Table 2.
Power (%) of seven methods to detect association of rare variants under seven scenarios for underlying genetic architecture using data simulated for BRCA2 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 |
19.5 |
2.5 |
0.5 |
2.5 |
1.5 |
4.5 |
5.5 |
41.0 |
7.5 |
6.0 |
7.0 |
6.0 |
14.5 |
11.0 |
57.5 |
18.0 |
21.5 |
15.0 |
15.5 |
29.5 |
18.5 |
| 2 |
0.05 |
15.5 |
4.5 |
1.5 |
3.0 |
2.0 |
3.0 |
5.0 |
26.5 |
9.5 |
3.0 |
6.0 |
7.0 |
7.5 |
10.0 |
44.0 |
21.0 |
14.0 |
15.0 |
11.5 |
18.5 |
18.0 |
| 3 |
0.05 |
13.0 |
2.5 |
0.5 |
2.0 |
2.0 |
2.5 |
2.5 |
27.5 |
4.0 |
4.0 |
4.0 |
2.5 |
3.5 |
4.5 |
45.5 |
13.5 |
15.5 |
8.0 |
9.0 |
17.0 |
11.5 |
| 4 |
0.05 |
14.0 |
3.5 |
1.5 |
2.5 |
1.5 |
3.5 |
3.0 |
27.0 |
9.5 |
4.0 |
6.5 |
6.0 |
7.5 |
8.5 |
39.5 |
18.5 |
7.5 |
13.5 |
13.5 |
16.0 |
16.0 |
| 5 |
0.05 |
14.5 |
3.0 |
0.5 |
2.0 |
1.5 |
2.5 |
3.5 |
31.0 |
8.0 |
3.0 |
5.5 |
3.5 |
7.0 |
8.0 |
47.0 |
12.5 |
15.0 |
10.5 |
9.0 |
17.0 |
13.0 |
| 6 |
0.05 |
15.0 |
2.5 |
0.5 |
0.5 |
1.0 |
1.5 |
1.0 |
30.0 |
9.5 |
4.0 |
7.0 |
7.0 |
4.0 |
9.0 |
45.5 |
21.0 |
8.0 |
17.0 |
15.0 |
14.0 |
21.0 |
| 7 |
0.05 |
18.0 |
0.5 |
0.0 |
0.5 |
0.0 |
1.5 |
1.5 |
29.5 |
2.5 |
3.0 |
1.0 |
1.0 |
3.0 |
2.5 |
44.0 |
9.0 |
8.5 |
5.0 |
3.5 |
9.0 |
10.0 |
| 1 |
0.10 |
14.5 |
1.5 |
3.0 |
1.5 |
2.5 |
7.5 |
3.5 |
30.5 |
8.0 |
13.0 |
6.0 |
8.0 |
15.5 |
8.5 |
48.5 |
19.0 |
24.0 |
14.5 |
20.5 |
31.0 |
20.0 |
| 2 |
0.10 |
9.5 |
2.0 |
1.0 |
1.5 |
2.0 |
3.5 |
3.0 |
24.5 |
10.5 |
4.5 |
7.0 |
7.5 |
8.5 |
9.0 |
40.0 |
22.0 |
15.5 |
18.0 |
19.5 |
18.5 |
23.0 |
| 3 |
0.10 |
11.5 |
1.5 |
1.5 |
1.0 |
2.0 |
3.0 |
2.5 |
27.0 |
5.0 |
9.0 |
4.0 |
4.5 |
8.5 |
6.0 |
41.5 |
12.5 |
20.5 |
10.5 |
10.5 |
22.5 |
13.5 |
| 4 |
0.10 |
11.0 |
3.0 |
2.0 |
2.5 |
1.0 |
2.5 |
2.5 |
20.5 |
7.0 |
4.0 |
5.0 |
3.5 |
9.5 |
5.5 |
39.5 |
18.0 |
13.0 |
11.5 |
12.5 |
16.0 |
14.0 |
| 5 |
0.10 |
13.5 |
2.5 |
3.0 |
1.5 |
2.0 |
3.5 |
2.5 |
24.0 |
6.0 |
6.0 |
4.0 |
3.0 |
9.0 |
7.0 |
40.5 |
18.0 |
15.5 |
12.0 |
13.5 |
18.0 |
14.5 |
| 6 |
0.10 |
6.5 |
0.5 |
0.0 |
0.0 |
0.0 |
0.0 |
0.5 |
17.0 |
4.5 |
1.0 |
2.5 |
3.0 |
3.0 |
3.5 |
36.0 |
13.0 |
7.0 |
7.5 |
8.5 |
11.5 |
10.5 |
| 7 |
0.10 |
7.5 |
1.5 |
1.5 |
2.0 |
1.0 |
3.0 |
2.0 |
22.5 |
4.0 |
5.0 |
4.0 |
4.0 |
8.0 |
4.0 |
40.5 |
15.5 |
13.5 |
9.0 |
10.5 |
17.0 |
13.0 |
| 1 |
0.20 |
20.0 |
9.0 |
12.0 |
9.5 |
12.0 |
22.5 |
11.0 |
41.0 |
18.0 |
27.0 |
17.0 |
25.0 |
39.5 |
21.0 |
59.0 |
31.5 |
47.5 |
28.0 |
38.0 |
55.0 |
30.0 |
| 2 |
0.20 |
8.5 |
1.0 |
2.5 |
0.5 |
1.5 |
4.5 |
2.5 |
22.0 |
5.5 |
11.0 |
5.0 |
8.0 |
13.5 |
7.0 |
45.0 |
18.5 |
27.0 |
12.0 |
21.5 |
30.0 |
17.0 |
| 3 |
0.20 |
9.0 |
3.0 |
5.0 |
3.0 |
6.5 |
9.0 |
4.0 |
25.5 |
9.0 |
17.5 |
9.0 |
13.0 |
20.0 |
10.5 |
44.5 |
17.0 |
34.0 |
16.0 |
22.0 |
34.5 |
19.5 |
| 4 |
0.20 |
8.5 |
1.0 |
1.0 |
0.5 |
1.0 |
1.5 |
1.0 |
21.5 |
6.5 |
6.0 |
4.0 |
6.0 |
9.0 |
5.5 |
38.0 |
15.0 |
16.0 |
13.0 |
12.0 |
20.5 |
17.5 |
| 5 |
0.20 |
12.5 |
4.0 |
2.5 |
4.0 |
1.0 |
4.5 |
4.0 |
29.0 |
8.0 |
5.5 |
6.0 |
6.0 |
12.5 |
8.5 |
43.5 |
17.5 |
17.5 |
14.0 |
15.0 |
24.0 |
18.0 |
| 6 |
0.20 |
5.5 |
2.0 |
1.0 |
2.5 |
1.0 |
2.5 |
3.0 |
21.5 |
4.0 |
3.0 |
5.0 |
3.5 |
7.0 |
6.0 |
35.0 |
15.5 |
12.0 |
10.0 |
11.0 |
15.5 |
15.0 |
| 7 | 0.20 | 8.5 | 2.5 | 1.0 | 1.5 | 1.0 | 1.5 | 3.0 | 21.0 | 6.0 | 3.0 | 5.0 | 5.0 | 3.5 | 7.0 | 42.0 | 16.5 | 9.0 | 13.0 | 12.5 | 14.0 | 16.0 |
Method with greatest power emboldened.
* See text for description of genetic architecture for each scenario.
RAML Rare admixture maximum likelihood, SKAT-O sequence kernel association test, T1 fixed threshold test 1 per cent MAF, T5 fixed threshold test 5 per cent MAF, WST weighted sum test, VTT variable threshold test, EREC estimated regression coefficient test.