Second we applied a case-control CNV enrichment test implemented in PLINK (http://pngu.mgh.harvard.edu/~purcell/plink/) to the eight gene sets (pathways) associated with SCZ de novo CNVs and seven gene sets associated with BD de novo CNVs. For analysis of de novo CNVs using PLINK we report the one-sided empirical p value based on 10,000 permutations. A category was defined as “enriched” if nominally significant (p < 0.05) by all case-only and case-control permutation tests. Pathway enrichment analysis was also applied to de novo CNVs in control, and significance was based on a single (control only) permutation test.
