Table 2. Frequency of somatic and germline mutations in 12 candidate susceptibility genes in 412 high-grade serous ovarian cancer cases from TCGA and germline mutations in up to 4,508 ovarian cancer cases and 3,368 controls.
| Gene | Somatic variants(412 TCGA cases) | Germline mutations | |||||
|---|---|---|---|---|---|---|---|
| Mutationa N (%) |
LOHb (%) |
TCGA cases N (%) |
HG serouscases (%) | Other cases N (%) |
Controls N (%) |
P-valuec | |
| N=2,210 | N=924 | N=3,368 | |||||
| APEX1 | 2 (0.49) | 29 | 1 (0.24) | 1 (0.03) | 2 (0.13) | 3 (0.09) | 0.52 |
| EME1 | 0 | 52 | 1 (0.24) | 3 (0.10) | 1 (0.07) | 3 (0.09) | 0.91 |
| FANCL | 2 (0.49) | 10 | 1 (0.24) | 18 (0.60) | 8 (0.54) | 28 (0.83) | 0.34 |
| MAD2L2 | 1 (0.24) | 34 | 2 (0.49) | 1 (0.03) | 0 | 0 | - |
| PARP3 | 1 (0.24) | 31 | 1 (0.24) | 6 (0.20) | 1 (0.07) | 13 (0.39) | 0.22 |
| POLN | 1 (0.24) | 42 | 3 (0.73) | 15 (0.50) | 10 (0.67) | 26 (0.77) | 0.09 |
| RAD54L | 2 (0.49) | 12 | 1 (0.24) | 4 (0.13) | 1 (0.20) | 6 (0.18) | 0.80 |
| SMUG1 | 0 | 18 | 1 (0.24) | 2 (0.07) | 1 (0.07) | 2 (0.06) | 0.71 |
| N=3,107 | N=1,491 | N=3,368 | |||||
| APLF | 2 (0.49) | 10 | 5 (1.21) | 92 (3.1) | 40 (2.7) | 121 (3.6) | 0.16 |
| APTX | 2 (0.49) | 40 | 1 (0.24) | 4 (0.13) | 4 (0.27) | 4 (0.12) | 0.97 |
| FANCM | 2 (0.49) | 41 | 1 (0.24) | 29 (0.96) | 6 (0.40) | 13 (0.39) | 0.008 |
| PARP2 | 1 (0.24) | 30 | 1 (0.24) | 4 (0.13) | 3 (0.20) | 5 (0.15) | 0.65 |
a germline mutation
b Loss of heterozygosity
c Comparison of high-grade serous cases with controls