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1-Mb Resolution Array-Based Comparative Genomic Hybridization Using a BAC Clone Set Optimized for Cancer Gene Analysis

¹ Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA ² Georgia State University, Atlanta, Georgia 30303, USA ³ Wellcome Trust Sanger Institute, Hinxton CB10 15A, UK ⁴ Children's Hospital Oakland-BACPAC Resources, Oakland, California 94609, USA ⁵ The Institute for Genomic Research, Rockville, Maryland 20850, USA

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 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.

⁶ Corresponding author.
E-MAIL weberb{at}mail.med.upenn.edu; FAX (215) 662-7617.

[Supplemental material is available online at www.genome.org.]

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