We calculated quality control measures on our HumanHap550 GWAS data based on statistical distributions to exclude DNA samples of poor quality and false-positive CNVs. The first quality control threshold used was the percentage of attempted SNPs that were successfully genotyped. Only samples with call rate >98% were included. The genome-wide intensity signal should have as little noise as possible. Only samples within the s.d. of the normalized intensity (LRR < 0.35) were included. All samples were required to be of European descent based on principle components analysis (Supplementary Fig. 9). Furthermore, case and control matching was insured by calculating a genomic inflation factor (which was 1.024) between groups. Wave artifacts roughly correlating with GC content resulting from hybridization bias of low full-length DNA quantity are known to interfere with the accurate inference of copy number variations57. Only samples where |GC base pair wave factor (GCWF)| < 0.05 were accepted. If the count of CNV calls made by PennCNV exceeds 70 (Supplementary Fig. 1), the DNA quality is usually poor. Therefore, only samples with CNV call count <70 were included. One
