To quantify the magnitude of signal fluctuation of genotyped samples, it is necessary to develop a summary measure of waviness. This measure should not be susceptible to the presence of CNVs (which generate extreme values in the signal intensity measures), and should be comparable between different cohorts, or even arrays with different density of markers (for example, the Illumina HumanHap300, HumanHap550 and HumanHap1M arrays). We have developed a score called wave factor (WF) that is based on median absolute deviation of signal intensities. We calculate the median signal intensity values (normalized signal intensity as LRR value) for every 1 Mb nonoverlapping window in the genome and denote them as Yi (i = 1 to ∼3000 for human genome). The windows containing less than 10 SNPs were excluded from the calculation. We then compute the correlation between median signal intensity and local GC content in all windows, and denote this value as rGC. In this study, rGC is calculated using all windows on chromosome 11. The WF score is defined as The first part of the equation is used to assign
