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 sample from any duplicate samples (such as those from monozygotic twins) was excluded. Supplementary Table 13 lists the number of samples excluded using each quality control measure.
