1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis

Joel Greshock, Tara L. Naylor, Adam Margolin, Sharon Diskin, Stephen H. Cleaver, P. Andrew Futreal, Pieter J. deJong, Shaying Zhao, Michael Liebman, Barbara L. Weber

Research output: Contribution to journalArticle

96 Citations (Scopus)

Abstract

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 aCGH 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 ∼4100 publicly available human bacterial artificial chromosome (BAC) clones evenly spaced at ∼1-Mb resolution across the genome, which includes direct coverage of ∼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.

Original languageEnglish (US)
Pages (from-to)179-187
Number of pages9
JournalGenome Research
Volume14
Issue number1
DOIs
StatePublished - Jan 2004
Externally publishedYes

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Bacterial Artificial Chromosomes
Comparative Genomic Hybridization
Neoplasm Genes
Clone Cells
Genetic Association Studies
Human Artificial Chromosomes
Software
Genome
Technology
DNA
Neoplasms

ASJC Scopus subject areas

  • Genetics

Cite this

1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. / Greshock, Joel; Naylor, Tara L.; Margolin, Adam; Diskin, Sharon; Cleaver, Stephen H.; Futreal, P. Andrew; deJong, Pieter J.; Zhao, Shaying; Liebman, Michael; Weber, Barbara L.

In: Genome Research, Vol. 14, No. 1, 01.2004, p. 179-187.

Research output: Contribution to journalArticle

Greshock, J, Naylor, TL, Margolin, A, Diskin, S, Cleaver, SH, Futreal, PA, deJong, PJ, Zhao, S, Liebman, M & Weber, BL 2004, '1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis', Genome Research, vol. 14, no. 1, pp. 179-187. https://doi.org/10.1101/gr.1847304
Greshock, Joel ; Naylor, Tara L. ; Margolin, Adam ; Diskin, Sharon ; Cleaver, Stephen H. ; Futreal, P. Andrew ; deJong, Pieter J. ; Zhao, Shaying ; Liebman, Michael ; Weber, Barbara L. / 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. In: Genome Research. 2004 ; Vol. 14, No. 1. pp. 179-187.
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