Comparative genomic hybridization (CGH) has been widely used for the analysis of copy number changes in tumors to identify genes involved in the development and pathogenesis of cancers. In conventional CGH, metaphase chromosomes are used as the target for hybridization (1). However, the resolution with which copy number changes can be detected using this technique is limited to approximately 3-5 Mb (2). By replacing the metaphase chromosomes with mapped sequences (typically from large insert clones such as BACs, PACs and cosmids), analysis resolution becomes dependent only on the insert size and the density of the clones used to construct the array.

For this purpose, the sequencing of the human genome has provided a valuable resource of mapped and sequenced clones. Due to the increased sensitivity and resolution compared to conventional CGH, array CGH is now not only being applied to the analysis of copy number alterations in tumors, but also to the identification of genomic imbalances (microdele-tions/microduplications) in patients with constitutional rearrangements and to rapidly map translocation breakpoints.

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