To test this effect more directly, we performed a serial dilution experiment and genotyped the same subject on the HumanHap550 array using five different DNA quantities (187.5, 375, 750, 1500 and 2250 ng; Figure 4D). This anonymous subject is chosen since we had sufficiently large amounts of DNA extracted from the same batch of whole blood without whole-genome amplification. We found that when DNA quantity is low (for example, 187.5 ng), the LRR values show patterns of positive waves; conversely, when DNA quantity is high (for example, 2250 ng), the LRR values show patterns of negative waves (Figure 5A). The GCWF values for the five samples with increasing DNA quantity are −0.044, −0.018, 0, 0.012 and 0.023, respectively, reflecting the direction and magnitude of signal fluctuation for each sample. The correlation between GCWF and DNA quantity (logarithm scale) is 0.994, indicating that GCWF is a reliable measure of the DNA quantity, which is usually not well controlled in genotyping experiments.
