Table 2.
Case-control analyses of mutated genes in the current cohort compared with population data.
| Gene | Number of mutant alleles | Odds ratio | p-value | 95% confidence intervals | |
|---|---|---|---|---|---|
| Lower | Upper | ||||
| (a) Odds ratio of mutated genes in the current cohort compared with the East-Asian population data, including male dataa | |||||
| PALB2 | 7 | 10.7 | <0.01 | 3.5 | 31.3 |
| BARD1 | 4 | 10.2 | <0.01 | 2.1 | 43.2 |
| BLM | 4 | 3.6 | 0.04 | 0.9 | 11.0 |
| ATM | 6 | 2.7 | 0.03 | 0.9 | 6.5 |
| BRIP1 | 2 | 2.4 | NS | 0.3 | 10.4 |
| RAD51D | 4 | 1.8 | NS | 0.5 | 5.2 |
| RAD51C | 1 | 1.7 | NS | 0.0 | 13.0 |
| RECQL | 1 | 1.5 | NS | 0.0 | 10.7 |
| FANCM | 2 | 1.4 | NS | 0.2 | 5.6 |
| CHEK2 | 1 | 1.3 | NS | 0.0 | 8.5 |
| RAD50 | 1 | 0.3 | NS | 0.0 | 1.8 |
| NF1 | 1 | 0.2 | NS | 0.0 | 1.3 |
| (b) Odds ratio of mutated genes in the current cohort compared with female only ExAC data without a distinction of ethnicityb | |||||
| PALB2 | 7 | 8.9 | <0.01 | 3.3 | 20.6 |
| BARD1 | 4 | 14.8 | <0.01 | 3.4 | 50.0 |
| BLM | 4 | 3.4 | 0.04 | 0.9 | 9.3 |
| ATM | 6 | 3.6 | 0.01 | 1.3 | 8.2 |
| BRIP1 | 2 | 2.9 | NS | 0.3 | 11.5 |
| RAD51D | 4 | 0.6 | NS | 0.2 | 1.5 |
| RAD51C | 1 | 2.0 | NS | 0.0 | 12.7 |
| RECQL | 1 | 0.8 | NS | 0.0 | 4.5 |
| FANCM | 2 | 0.5 | NS | 0.1 | 1.9 |
| CHEK2 | 1 | 0.4 | NS | 0.0 | 2.0 |
| RAD50 | 1 | 0.2 | NS | 0.0 | 1.2 |
| NF1 | 1 | 0.1 | NS | 0.0 | 0.7 |
ExAC data were excluding the Cancer Genome Atlas (TCGA) data. Allele count information for gender was not available for HGVD or TMM. ExAC provides allele count data for gender and ethnicity separately but not together. The use of similar ethnicity data as the control prohibits further filtering of the allele count data based on gender, and vice versa.
HGMD Human Gene Mutation Database, HGVD Human Genetic Variation Database, TMM Tohoku Medical Megabank Project, ExAC Exome Aggregation Consortium, NS Non-significant.
aData were combined from HGVD (1208 Japanese), TMM (3554 Japanese), and East-Asian ExAC (3933 east Asian people) (total 8695; all databases include male data) databases and used as the control to compute the odds ratios for each gene (not for each variant).
bFemale ExAC without distinction of ethnicity (22,937 females) was used as the control to compute the odds ratio for each gene (not for each variant). p-values and odds ratios (Fisher exact test) for each gene are shown with upper and lower 95% confidence intervals.