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

Nature Genetics volume 23, pages 41–46 (1999)Cite this article

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 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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Figure 1: cDNA microarray analysis of DNA copy-number changes.
Figure 2: Measuring X-chromosomal DNA copy-number variation.
Figure 3: Genome-wide mapping of DNA copy-number variation for breast cancer cell line BT474.
Figure 4: High-resolution analysis of recurrent amplicons in breast cancer.
Figure 5: Parallel analysis of DNA copy number and gene expression.

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References

  1. Kallioniemi, A. et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258, 818–821 (1992).

    Article  CAS  Google Scholar 

  2. Solinas-Toldo, S. et al. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20, 399–407 (1997).

    Article  CAS  Google Scholar 

  3. Pinkel, D. et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genet. 20, 207–211 (1998).

    Article  CAS  Google Scholar 

  4. Geschwind, D.H. et al. Klinefelter's syndrome as a model of anomalous cerebral laterality: testing gene dosage in the X chromosome pseudoautosomal region using a DNA microarray. Dev. Genet. 23, 215–229 (1998).

    Article  CAS  Google Scholar 

  5. Schuler, G.D. et al. A gene map of the human genome. Science 274, 540–546 (1996).

    Article  CAS  Google Scholar 

  6. Deloukas, P. et al. A physical map of 30,000 human genes. Science 282, 744–746 (1998).

    Article  CAS  Google Scholar 

  7. Schena, M., Shalon, D., Davis, R.W. & Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470 (1995).

    Article  CAS  Google Scholar 

  8. DeRisi, J. et al. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nature Genet. 14, 457–460 (1996).

    Article  CAS  Google Scholar 

  9. Iyer, V. et al. The transcriptional program in the response of human fibroblasts to serum. Science 283, 83–87 (1999).

    Article  CAS  Google Scholar 

  10. Kallioniemi, O.P. et al. ERBB2 amplification in breast cancer analyzed by fluorescence in situ hybridization. Proc. Natl Acad. Sci. USA 89, 5321–5325 (1992).

    Article  CAS  Google Scholar 

  11. Lucito, R. et al. Genetic analysis using genomic representations. Proc. Natl Acad. Sci. USA 95, 4487–4492 (1998).

    Article  CAS  Google Scholar 

  12. Gyapay, G. et al. A radiation hybrid map of the human genome. Hum. Mol. Genet. 5, 339–346 (1996).

    Article  CAS  Google Scholar 

  13. Kallioniemi A. et al. Detection and mapping of amplified DNA sequences in breast cancer by comparative genomic hybridization. Proc. Natl Acad. Sci. USA 91, 2156–2160 (1994).

    Article  CAS  Google Scholar 

  14. Gelmini, S. et al. Quantitative polymerase chain reaction-based homogeneous assay with fluorogenic probes to measure c-erbB-2 oncogene amplification. Clin. Chem. 43, 752–758 (1997).

    CAS  Google Scholar 

  15. Barlund, M. et al. Increased copy number at 17q22–q24 by CGH in breast cancer is due to high-level amplification of two separate regions. Genes Chromosomes Cancer 20, 372–376 (1997).

    Article  CAS  Google Scholar 

  16. Kallioniemi, O.P. et al. Optimizing comparative genomic hybridization for analysis of DNA sequence copy number changes in solid tumors. Genes Chromosomes Cancer 10, 231–243 (1994).

    Article  CAS  Google Scholar 

  17. Stein, D. et al. The SH2 domain protein GRB-7 is co-amplified, overexpressed and in a tight complex with HER2 in breast cancer. EMBO J. 13, 1331–1340 (1994).

    Article  CAS  Google Scholar 

  18. Tomasetto C. et al. Identification of four novel human genes amplified and overexpressed in breast carcinoma and localized to the q11–q21.3 region of chromosome 17. Genomics 28, 367–376 (1995).

    Article  CAS  Google Scholar 

  19. Guan, X.Y. et al. Hybrid selection of transcribed sequences from microdissected DNA: isolation of genes within amplified region at 20q11–q13.2 in breast cancer. Cancer Res. 56, 3446–3450 (1996).

    CAS  PubMed  Google Scholar 

  20. Anzick, S.L. et al. AIB1, a steroid receptor coactivator amplified in breast and ovarian cancer. Science 277, 965–968 (1997).

    Article  CAS  Google Scholar 

  21. Williamson, J.A. et al. Chromosomal mapping of the human and mouse homologues of two new members of the AP-2 family of transcription factors. Genomics 35, 262–264 (1996).

    Article  CAS  Google Scholar 

  22. Sen, S., Zhou, H. & White, R.A. A putative serine/threonine kinase encoding gene BTAK on chromosome 20q13 is amplified and overexpressed in human breast cancer cell lines. Oncogene 14, 2195–2200 (1997).

    Article  CAS  Google Scholar 

  23. Shalon, D., Smith, S.J. & Brown, P.O. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6, 639–645 (1996).

    Article  CAS  Google Scholar 

  24. DeRisi, J.L., Iyer, V.R. & Brown, P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680–686 (1997).

    Article  CAS  Google Scholar 

  25. Lennon, G., Auffray, C., Polymeropoulos, M. & Soares, M.B. The I.M.A.G.E. Consortium: an integrated molecular analysis of genomes and their expression. Genomics 33, 151–152 (1996).

    Article  CAS  Google Scholar 

  26. Boguski, M.S. & Schuler, G.D. ESTablishing a human transcript map. Nature Genet. 10, 369–371 (1995).

    Article  CAS  Google Scholar 

  27. Schuler, G.D. Pieces of the puzzle: expressed sequence tags and the catalog of human genes. J. Mol. Med. 75, 694–698 (1997).

    Article  CAS  Google Scholar 

  28. Alitalo, K., Schwab, M., Lin, C.C., Varmus, H.E. & Bishop, J.M. Homogeneously staining chromosomal regions contain amplified copies of an abundantly expressed cellular oncogene (c-myc) in malignant neuroendocrine cells from a human colon carcinoma. Proc. Natl Acad. Sci. USA 80, 1707–1711 (1983).

    Article  CAS  Google Scholar 

  29. Takahashi, T. et al. p53: a frequent target for genetic abnormalities in lung cancer. Science 246, 491–494 (1989).

    Article  CAS  Google Scholar 

  30. Saxena, R. et al. The DAZ gene cluster on the human Y chromosome arose from an autosomal gene that was transposed, repeatedly amplified and pruned. Nature Genet. 14, 292–299 (1996).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank K. Ranade for assistance with quantitative PCR analysis; R. Sutton, C. Rees and members of the Brown and Botstein Labs for helpful discussions; and J. Doda for human mitochondrial DNA. This work was supported by grants from the National Cancer Institute, the National Human Genome Research Institute and the Howard Hughes Medical Institute. J.R.P. is a Physician Postdoctoral Fellow and P.O.B. is an Associate Investigator of the Howard Hughes Medical Institute. C.M.P. is a SmithKline Beecham Pharmaceuticals Fellow of the Life Sciences Research Foundation. M.B.E. is supported by a postdoctoral fellowship from the Alfred E. Sloan Foundation.

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Authors and Affiliations

  1. Howard Hughes Medical Institute, Stanford Medical Center, Stanford, 94305, California, USA

    Jonathan R. Pollack & Patrick O. Brown

  2. Department of Genetics, Stanford Medical Center, Stanford, 94305, California, USA

    Charles M. Perou, Michael B. Eisen, Alexander Pergamenschikov, Cheryl F. Williams & David Botstein

  3. Department of Biochemistry, Stanford Medical Center, Stanford, 94305, California, USA

    Ash A. Alizadeh & Patrick O. Brown

  4. Department of Surgery, Stanford Medical Center, Stanford, 94305, California, USA

    Stefanie S. Jeffrey

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Correspondence to Patrick O. Brown.

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Pollack, J., Perou, C., Alizadeh, A. et al. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 23, 41–46 (1999). https://doi.org/10.1038/12640

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