was also utilized to test if the 12 SCZ-associated CNV regions (without any additional genomic window) tended to hit the differentially expressed genes more than expected by randomly generated regions in the genome matched to the associated regions in terms of the number of overlapping genes. After conditioning on DLPFC expression, the 12 regions spanned 127 genes. 10,000 permutations were performed. c) De novo mutations: DNENRICH7 (https://psychgen.u.hpc.mssm.edu/dnenrich) was employed to measure if the 756 nonsynonymous (114 loss-of-function) SCZ mutations affected the differentially expressed genes more than expected by randomly generated de novo mutations matched to the observed mutations for their trinucleotide base context and functional consequence and then placed in the genome uniformly at random to account for gene size (e.g., larger genes tend to have more mutations). Conditioning on DLPFC expression, there were 103 loss-of-function mutations in 101 genes, and a total of 638 nonsynonymous mutations across 605 genes. 50,000 permutations were employed for each test. The two tests, for nonsynonymous and loss-of-function mutations, were combined by taking the minimum P value after Bonferroni correction for the 2 tests. d) Rare variants: PLINK/Seq and SMP5 (http://atgu.mgh.harvard.edu/plinkseq) were used to assess whether the exome-sequenced SCZ cases exhibited a burden of
