Comparison of comparative genomic hybridization technologies across microarray platforms.
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.
Hester
Susan D
SD
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
Reid
Laura
L
Nowak
Norma
N
Jones
Wendell D
WD
Parker
Joel S
JS
Knudtson
Kevin
K
Ward
William
W
Tiesman
Jay
J
Denslow
Nancy D
ND
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