Genome-wide analysis of genetic alterations in tumor cell lines by Ccap BAC microarray

Abstract

Recently, the first Ccap BAC microarray has been developed and printed by the NCI and the Cold Spring Harbor Laboratory. This array contains over 1,300 Ccap BAC clones and all of these BAC clones have been mapped by high-resolution fluorescence-in-situ-hybridization (FISH) to single sites on chromosomes. The Ccap BAC set is also physically mapped and can be localized by alignment of BAC end sequences to the finished HGP contig. Ccap BAC clones are localized at 12-Mb intervals across the entire genome. Information about those clones is available on a publicly accessible web site http://www.ncbi.nlm.nih.gov/CCAP BAC clones were amplified by DOP-PCR and printed onto glass slides. Using this Ccap BAC array, several tumor cell lines have been analyzed. The CGH microarray data have been validated by chromosomal CGH and SKY on the same cell lines. Copy number changes of small regions (microdeletions and duplications) were confirmed by interphase FISH. Our data demonstrated that Ccap BAC arrays were able to define copy number changes of whole chromosome or chromosome regions in cancer cell lines. The Ccap BAC array provides a valuable tool, which not only allows definition of a target area of gain or loss from cancer samples, but also leads seamlessly from a cytogenetic band to the primary DNA sequence allowing integration of molecular cytogenetics and genomics