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Genome-wide analysis of DNA copy number variation in breast cancer using DNA microarrays

Nature Genetics volume 23, page 69 (1999)Cite this article

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Gene amplifications and deletions frequently have pathogenetic roles in cancer. 30,000 radiation-hybrid mapped cDNAs provide a genomic resource to map these lesions with high resolution. We developed a cDNA microarray-based comparative genomic hybridisation method for analysing DNA copy number changes across thousands of genes simultaneously. Using this procedure, we could reliably detect DNA copy number alterations of twofold or less. In breast cancer cell lines, we have mapped regions of DNA copy number variation at high resolution, revealing previously unrecognised genomic amplifications and deletions, and new complexities of amplicon structure. Recurrent regions of DNA amplification, which may harbour novel oncogenes, were readily identified. Alterations of DNA copy number and gene expression could be compared and correlated in parallel analyses.

We have now collected genome-wide DNA copy number information on a set of 9 breast cancer cell lines and over 35 primary breast tumours. For the breast tumours, DNA copy number information is being compared and correlated with data already collected on p53 status, microarray gene expression profiles, and treatment response and clinical outcome. The results of this analysis will be presented.

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Authors and Affiliations

  1. Stanford Medical Center, Stanford, California, USA

    Jonathan R. Pollack, Charles M. Perou, Ash A. Alizadeh, Christian Rees, Michael B. Eise, Alexander Pergamenschikov, Cheryl F. Williams, Matt van de Rijn, Stefanie S. Jeffrey, David Botstein & Patrick O. Brown

  2. The Norwegian Radium Hospital, Motebello Oslo, Norway

    Therese Sorlie, Hilde Johnsen, Per E. Lonning, Stephanie Geisler, Turid Aas & Anne-Lise Borresen-Dale

  3. the Haukeland University Hospital, Bergen, Norway

    Therese Sorlie, Hilde Johnsen, Per E. Lonning, Stephanie Geisler, Turid Aas & Anne-Lise Borresen-Dale

Authors
  1. Jonathan R. Pollack
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  2. Charles M. Perou
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  3. Therese Sorlie
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  4. Ash A. Alizadeh
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  5. Christian Rees
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  6. Michael B. Eise
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  7. Alexander Pergamenschikov
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  8. Cheryl F. Williams
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  9. Matt van de Rijn
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  10. Stefanie S. Jeffrey
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  11. Hilde Johnsen
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  12. Per E. Lonning
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  13. Stephanie Geisler
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  14. Turid Aas
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  15. Anne-Lise Borresen-Dale
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  16. David Botstein
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  17. Patrick O. Brown
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Pollack, J., Perou, C., Sorlie, T. et al. Genome-wide analysis of DNA copy number variation in breast cancer using DNA microarrays. Nat Genet 23 (Suppl 3), 69 (1999). https://doi.org/10.1038/14385

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