title: Detection of gene amplification by genomic hybridization to cDNA microarrays.
abstract: Gene amplification is one of the major mechanisms of oncogene activation in tumorigenesis. To facilitate the identification of genes mapping to amplified regions, we have used a technique based on the hybridization of total genomic DNA to cDNA microarrays. To aid detection of the weak signals generated 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 detected by this approach. The technique was validated using cancer cell lines with several known gene amplifications, such as those affecting MYC, MYCN, ERBB2, 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 expression of ZNF133. Parallel analysis of genomic DNA for copy number and cDNA for expression now provides rapid approach to the identification of amplified genes and chromosomal regions in tumor cells.
authors.affiliation: Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesa, Maryland 20892, USA.
authors.forename: M A
authors.initials: MA
authors.lastname: Heiskanen
authors.forename: M L
authors.initials: ML
authors.lastname: Bittner
authors.forename: Y
authors.initials: Y
authors.lastname: Chen
authors.forename: J
authors.initials: J
authors.lastname: Khan
authors.forename: K E
authors.initials: KE
authors.lastname: Adler
authors.forename: J M
authors.initials: JM
authors.lastname: Trent
authors.forename: P S
authors.initials: PS
authors.lastname: Meltzer
mesh_terms: D051358:Cyclin-Dependent Kinase 4; D018844:Cyclin-Dependent Kinases / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics*; D005784:Gene Amplification; D018734:Genes, erbB-2; D016259:Genes, myc; D006801:Humans; D009693:Nucleic Acid Hybridization; D009857:Oncogenes; D011518:Proto-Oncogene Proteins; D014407:Tumor Cells, Cultured
chemical_list: D018076:DNA, Complementary; D011518:Proto-Oncogene Proteins; C495900:CDK4 protein, human; D051358:Cyclin-Dependent Kinase 4; D018844:Cyclin-Dependent Kinases