We proposed two measures for wavy patterns of any genotyped sample. The main advantages of these measures are that they are not dependent on an external data model or reference sample, and can be applied to many different technical platforms and different array designs. We further showed that the GCWF measure correlates strongly with DNA quantity, and can be used to evaluate the effectiveness of reducing genomic waves. Besides GCWF, we have also tried other measures of autocorrelation, including the correlation of signal intensities of neighboring markers with lag 1, lag 10, lag 100 and lag 500 distance (Supplementary Table 5). Although, the autocorrelation measure does reflect the general trend of correlation between nearby markers (with positive values), they are poor predictors of DNA quantity and were not useful in evaluating the magnitude or directionality of waves.
