We initially suspected that DNA quality, such as DNA degradation or protein contamination, could be a direct cause of genomic waves, since strong waves are less frequently observed for DNA samples purchased from standardized cell line repositories than for DNA extracted from patient samples. Using a set of 1444 DNA samples genotyped by the Illumina HumanHap550 arrays, we investigated the relationship between DNA quality and the magnitude of waves. We first calculated the GCWF for each of the 1444 DNA samples. Figure 4A illustrates that DNA purity, as estimated by the 260/280 ratio of DNA samples, does not correlate with GCWF. To investigate the possibility of DNA degradation affecting waviness, we performed an electrophoresis assay (Figure 4B) on a representative set of 18 cases, including six with little genomic wave, six with strong positive waves and six with strong negative waves. We did not observe evidence of increased DNA degradation for samples with positive or negative waves (examples of gel patterns for degraded DNA samples were given in Supplementary Figure 2).
