We next investigated whether the quantity of DNA is the predominant factor in generating genomic waves. For the Illumina Infinium assay, the recommended DNA quantity for each sample is 750 ng; however, in many large studies, variable concentrations of DNA are typically available for different samples, and it is generally difficult to control DNA quantity for all genotyped samples accurately. We compared the GCWF for each of the 1444 DNA samples described above with the total quantity of DNA hybridized as estimated from available pico-green DNA concentration measurements (Figure 4C). We observed a positive correlation between DNA quantity and waviness (Pearson correlation coefficient = 0.4371).
