For a subset of 11,529 samples, we identified for each coding exon39 the three closest probes, requiring at least one probe on both sides within 100 kbp of the exon. We required that all probes map within 200 kbp, yielding 65,704 unique cassettes targeting 186,014 autosomal coding exons. We then determined the average cassette intensity for each sample and normalized this by array type. Subsequently, we considered filtered cassettes by the following criteria: 10–100 samples with scores at least 5 standard deviations below average; the subset of samples at less than 5 standard deviations below average compose at least 10% of samples with scores less than 3 standard deviations below average (a measure of cluster separation); and no overlap of the target exon (note, individual probes were not filtered given the heterogeneity of platforms and potential for atypical CNVs) with common copy number polymorphisms or deletions seen in multiple control individuals16,42,43,59. This yielded 829 candidates for follow-up, each of which were manually reviewed to eliminate cassettes in which all candidate deletions clustered within a single array type suggestive of a
