Since different SNP genotyping arrays show the same phase and period of genomic waves, we assume that certain local genomic features may determine the magnitude of waves in local genomic regions. Previous studies in array-CGH platforms and Affymetrix SNP genotyping platforms suggested correlation between intensity of the clones/probes and the local GC content (4,6). However, GC content is correlated with many genomic features, and these features have not been investigated to find the most likely predictor of waves.
