Table 3.
Tests of association for uncommon (MAF < 1%) and rare (MAF < 0.1%) missense variants identified in BRIP1, BARD1, NBN, and PALB2 in ovarian cancer case patients using a simple burden test and the rare admixture maximum likelihood test
| Type of missense | MAF frequency, % | No. of variants | P* | |
|---|---|---|---|---|
| RAML | Simple burden | |||
| BARD1 | ||||
| Damaging | <1.0 | 28 | .50 | .63 |
| Nondamaging | <1.0 | 41 | .68 | .28 |
| Combined | <1.0 | 69 | .69 | .88 |
| Damaging | <0.1 | 27 | .39 | .25 |
| Nondamaging | <0.1 | 39 | .86 | .90 |
| Combined | <0.1 | 66 | .74 | .68 |
| BRIP1 | ||||
| Damaging | <1.0 | 35 | .01 | .05 |
| Nondamaging | <1.0 | 54 | .02 | .20 |
| Combined | <1.0 | 89 | 7.4 x 10–4 | .02 |
| Damaging | <0.1 | 34 | <.01 | .05 |
| Nondamaging | <0.1 | 52 | .02 | .03 |
| Combined | <0.1 | 86 | 5.5 x 10–4 | 1.5 x 10–4 |
| NBN | ||||
| Damaging | <1.0 | 51 | .28 | .73 |
| Nondamaging | <1.0 | 32 | .98 | .66 |
| Combined | <1.0 | 83 | .37 | .99 |
| Damaging | <0.1 | 29 | .71 | .69 |
| Nondamaging | <0.1 | 51 | .28 | .73 |
| Combined | <0.1 | 80 | .24 | .49 |
| PALB2 | ||||
| Damaging | <1.0 | 26 | .36 | .33 |
| Nondamaging | <1.0 | 64 | <.01 | .04 |
| Combined | <1.0 | 90 | .13 | .20 |
| Damaging | <0.1 | 25 | .39 | .26 |
| Nondamaging | <0.1 | 62 | .01 | .03 |
| Combined | <0.1 | 87 | .14 | .20 |
* All P values presented are two-sided. MAF = minor allele frequency; RAML = rare admixture likelihood test.