A comparison of the CNV landscape between cases and controls reveals striking differences and some general genomic architectural features (Figure 2). To ameliorate the effects of breakpoint imprecision and multi-platform comparisons, we contrasted the number of deletions (or duplications) present in cases versus controls in 200 kbp windows along the human genome using a Fisher’s exact test (Supplementary Table 7, Supplementary Figure 3). This analysis identified 80 genomic regions that were at least weakly enriched for CNVs (counting deletions and duplications separately) among cases (at least five windows with p < 0.1), 27 of which exhibit strong evidence for enrichment (p < 0.001). Notably, 27.5% (22/80) of the enriched CNV-loci reside at genomic hotspots flanked by large (>10 kbp) blocks of highly similar (>90%) segmental duplication (SD) and include most known genomic disorders (Supplementary Table 7). An additional 46 enrichments represent large CNVs near telomeres (Supplementary Figure 4). While we observed enrichments at one or both ends of all chromosomes, 12 chromosome ends showed particularly strong (p < 0.001) enrichment. Of the 80-CNV loci, 15 are novel or are supported
