We examined the fully independent case–control data sets for rare CNVs at the novel loci affected by case de novos, including CNVs only of the same class that had been observed to have occurred as de novos (that is, deletions, duplications or both where relevant) (Supplementary Section 7) that intersected at least one exon of a gene (details in Supplementary Table S1). Even after an extremely conservative approach of excluding all CNVs (deletions and duplications) at known schizophrenia loci represented among our de novos (3q29, 15q11.2, 15q13.3 and 16p11.2), we found rates of 0.4% (32/7907) in cases and 0.21% (22/10 585) in controls, a twofold enrichment (Fisher one-tailed P=0.012). We did not obtain evidence for association to individual CNV loci at a level that would survive correction for multiple testing (N=19 excluding the known schizophrenia loci, giving a Bonferroni corrected threshold of P=0.0025). However, nominally significant associations (P uncorrected <0.05) were observed for deletions at DLG2 (P=0.02) and MSRA (P=0.03), whereas the EHMT1 locus just failed to reach this uncorrected threshold (P=0.055). Of interest, although not even nominally significant, we
