We next evaluated both CNV intervals and RefSeq transcripts mapping within rare CNVs that were recurrently observed as restricted to or over-represented in cases (Table 3). To avoid biasing our interpretation, we also evaluated a randomly selected subset of controls of equal size (N=460) and identified genes that were either restricted to or overrepresented in unaffected individuals (n=41 genes, data not shown). While these could potentially include protective alleles, we reasoned that the majority would have no association with disease and consequently, we added this number to the total found in cases (N=26) as the basis for a correction for multiple comparisons in evaluating association (N=67 total events). To ensure comparable CNV detection from different array types, CNVs in both cases and controls were detected using probes shared among the arrays (n=213,819).
