Table 2 Other Parameter Settings

Number of Simulations

1000 runs times 30 replicates for each sample size scenario

Upper Threshold for MAF

0.01 and 0.05

Variant Weighting

Madsen and Browning [12]

Disease Prevalence

5%

Number of Disease Loci

10

Odds Ratio (OR)

All disease loci with OR 2.5; Half of disease loci with risk effect, the other half with protective effect