Secondly, in the case–control GWAS discovery sample, we performed 10 000 permutations of the case–control status to see how often we get directionally consistent nominal minimal one-sided P-values of ≤0.025 as observed for 20 out of the 25 CNVRs detected in the family-based discovery GWAS sample. In none of the permutations we observed more than 20 such directionally consistent CNVR findings; in two permutation samples, we observed exactly 20 (taken together resulting in an empirical P-value of 2 × 10−4); the median was 10 directionally consistent CNVR findings in the 10 000 permutations.
