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

ABSTRACT:

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 t

SUBMITTER: Eckel-Passow JE 

PROVIDER: S-EPMC3146450 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature