Table 3.
Comparison of mutant allele frequency in case–control association study
| Gene1 | TCGA OC cases | ExAC population controls2 | OR | p‐value3 | |||
|---|---|---|---|---|---|---|---|
| Total chr count4 | Allele frequency | Allele count | Total chr count | Allele frequency | |||
| BRCA1 | 762 | 4.46% | 245 | 54,346 | 0.45% | 10.31 | 7.22E−22 |
| TTC28 | – | – | 47 | 5,400 | 0.87% | – | – |
| FREM2 | 714 | 0.98% | 592 | 54,346 | 1.09% | 0.90 | 1.00 |
| VPS13B | 762 | 1.57% | 600 | 54,346 | 1.10% | 1.43 | 0.22 |
| COL6A3 | 714 | 1.54% | 651 | 54,346 | 1.20% | 1.29 | 0.38 |
| ANKRD11 | 714 | 1.82% | 339 | 54,346 | 0.62% | 2.95 | 7.92E−04 |
| EP300 | 762 | 1.44% | 393 | 54,346 | 0.72% | 2.01 | 2.99E−02 |
| POLE | 738 | 2.17% | 444 | 54,346 | 0.82% | 2.69 | 5.71E−04 |
| BRIP1 | 762 | 0.39% | 135 | 54,346 | 0.25% | 1.59 | 0.44 |
| MSH2 | 762 | 0.92% | 161 | 54,346 | 0.30% | 3.12 | 9.19E−03 |
| BRCA2 | 762 | 3.15% | 349 | 54,346 | 0.64% | 5.03 | 7.26E−10 |
1
The novel OC predisposition candidate genes were in bold. Genes were in the same order as in Table 2.
2
Variants were from Non‐Finnish European population of ExAC with samples from TCGA excluded.
3
Fisher exact test p‐value for comparing allele counts between OC cohort and ExAC. p values that were statistically significant after Bonferroni correction for 10 genes (p‐value <5 × 10−3) are in bold.
4
The samples with genotypes missed for all the variants of the corresponding gene were excluded.