1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis.
Array-based comparative genomic hybridization (aCGH) is a recently developed tool for genome-wide determination of DNA copy number alterations. This technology has tremendous potential for disease-gene discovery in cancer and developmental disorders as well as numerous other applications. However, widespread utilization of a CGH has been limited by the lack of well characterized, high-resolution clone sets optimized for consistent performance in aCGH assays and specifically designed analytic software. We have assembled a set of approximately 4100 publicly available human bacterial artificial chromosome (BAC) clones evenly spaced at approximately 1-Mb resolution across the genome, which includes direct coverage of approximately 400 known cancer genes. This aCGH-optimized clone set was compiled from five existing sets, experimentally refined, and supplemented for higher resolution and enhancing mapping capabilities. This clone set is associated with a public online resource containing detailed clone mapping data, protocols for the construction and use of arrays, and a suite of analytical software tools designed specifically for aCGH analysis. These resources should greatly facilitate the use of aCGH in gene discovery.
Greshock
Joel
J
Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
Naylor
Tara L
TL
Margolin
Adam
A
Diskin
Sharon
S
Cleaver
Stephen H
SH
Futreal
P Andrew
PA
deJong
Pieter J
PJ
Zhao
Shaying
S
Liebman
Michael
M
Weber
Barbara L
BL
D045744:Cell Line, Tumor; D002874:Chromosome Mapping / Q000592:standards; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D003001:Cloning, Molecular / Q000379:methods*; D004273:DNA, Neoplasm / Q000032:analysis; D018628:Gene Dosage; D052138:Genes, Neoplasm / Q000235:genetics*; D015894:Genome, Human; D006801:Humans; D020407:Internet / Q000639:trends; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016415:Sequence Alignment / Q000379:methods; D012984:Software
D004273:DNA, Neoplasm