• Jonathan R. Pollack
Part of the Methods in Molecular Biology™ book series (MIMB, volume 556)


DNA microarray technology has revolutionized biological research by enabling genome-scale explorations. This chapter provides an overview of DNA microarray technology and its application to characterizing the physical genome, with a focus on cancer genomes. Specific areas discussed include investigations of DNA copy number alteration (and loss of heterozygosity), DNA methylation, DNA–protein (i.e., chromatin and transcription factor) interactions, DNA replication, and the integration of diverse genome-scale data types. Also provided is a perspective on recent advances and future directions in characterizing the physical genome.

Key words

DNA microarray array CGH SNP array methylation array ChIP-chip 


  1. 1.
    Fodor, S. P., Rava, R. P., Huang, X. C., Pease, A. C., Holmes, C. P., and Adams, C. L. (1993) Multiplexed biochemical assays with biological chips. Nature 364, 555–556.PubMedCrossRefGoogle Scholar
  2. 2.
    Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470.PubMedCrossRefGoogle Scholar
  3. 3.
    Alizadeh, A. A., Eisen, M. B., Davis, R. E., Ma, C., Lossos, I. S., Rosenwald, A. et al. (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403, 503–511.PubMedCrossRefGoogle Scholar
  4. 4.
    Perou, C. M., Sorlie, T., Eisen, M. B., van de Rijn, M., Jeffrey, S. S., Rees, C. A., et al. (2000) Molecular portraits of human breast tumours. Nature 406, 747–752.PubMedCrossRefGoogle Scholar
  5. 5.
    van't Veer, L. J., Dai, H., van de Vijver, M. J., He, Y. D., Hart, A. A., Mao, M., et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530–536.CrossRefGoogle Scholar
  6. 6.
    Lengauer, C., Kinzler, K. W., and Vogelstein, B. (1998) Genetic instabilities in human cancers. Nature 396, 643–649.PubMedCrossRefGoogle Scholar
  7. 7.
    Shaffer, L. G., and Bejjani, B. A. (2006) Medical applications of array CGH and the transformation of clinical cytogenetics. Cytogenet Genome Res 115, 303–309.PubMedCrossRefGoogle Scholar
  8. 8.
    Pinkel, D., and Albertson, D. G. (2005) Comparative genomic hybridization. Annu Rev Genomics Hum Genet 6, 331–354.PubMedCrossRefGoogle Scholar
  9. 9.
    Herman, J. G., and Baylin, S. B. (2003) Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med 349, 2042–2054.PubMedCrossRefGoogle Scholar
  10. 10.
    Wold, B., and Myers, R. M. (2008) Sequence census methods for functional genomics. Nat Methods 5, 19–21.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Jonathan R. Pollack
    • 1
  1. 1.Department of PathologyStanford UniversityStanfordUSA

Personalised recommendations