Of the samples that passed quality control, we identified 1,139 CNV regions with length greater than 50 kb and number of probes not less than 10 (Lin et al., 2011). Among them, only 141 CNV regions have frequency higher than 1%. All of these CNV regions had previously been documented in the database of genetic variants (Zhang et al., 2006). Level of agreement across the various algorithms was moderate (see Supplementary Table S1). Thus, after adjusting for multiple tests, our significance threshold for association analyses is 0.05/141=3.54 × 10−4.
