Our results confirm the finding from previous studies that the results from SKAT can be biased. Specifically, we observed a λ of 0.797. Values less than 1 suggest that the observed test statistics are smaller than expected when compared with the complete null hypothesis assuming no effect for any of the sets. The permutation p-values were comparable to the observed p-values from SKAT (Table 2), with the permutation p-values being slightly more conservative in some cases, and unrelated to the variant set size (Figure S1).
