title: Comparison of comparative genomic hybridization technologies across microarray platforms.
abstract: In the 2007 Association of Biomolecular Resource Facilities Microarray Research Group project, we analyzed HL-60 DNA with five platforms: Agilent, Affymetrix 500K, Affymetrix U133 Plus 2.0, Illumina, and RPCI 19K BAC arrays. Copy number variation was analyzed using circular binary segmentation (CBS) analysis of log ratio scores from four independently assessed hybridizations of each platform. Data obtained from these platforms were assessed for reproducibility and the ability to detect formerly reported copy number variations in HL-60. In HL-60, all of the tested platforms detected genomic DNA amplification of the 8q24 locus, trisomy 18, and monosomy X; and deletions at loci 5q11.2~q31, 9p21.3~p22, 10p12~p15, 14q22~q31, and 17p12~p13.3. In the HL-60 genome, at least two of the five platforms detected five novel losses and five novel gains. This report provides guidance in the selection of platforms based on this wide-ranging evaluation of available CGH platforms.
authors.affiliation: Cellular Toxicology Branch, National Health and Environmental Effects Laboratory, U.S. Environmental Protection Agency, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711, USA. hester.susan@epa.gov
authors.forename: Susan D
authors.initials: SD
authors.lastname: Hester
authors.forename: Laura
authors.initials: L
authors.lastname: Reid
authors.forename: Norma
authors.initials: N
authors.lastname: Nowak
authors.forename: Wendell D
authors.initials: WD
authors.lastname: Jones
authors.forename: Joel S
authors.initials: JS
authors.lastname: Parker
authors.forename: Kevin
authors.initials: K
authors.lastname: Knudtson
authors.forename: William
authors.initials: W
authors.lastname: Ward
authors.forename: Jay
authors.initials: J
authors.lastname: Tiesman
authors.forename: Nancy D
authors.initials: ND
authors.lastname: Denslow
mesh_terms: D000465:Algorithms; D016022:Case-Control Studies; D002869:Chromosome Aberrations; D002872:Chromosome Deletion; D022202:Chromosomes, Artificial, Bacterial; D055028:Comparative Genomic Hybridization / Q000379:methods*; D018628:Gene Dosage; D014644:Genetic Variation; D015894:Genome, Human; D018922:HL-60 Cells; D006801:Humans; D021141:Nucleic Acid Amplification Techniques; D020411:Oligonucleotide Array Sequence Analysis / Q000191:economics / Q000379:methods*; D012015:Reference Standards; D015203:Reproducibility of Results; D012984:Software