Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.

ABSTRACT: Whole-genome microarrays with large-insert clones designed to determine DNA copy number often show variation in hybridization intensity that is related to the genomic position of the clones. We found these 'genomic waves' to be present in Illumina and Affymetrix SNP genotyping arrays, confirming that they are not platform-specific. The causes of genomic waves are not well-understood, and they may prevent accurate inference of copy number variations (CNVs). By measuring DNA concentration for 1444 samples and by genotyping the same sample multiple times with varying DNA quantity, we demonstrated that DNA quantity correlates with the magnitude of waves. We further showed that wavy signal patterns correlate best with GC content, among multiple genomic features considered. To measure the magnit

SUBMITTER: Diskin SJ 

PROVIDER: S-EPMC2577347 | biostudies-literature | 2008 Nov

REPOSITORIES: biostudies-literature