In order to implement a genome-wide screen for the effect of common CNVs on schizophrenia predisposition, the number of deletions and duplications affecting each SNP was counted up and compared between cases and controls using Fisher's exact test. For each population, separate analyses were done for deletions, duplications and loci affected by both deletions and duplications. To enter the deletion analysis, a SNP had to be deleted in 3 or more samples and duplicated in fewer than 2 samples, for the duplication analysis a SNP had to be duplicated in 3 or more samples and deleted in fewer than 2 samples and the third analysis included all SNPs that are deleted in 2 or more samples and duplicated in 2 or more samples. Events that only occurred in one or two individuals were not analyzed. For the screen for schizophrenia-specific recurring events, we performed the same statistical test, and again stipulated that the event must occur in at least three individuals, but this time we did not filter out sites that were affected by duplications from the deletion analysis nor those affected by deletions from the duplication analysis, in order to maximize the search space for each test.
