In summary, we describe the presence of genomic waves in several high-density SNP genotyping platforms and present experiments and analyses to investigate the major causes of these patterns. Moreover, we propose a simple computational procedure that generates adjusted signal intensities to reduce the effects of genomic waves and to improve the accuracy of CNV inference. With the increasing use of SNP genotyping platforms for genome-wide association studies and genome-wide CNV analysis, our method will be useful for taking full advantage of all available samples.
