Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform

Background: Copy number data are routinely being extracted from genome-wide association study chips using a variety of software. We empirically evaluated and compared four freely-available software packages designed for Affymetrix SNP chips to estimate copy number: Affymetrix Power Tools (APT), Aroma.Affymetrix, PennCNV and CRLMM. Our evaluation used 1,418 GENOA samples that were genotyped on the Affymetrix Genome-Wide Human SNP Array 6.0. We compared bias and variance in the locus-level copy number data, the concordance amongst regions of copy number gains/deletions and the false-positive rate amongst deleted segments. Results: APT had median locus-level copy numbers closest to a value of two, whereas PennCNV and Aroma.Affymetrix had the smallest variability associated with the median copy number. Of those evaluated, only PennCNV provides copy number specific quality-control metrics and identified 136 poor CNV samples. Regions of copy number variation (CNV) were detected using the hi...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Jeanette E. Eckel-Passow, Elizabeth J. Atkinson, Sooraj Maharjan, Sharon L. R. Kardia, Mariza de Andrade
• Keywords: Background Copy, Biometrics, BMCBI 2011, Copy Numbers, Hidden Markov Models