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 by the same cassette), excluding exons within known common CNVs16,40,41. After a series of data normalization and quality-control steps, we identified 829 cassettes in which a small (10–100) set of samples exhibited probe intensities that clustered well below the population-wide mean. Each of these was manually reviewed to eliminate artifacts and select for genes with greater potential for disease involvement; 19 were selected for follow-up and organized into two subjectively defined tiers of quality (Table 3).
