) | GWAS Catalog | P&T: p ≤ 5 × 10−9 | 24 | 0.0813 | 0.615 (0.608,0.623) | 1.53 (1.48,1.57) | 3.05 (2.55,3.64) |
| Squamous cell carcinoma (172.22) | Large GWAS: Chahal et al.50 | P&T: p ≤ 1.6 × 10−8 | 9 | 0.0819 | 0.571 (0.563,0.579) | 1.33 (1.30,1.37) | 1.93 (1.56,2.39) |
Cancer traits are sorted by observed case counts in UKB; references of studies contributing to GWAS Catalog PRSs are listed in Table S4.
a
PRSs were scaled to mean = 0 and SD = 1.
b
Top 1% versus rest.