Table 3. Power Comparison when Causal Variants All Increase Trait Values and Explain the Same Amount of Trait Variance.
| 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% | 4.3 | 4.2 | 9.1 | 20.8 | 88.7 | 94.9 | 90.8 | 67.0 |
| 80% | 66.9 | 86.6 | 85.4 | 20.1 | 85.5 | 97.1 | 93.8 | 27.0 | |
|
| |||||||||
| 0.05 | 20% | 3.8 | 5.1 | 9.3 | 9.8 | 78.8 | 98.0 | 90.1 | 53.0 |
| 80% | 38.6 | 88.5 | 82.1 | 9.4 | 56.0 | 97.9 | 92.6 | 12.4 | |
Simulated samples each had 5,000 individuals, organized in families with pedigree 10 structure (See Figure 1). Causal variants were selected among those identified in simulated 1,000 base-pair sequences and explained 1% of trait variance. Each causal variant explained the same amount of trait variance. All 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.