Genome-wide analysis of DNA copy-number changes using cDNA microarrays

Gene amplifications and deletions frequently contribute to tumorigenesis. C haracterization of these DNA copy-number changes is important for both the basic understanding of cancer and its diagnosis. Comparative genomic hybrid ization (CGH) was developed to survey DNA copy-number variations across a w hole genome(1). With CCH, differentially labelled test and reference genomi c DNAs are co-hybridized to normal metaphase chromosomes, and fluorescence ratios along the length of chromosomes provide a cytogenetic representation of DNA copy-number variation. CCH, however, has a limited (similar to 20 M b) mapping resolution, and higher-resolution techniques, such as fluorescen ce in situ hybridization (FISH), are prohibitively labour-intensive on a ge nomic scale. Array-based CCH, in which fluorescence ratios at arrayed DNA e lements provide a locus-by-locus measure of DNA copy-number variation, repr esents another means of achieving increased mapping resolution(2-4) Publish ed array CGH methods have relied on large genomic clone (for example BAC) a rray targets and have covered only a small fraction of the human genome. cD NAs representing over 30,000 radiation-hybrid (RH)-mapped human genes(5,6) provide an alternative and readily available genomic resource for mapping D NA copy-number changes. Although cDNA microarrays have been used extensivel y to characterize variation in human gene expression(7-9), human genomic DN A is a far more complex mixture than the mRNA representation of human cells . Therefore, analysis of DNA copy-number variation using cDNA microarrays w ould require a sensitivity of detection an order of magnitude greater than has been routinely reported(7). We describe here a cDNA microarray-based CG H method, and its application to DNA copy-number variation analysis in brea st cancer cell lines and tumours, Using this assay, we were able to identif y gene amplifications and deletions genome-wide and with high resolution, a nd compare alterations in DNA copy number and gene expression.