Table 1.
Overall ability of the four rare variant methods to identify genes as significantly associated with the phenotype
| Method | Nominal α = 0.05 | Nominal α = 0.005 | ||||
|---|---|---|---|---|---|---|
| Total number of significant associations | Number of significant associations that are actually causal | True discoveries (%) | Total number of significant associations | Number of significant associations that are actually causal | True discoveries (%) | |
| Only SNPs with MAF < 5% | ||||||
| WS | 281.0 | 5.69 | 2.03 | 52.5 | 1.56 | 2.97 |
| CMAT | 201.4 | 4.42 | 2.19 | 38.4 | 1.31 | 3.44 |
| CMC | 256.5 | 3.80 | 1.48 | 38.2 | 0.92 | 2.41 |
| PR | 184.6 | 4.46 | 2.41 | 27.9 | 1.17 | 4.20 |
| All SNPs | ||||||
| WS | 348.7 | 6.81 | 1.95 | 76.1 | 2.05 | 2.69 |
| CMAT | 294.9 | 4.63 | 1.57 | 63.8 | 1.46 | 2.28 |
| CMC | 361.1 | 5.16 | 1.43 | 64.6 | 1.23 | 1.90 |
| PR | 285.6 | 4.74 | 1.66 | 53.7 | 1.39 | 2.59 |
| Nonsynonymous SNPs only | ||||||
| WS | 206.1 | 5.25 | 2.54 | 42.3 | 1.78 | 4.20 |
| CMAT | 173.3 | 4.19 | 2.42 | 35.7 | 1.44 | 4.03 |
| CMC | 223.3 | 4.99 | 2.23 | 38.5 | 1.33 | 3.46 |
| PR | 168.7 | 3.88 | 2.30 | 29.4 | 1.38 | 4.69 |
All values are averaged over 200 replicates. WS, weighted sum; CMAT, cumulative minor allele test; CMC, combined multivariate and collapsing; PR, proportion regression.