Table 4 Power (%) of RAML and SKAT methods to detect association of rare variants under seven scenarios for underlying genetic architecture using data simulated for BRCA1 in 4000 cases and 4000 controls
Threshold for significance | |||||||
|---|---|---|---|---|---|---|---|
P < 0.001 | P < 0.01 | P < 0.05 | |||||
Scenario* | Proportion of variants associated | RAML | SKAT-O | RAML | SKAT-O | RAML | SKAT-O |
1 | 0.05 | 47.5 | 31.5 | 61.0 | 44.0 | 73.5 | 58.5 |
2 | 0.05 | 39.5 | 24.0 | 53.5 | 36.0 | 64.5 | 49.0 |
3 | 0.05 | 43.0 | 29.5 | 61.5 | 43.0 | 70.5 | 55.0 |
4 | 0.05 | 33.5 | 22.5 | 49.5 | 29.0 | 59.5 | 42.5 |
5 | 0.05 | 39.5 | 25.5 | 57.0 | 39.5 | 62.0 | 51.5 |
6 | 0.05 | 33.5 | 21.5 | 43.0 | 29.5 | 57.0 | 41.5 |
7 | 0.05 | 37.5 | 30.5 | 51.0 | 38.0 | 56.5 | 45.5 |
1 | 0.10 | 40.0 | 34.5 | 58.0 | 50.0 | 76.0 | 66.0 |
2 | 0.10 | 36.0 | 29.0 | 50.5 | 42.5 | 65.5 | 58.0 |
3 | 0.10 | 32.5 | 28.5 | 53.0 | 42.5 | 67.5 | 58.0 |
4 | 0.10 | 31.0 | 22.0 | 45.5 | 35.5 | 59.0 | 48.5 |
5 | 0.10 | 33.5 | 25.0 | 55.0 | 39.5 | 71.0 | 59.5 |
6 | 0.10 | 32.5 | 21.5 | 48.5 | 31.5 | 62.0 | 48.5 |
7 | 0.10 | 31.5 | 23.0 | 44.0 | 35.0 | 60.5 | 46.5 |
1 | 0.20 | 47.5 | 50.0 | 71.0 | 67.5 | 83.5 | 81.0 |
2 | 0.20 | 26.5 | 34.5 | 49.0 | 46.0 | 69.5 | 68.0 |
3 | 0.20 | 41.0 | 40.5 | 59.5 | 52.5 | 74.0 | 67.0 |
4 | 0.20 | 26.0 | 26.0 | 44.5 | 40.0 | 67.5 | 55.5 |
5 | 0.20 | 35.0 | 26.5 | 51.5 | 44.5 | 70.0 | 64.5 |
6 | 0.20 | 27.5 | 24.5 | 45.5 | 37.0 | 62.5 | 55.0 |
7 | 0.20 | 23.5 | 19.0 | 46.0 | 35.5 | 63.0 | 59.5 |