To further validate the performance of the wave adjustment procedure, we analyzed the five samples used in the serial dilution experiment (Figure 5). Before adjustment, the GCWF values for the five samples ranged from −0.044 to 0.023, which correlated with the DNA quantity (Figure 5B). However, after adjustment, the GCWF values for the five samples were 0, −0.001, 0, 0 and −0.003, respectively, supporting the effectiveness of wave adjustment procedure. We next generated CNV calls in the BeadStudio software using the cnvPartition algorithm (the default CNV-calling algorithm developed by Illumina), as well as the PennCNV algorithm (18) without and with wave adjustment (Figure 6). The cnvPartition algorithm is used here as an alternative approach to independently support CNV calls in the absence of experimental data. The CNV calls are represented as colored bars in the corresponding chromosome positions in the graph for each sample and for each algorithm. Using the cnvPartition algorithm, we detected 16, 10, 7, 13 and 11 CNV calls for the five samples with increasing DNA quantity. With the PennCNV algorithm without wave adjustment, we detected 24,
