While the data suggest that as much as 14.2% of DD may be explained by large CNVs, many causal mutations remain to be identified. We sought to determine if novel, smaller CNVs could be identified among these patients assuming that breakpoints would not necessarily be recurrent and individually relevant events would be rare (<0.1%); such variants may, in principle, identify novel candidate genes, refine the molecular basis for the phenotypic consequences of larger CNVs, and broaden the predictive power of a given microarray experiment. Therefore, we conducted a directed search for small, exon-affecting CNVs, reasoning that such variants are more likely to have disease relevance and be amenable to follow-up. For each consensus coding sequence (CCDS) exon39, we determined the average intensity for the three closest probes (termed a “cassette”) in each sample and, in turn, identified cassettes exhibiting outlier intensities that may be indicative of deletions (see Methods, Supplementary Figure 6). Note that because this strategy is exon-centric, it is partially platform and breakpoint independent. We analyzed 186,014 autosomal coding exons using 65,704 cassettes (multiple exons are often targeted
