Table 2.
Estimated genome-wide significance thresholds for a combined analytic strategy including window-based tests of rare genetic variation and single-marker tests for common variants
| MAF threshold defining rare variants | Test statistic | Number of tests (single marker and windows) on chromosome 3 | Genome-wide estimate of the number of independent tests | Predicted genome-wide significance threshold |
|---|---|---|---|---|
| 0.005 | SKAT | 869,354 | 5,933,687 | 8.43 × 10−9 |
| 0.005 | Burden | 7,237,279 | 6.91 × 10−9 | |
| 0.005 | SKAT-O | 8,547,380 | 5.85 × 10−9 | |
| 0.01 | SKAT | 797,907 | 4,412,096 | 1.13 × 10−8 |
| 0.01 | Burden | 5,735,011 | 8.72 × 10−9 | |
| 0.01 | SKAT-O | 6,019,458 | 8.31 × 10−9 | |
| 0.05 | SKAT | 613,066 | 2,746,888 | 1.82 × 10−8 |
| 0.05 | Burden | 3,142,544 | 1.59 × 10−8 | |
| 0.05 | SKAT-O | 4,306,272 | 1.16 × 10−8 |
Results are derived from simulations.