Table 1 Power (%) of seven methods to detect association of rare variants under seven scenarios for underlying genetic architecture using data simulated for BRCA1 in 2000 cases and 2000 controls
Threshold for significance | ||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
P < 0.001 | P < 0.01 | P < 0.05 | ||||||||||||||||||||
Scenario* | Proportion of variants associated | RAML | SKAT-O | T1 | T5 | WST | VTT | EREC | RAML | SKAT-O | T1 | T5 | WST | VTT | EREC | RAML | SKAT-O | T1 | T5 | WST | VTT | EREC |
1 | 0.05 | 5.0 | 4.5 | 3.0 | 2.5 | 2.0 | 3.0 | 3.0 | 15.0 | 11.0 | 10.0 | 7.5 | 8.0 | 7.0 | 10.0 | 30.0 | 29.0 | 22.5 | 18.5 | 20.5 | 19.5 | 26.0 |
2 | 0.05 | 5.0 | 6.5 | 1.5 | 2.0 | 1.0 | 1.5 | 3.0 | 11.5 | 11.5 | 4.5 | 6.0 | 5.5 | 9.0 | 8.0 | 28.0 | 21.5 | 14.5 | 10.5 | 13.5 | 17.0 | 16.0 |
3 | 0.05 | 7.5 | 5.0 | 2.5 | 0.5 | 1.5 | 1.5 | 4.0 | 13.5 | 11.0 | 7.0 | 6.0 | 7.0 | 7.0 | 8.0 | 25.5 | 26.0 | 16.0 | 19.5 | 17.0 | 17.5 | 22.5 |
4 | 0.05 | 7.0 | 4.0 | 2.0 | 1.0 | 1.0 | 1.0 | 2.5 | 14.0 | 12.5 | 5.0 | 3.5 | 5.0 | 4.5 | 8.0 | 26.0 | 23.5 | 12.5 | 12.0 | 9.5 | 10.0 | 21.0 |
5 | 0.05 | 6.5 | 5.0 | 2.0 | 2.0 | 1.5 | 2.0 | 3.5 | 14.5 | 9.5 | 5.0 | 2.5 | 3.5 | 5.5 | 6.5 | 27.5 | 18.0 | 11.5 | 8.0 | 10.0 | 13.5 | 14.5 |
6 | 0.05 | 9.0 | 4.5 | 1.0 | 0.5 | 0.5 | 1.0 | 3.5 | 16.0 | 11.0 | 5.0 | 4.0 | 3.0 | 3.0 | 8.5 | 26.0 | 20.5 | 12.5 | 10.5 | 11.0 | 10.5 | 18.5 |
7 | 0.05 | 8.5 | 5.0 | 1.0 | 1.5 | 0.5 | 1.5 | 4.0 | 16.0 | 8.0 | 3.0 | 4.0 | 3.5 | 4.0 | 7.5 | 24.5 | 21.5 | 8.0 | 8.5 | 6.5 | 10.0 | 16.5 |
1 | 0.10 | 7.5 | 6.0 | 6.0 | 2.0 | 5.0 | 4.5 | 5.5 | 14.5 | 16.0 | 11.0 | 8.0 | 10.0 | 11.0 | 15.0 | 30.0 | 30.0 | 24.5 | 21.5 | 20.0 | 20.5 | 25.0 |
2 | 0.10 | 2.5 | 3.5 | 1.5 | 2.0 | 1.5 | 0.5 | 1.5 | 8.5 | 8.5 | 6.0 | 5.5 | 7.0 | 6.5 | 10.5 | 26.0 | 24.0 | 19.5 | 17.5 | 17.5 | 17.5 | 20.5 |
3 | 0.10 | 4.5 | 5.0 | 3.0 | 2.5 | 3.0 | 1.5 | 3.5 | 10.5 | 8.5 | 7.0 | 4.5 | 5.5 | 7.5 | 8.5 | 22.0 | 19.5 | 15.0 | 11.5 | 14.0 | 15.5 | 18.5 |
4 | 0.10 | 3.5 | 3.0 | 2.0 | 2.0 | 1.5 | 1.5 | 2.5 | 9.5 | 10.5 | 6.0 | 3.0 | 4.5 | 3.5 | 7.5 | 22.0 | 18.5 | 13.5 | 13.0 | 13.0 | 12.5 | 17.5 |
5 | 0.10 | 4.0 | 4.5 | 3.0 | 1.0 | 1.5 | 3.0 | 2.5 | 10.5 | 9.0 | 5.5 | 3.0 | 5.0 | 5.5 | 9.0 | 23.0 | 21.0 | 13.0 | 11.5 | 14.0 | 14.5 | 22.0 |
6 | 0.10 | 2.5 | 3.5 | 1.5 | 1.0 | 1.5 | 1.0 | 1.5 | 9.0 | 9.0 | 5.0 | 2.5 | 5.5 | 3.5 | 5.5 | 21.0 | 18.0 | 10.0 | 9.0 | 9.0 | 11.0 | 16.5 |
7 | 0.10 | 4.0 | 3.0 | 1.0 | 1.0 | 0.5 | 2.0 | 3.5 | 11.0 | 10.5 | 2.5 | 5.0 | 3.0 | 3.0 | 7.5 | 25.5 | 20.0 | 11.5 | 11.5 | 12.0 | 12.5 | 17.0 |
1 | 0.20 | 6.5 | 7.5 | 7.5 | 4.0 | 5.5 | 4.5 | 7.5 | 23.5 | 27.5 | 23.5 | 18.5 | 24.5 | 20.5 | 25.5 | 40.0 | 44.5 | 44.0 | 40.0 | 44.5 | 39.0 | 43.5 |
2 | 0.20 | 4.0 | 6.5 | 4.5 | 2.0 | 4.5 | 4.0 | 4.5 | 14.0 | 12.5 | 14.0 | 7.0 | 10.0 | 9.5 | 12.5 | 23.0 | 26.5 | 23.5 | 16.5 | 22.5 | 23.0 | 24.0 |
3 | 0.20 | 5.0 | 6.0 | 5.5 | 3.5 | 5.0 | 5.5 | 5.0 | 14.5 | 17.0 | 15.0 | 12.5 | 16.5 | 13.0 | 17.0 | 27.5 | 36.5 | 31.0 | 28.5 | 34.0 | 30.0 | 35.5 |
4 | 0.20 | 2.5 | 3.0 | 1.5 | 1.5 | 1.5 | 1.0 | 2.0 | 7.5 | 10.5 | 5.0 | 6.5 | 5.5 | 5.0 | 8.0 | 18.5 | 21.5 | 16.0 | 14.0 | 16.5 | 17.0 | 18.5 |
5 | 0.20 | 4.5 | 5.0 | 1.0 | 1.0 | 1.5 | 1.0 | 2.5 | 10.5 | 9.0 | 7.0 | 4.0 | 4.5 | 6.0 | 8.0 | 24.0 | 25.5 | 17.5 | 13.5 | 15.0 | 14.5 | 20.5 |
6 | 0.20 | 0.5 | 1.0 | 0.0 | 0.0 | 0.5 | 0.0 | 0.5 | 6.5 | 6.5 | 3.5 | 2.5 | 2.0 | 1.5 | 4.5 | 17.0 | 20.0 | 10.0 | 12.0 | 11.0 | 8.5 | 18.5 |
7 | 0.20 | 3.0 | 3.5 | 0.5 | 0.5 | 1.0 | 0.5 | 0.5 | 9.0 | 9.5 | 3.0 | 4.0 | 2.5 | 3.5 | 6.5 | 23.5 | 21.5 | 12.0 | 9.5 | 12.0 | 12.0 | 17.5 |