Table 1.
Results of Associations at Prostate Cancer GWAS Loci in Men of African descent
| Sample Size | Risk Allele Frequency | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chr | Locus | SNP | Position (bp) |
Risk Allele |
Cases | Controls | Cases | Controls | aOR (95% CI)* | P- value |
OR in EDM** |
MAF in EDM** |
| 2 | EHBP1 | rs721048 | 62,985,234 | A | 2083 | 2116 | 0.05 | 0.04 | 1.02 (0.82 - 1.26) | 0.882 | 1.15(1) | 0.19 |
| 3 | 3p12.1 | rs2660753 | 87,193,363 | T | 1796 | 1415 | 0.50 | 0.49 | 1.05 (0.95 - 1.17) | 0.338 | 1.18(2) | 0.11 |
| 6 | SLC22A3 | rs9364554 | 160,753,653 | T | 2652 | 2659 | 0.07 | 0.07 | 1.05 (0.90 - 1.24) | 0.513 | 1.17(2) | 0.29 |
| 7 | JAZF1 | rs10486567 | 27,943,087 | C | 2899 | 2538 | 0.74 | 0.71 | 1.18 (1.08 - 1.29) | 0.0002 | 1.21(3) | 0.77 |
| 7 | LMTK2 | rs6465657 | 97,654,262 | C | 3266 | 2631 | 0.87 | 0.87 | 1.03 (0.91 - 1.15) | 0.666 | 1.12(2) | 0.46 |
| 8 | 8p21 | rs6982080 | 29,686,860 | G | 844 | 536 | 0.28 | 0.28 | 1.08 (0.90 - 1.29) | 0.432 | 1.03(3) | 0.31 |
| 9 | DAB2IP | rs1571801 | 123,467,193 | T | 1709 | 1413 | 0.15 | 0.14 | 1.07 (0.92 - 1.24) | 0.385 | 1.30(4) | 0.24 |
| 10 | MSMB | rs7920517 | 51,202,626 | G | 849 | 541 | 0.74 | 0.71 | 1.13 (0.93 - 1.36) | 0.217 | 1.22(2) | 0.48 |
| 10 | MSMB | rs10993994 | 51,219,501 | T | 3374 | 2982 | 0.62 | 0.60 | 1.12 (1.03 - 1.21) | 0.005 | 1.25(2) | 0.4 |
| 10 | MSMB | rs7904463 | 51,229,474 | T | 501 | 563 | 0.69 | 0.66 | 1.13 (0.92 - 1.39) | 0.252 | 1.06(5) | 0.67 |
| 10 | MINPP1 | rs12771728 | 89,345,292 | C | 850 | 541 | 0.19 | 0.19 | 1.03 (0.83 - 1.27) | 0.788 | 1.06(3) | 0.34 |
| 10 | CTBP2 | rs4962416 | 126,686,861 | G | 1202 | 1388 | 0.17 | 0.17 | 0.99 (0.85 - 1.16) | 0.933 | 1.18(3) | 0.27 |
| 11 | 11q13 | rs1241845 | 68,691,994 | A | 862 | 876 | 0.12 | 0.13 | 0.94 (0.76 - 1.16) | 0.539 | 1.16(6) | 0.28 |
| 11 | 11q13 | rs7931342 | 68,751,072 | G | 2445 | 2018 | 0.79 | 0.77 | 1.15 (1.03 - 1.29) | 0.014 | 1.19(2) | 0.49 |
| 11 | 11q13.2 | rs10896449 | 68,751,242 | G | 2056 | 1898 | 0.70 | 0.68 | 1.12 (1.01 - 1.24) | 0.031 | 1.17(3) | 0.28 |
| 12 | Chr. 12 | rs902774 | 51,560,170 | A | 849 | 541 | 0.09 | 0.09 | 1.02 (0.77 - 1.34) | 0.914 | 1.03(2) | 0.15 |
| 15 | IL16 | rs4072111 | 79,365,193 | T | 857 | 539 | 0.04 | 0.05 | 0.87 (0.58 - 1.31) | 0.509 | 1.29(3) | 0.11 |
| 16 | CDH13 | rs4782726 | 81,258,833 | A | 849 | 535 | 0.32 | 0.32 | 0.99 (0.83 - 1.19) | 0.929 | 1.20(3) | 0.18 |
| 17 | HNF1B | rs11649743 | 33,149,091 | C | 862 | 874 | 0.94 | 0.93 | 1.10 (0.83 - 1.45) | 0.505 | 1.28(7) | 0.8 |
| 17 | HNF1B | rs4430796 | 33,172,152 | T | 3112 | 2911 | 0.35 | 0.33 | 1.08 (1.00 - 1.18) | 0.053 | 1.22(8) | 0.49 |
| 17 | HNF1B | rs7501939 | 33,175,268 | C | 1305 | 1513 | 0.50 | 0.50 | 0.97 (0.87 - 1.09) | 0.651 | 1.19(8) | 0.58 |
| 19 | KLK2/3 | rs887391 | 46,677,463 | T | 851 | 875 | 0.50 | 0.49 | 1.03 (0.90 - 1.18) | 0.671 | 1.13(9) | 0.76 |
| 19 | KLK2/3 | rs2735839 | 56,056,434 | A | 2773 | 2680 | 0.32 | 0.31 | 1.07 (0.99 - 1.18) | 0.093 | 1.20(2) | 0.15 |
| 22 | 22q13 | rs9623117 | 38,782,064 | C | 987 | 1077 | 0.76 | 0.76 | 0.99 (0.86 - 1.15) | 0.937 | 1.25(40) | 0.21 |
| X | NUDT10/11 | rs5945572 | 51,246,422 | A | 1764 | 1235 | 0.31 | 0.28 | 1.11 (1.02 - 1.20) | 0.02 | 1.23(1) | 0.35 |
| X | NUDT10/11 | rs5945619 | 51,258,411 | G | 1390 | 1845 | 0.41 | 0.36 | 1.09 (1.00 - 1.18) | 0.039 | 1.19(2) | 0.36 |
aOR: per allele OR adjusting for age and study centers.
OR (per allele OR) in EDM were estimated from: (a) estimations in the original publications whenever they are available (1,2,5,6,7,8,9,19), (b) recalculations based on number of genotype counts in cases and controls when available(4), (c) Specifically for SNPs reported in Thomas et al. (3), ORs for heterozygous carriers were used as a proxy for aORs when OR for homozygous carriers were higher than OR for heterozygous carriers. For SNPs rs4072111 and rs4782726, increased in prostate cancer risk were only seen in homozygous carriers. Therefore, the square-root of OR in homozygous carriers were used as estimates.