Previous studies have shown that under certain conditions SKAT can be biased when calculating p-values (Lee et al., 2012a, Ionita-Laza et al., 2013). To check the significance of the results with q-values < 0.30, we conducted 100,000 permutations. Specifically, we permuted the phenotypes in each sample separately to preserve the genetic architecture in each study. The analyses were then conducted on the combined permuted data.
