To demonstrate that wave adjustment leads to improved CNV detection, we analyzed a recently genotyped three-generation pedigree with 51 individuals (Supplementary Figure 7). The DNA were extracted from fibroblast cell lines, and were then subject to Illumina HumanHap550 arrays without appropriate dilution to ensure optimal DNA quantity used in genotyping. As a result, a large fraction of the samples show visually discernable genomic waves and this hinders accurate CNV inference. Excluding the three samples that failed genotyping, for the remaining 48 samples, the GCWF values range from −0.09 to 0.01, with interquantile range of −0.05 to −0.02. After signal adjustment, all samples have GCWF values between −0.004 and 0.004, with interquantile range of −0.002 to 0.001, suggesting effective elimination of wavy patterns in these samples by our wave adjustment procedure.
