Table 2. Power Comparison when Causal Variants Can Have Opposite Effects.
| MAF Cutoff | Causal Percentage | Group by MAF Cutoff | Group Only Causal Variants | ||||||
|---|---|---|---|---|---|---|---|---|---|
|
| |||||||||
| Burden | Madsen-Browning | VT | SKAT | Burden | Madsen-Browning | VT | SKAT | ||
| 0.01 | 20% | 4.6 | 0.4 | 6.0 | 36.7 | 38.9 | 21.1 | 43.4 | 83.2 |
| 80% | 30.5 | 10.4 | 33.4 | 60.0 | 42.6 | 18.8 | 42.2 | 69.0 | |
|
| |||||||||
| 0.05 | 20% | 11.7 | 1.3 | 15.0 | 35.7 | 55.4 | 22.3 | 58.3 | 88.3 |
| 80% | 44.0 | 7.8 | 47.1 | 74.7 | 55.1 | 12.2 | 54.3 | 81.6 | |
Simulated samples each had 5,000 individuals, organized in families with pedigree10 structure (See Figure 1). Causal variants were selected among those identified in simulated 1,000 base-pair sequences and explained 1% of trait variance. Among causal variants, 20% were randomly selected to be trait-decreasing, and the rest causal variants were trait-increasing. Power is tabulated as a percentage of simulations exceeding significance threshold. Significance level α = 2.5 × 10-6 was used in all simulations.