Detection of gene amplification by genomic hybridization to cDNA microarrays

Gene amplification is one of the major mechanisms of oncogene activation in tumorigenesis, To facilitate the identification of genes mapping to amplif ied regions, we have used a technique based on the hybridization of total g enomic DNA to cDNA microarrays, To aid detection of the weak signals genera ted in this complex hybridization, we have used a tyramide-based technique that allows amplification of a fluorescent signal up to 1000-fold. Dilution experiment suggests that amplifications of 5-fold and higher can be detect ed by this approach. The technique was validated using cancer cell lines wi th several known gene amplifications, such as those affecting MYC, MYCN, ER BB2, and CDK4, In addition to the detection of the known amplifications, we identified a novel amplified gene, ZNF133, in the neuroblastoma cell line NGP, Hybridization of NGP cDNA on an identical array also revealed over exp ression of ZNF133. parallel analysis of genomic DNA for copy number and cDN A for expression now provides rapid approach to the identification of ampli fied genes and chromosomal regions in tumor cells.