Besides array-CGH platforms, other CNV detection platforms of similar nature may also be susceptible to genomic waves. In our genotyping experiments using the Illumina HumanHap550 arrays, we have observed obvious genomic waves in many batches of samples. In our studies, even for DNA samples available from commercial cell line repositories, typically ∼10% show strong wavy patterns that are visually discernable in the BeadStudio software (Illumina Inc., San Deigo, CA, USA). The presence of genomic waves may adversely affect the performance of CNV calling algorithms and can result in inflated false positive calls. It is of great interest to perform a comprehensive analysis of signal intensity patterns across several SNP genotyping platforms, investigate the causes of genomic waves and find ways to reduce these waves from both experimental and computational perspectives.
