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

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  • Pollack, Jonathan R.
    • Other Affiliation: Howard Hughes Medical Institute, Stanford, California 93405, USA
  • Perou, Charles M.
  • Alizadeh, Ash A.
    • Other Affiliation: Department of Biochemistry, Stanford Medical Center, Stanford, California 94305, USA
  • Eisen, Michael B.
    • Other Affiliation: Department of Genetics, Stanford Medical Center, Stanford, California 94305, USA
  • Pergamenschikov, Alexander
    • Other Affiliation: Department of Genetics, Stanford Medical Center, Stanford, California 94305, USA
  • Williams, Cheryl F.
    • Other Affiliation: Department of Genetics, Stanford Medical Center, Stanford, California 94305, USA
  • Jeffrey, Stefanie S.
    • Other Affiliation: Department of Surgery, Stanford Medical Center, Stanford, California 94305, USA
  • Botstein, David
    • Other Affiliation: Department of Genetics, Stanford Medical Center, Stanford, California 94305, USA
  • Brown, Patrick O.
    • Other Affiliation: Howard Hughes Medical Institute, and Department of Biochemistry, Stanford Medical Center, Stanford, California 94305, USA
Abstract
  • Gene 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 copynumber 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 resolution2–4. 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 expression7–9, 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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  • Article
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  • In Copyright
Journal title
  • Nature Genetics
Journal volume
  • 23
Journal issue
  • 1
Page start
  • 41
Page end
  • 46
Language
  • English
Version
  • Postprint
ISSN
  • 1061-4036

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