Nature Genetics
23, 41 - 46 (1999)
doi:10.1038/12640
Genome-wide analysis of DNA copy-number changes using cDNA microarraysJonathan R. Pollack1, Charles M. Perou2, Ash A. Alizadeh3, Michael B. Eisen2, Alexander Pergamenschikov2, Cheryl F. Williams2, Stefanie S. Jeffrey4, David Botstein2
& Patrick O. Brown1, 31
Howard Hughes Medical Institute, Stanford Medical Center, Stanford, California 94305, USA. 2
Department of Genetics, Stanford Medical Center, Stanford, California 94305, USA. 3
Department of Biochemistry, Stanford Medical Center, Stanford, California 94305, USA. 4
Department of Surgery, Stanford Medical Center, Stanford, California 94305, USA.
Correspondence should be addressed to Patrick O. Brown pbrown@cmgm.stanford.eduGene amplifications and deletions frequently contribute to tumorigenesis. Characterization of these DNA copy-number changes is important for both the basic understanding of cancer and its diagnosis. Comparative genomic hybridization (CGH) was developed to survey DNA copy-number variations across a whole genome1. With CGH, differentially labelled test and reference genomic 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. CGH, however, has a limited (~20 Mb) mapping resolution, and higher-resolution techniques, such as fluorescence in situ hybridization (FISH), are prohibitively labour-intensive on a genomic scale. Array-based CGH, in which fluorescence ratios at arrayed DNA elements provide a locus-by-locus measure of DNA copy-number variation, represents another means of achieving increased mapping resolution2,
3,
4. Published array CGH methods have relied on large genomic clone (for example BAC) array targets and have covered only a small fraction of the human genome. cDNAs representing over 30,000 radiation-hybrid (RH)−mapped human genes5,
6 provide an alternative and readily available genomic resource for mapping DNA copy-number changes. Although cDNA microarrays have been used extensively to characterize variation in human gene expression7,
8,
9, human genomic DNA is a far more complex mixture than the mRNA representation of human cells. Therefore, analysis of DNA copy-number variation using cDNA microarrays would require a sensitivity of detection an order of magnitude greater than has been routinely reported7. We describe here a cDNA microarray-based CGH method, and its application to DNA copy-number variation analysis in breast cancer cell lines and tumours. Using this assay, we were able to identify gene amplifications and deletions genome-wide and with high resolution, and compare alterations in DNA copy number and gene expression.
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