Using log R ratio and B allele frequency measures for all markers, the CNV calls were generated by PennCNV software (Version 2009Aug27) (14). The quality-control procedure was described in detail in supplementary Fig. 2. We removed samples with low quality of signal intensity values, so that the remaining samples have log R ratio <0.3, B allele frequency_drift <0.01, wave factor <0.05, and that the number of calls is <50. We removed CNV calls with <10 SNPs or with a confidence score <10, sparse calls (average intermarker distance >50 kb), calls in the immunoglobulin regions, and calls in centromeric regions and telomeric regions (100 kb within the start or end of the chromosomes). The overlapping genes or exons for CNV calls were annotated using the scan_region.pl program, based on RefSeq gene annotation (15). We compiled a set of common CNV regions (cCNVRs), which occur at >1% frequency, and then classified the CNV call as common or rare by the scan_region.pl program: if >50% of a CNV call overlaps with a cCNVR, it is referred to as a common CNV. The comparison
