Table 1. Power when Causal Variants All Increase Trait Values and Have the Same Effect Sizes.
| MAF Cutoff | Causal Percentage | Group by MAF Cutoff | Group Only Causal Variantsb | ||||||
|---|---|---|---|---|---|---|---|---|---|
|
| |||||||||
| Burden | Madsen-Browning | VT | SKATa | Burden | Madsen-Browning | VT | SKAT | ||
| 0.01 | 20% | 9.7 | 3 | 13.1 | 36.6 | 94.3 | 86.7 | 92.9 | 82.6 |
| 80% | 82.4 | 64.7 | 88.1 | 61 | 96 | 82.1 | 94.3 | 70.7 | |
|
| |||||||||
| 0.05 | 20% | 14.6 | 2.6 | 24.9 | 36.3 | 95.4 | 75.3 | 93.8 | 86.5 |
| 80% | 81.3 | 39.5 | 89.2 | 75 | 96.3 | 55.3 | 94.3 | 82.9 | |
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. Each causal variant had the same effect size and direction. Power is tabulated as a percentage of simulations exceeding significance threshold. Significance level α = 2.5 × 10-6 was used in all simulations.
a
Power calculated from Madsen-Browning weighted SKAT.
b
Power when grouping only causal variants. This column represents the largest power we can achieve for each simulation setting.