The CNV burden for each sample was determined by counting all CNVs and stratifying them by size into four categories: <10 kb, 10–100 kb, 100–500 kb and >500 kb. All calls for CNVs >500 kb (“large CNVs”) were confirmed individually by plotting the LogR ratio and B allele frequency for the SNPs in the region (Figure S4). The CNV burden was then contrasted between cases and controls using Fisher’s exact test.
