Abstract
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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
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.
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.
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.
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.
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.
Lengauer, C., Kinzler, K. W., and Vogelstein, B. (1998) Genetic instabilities in human cancers. Nature 396, 643–649.
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.
Pinkel, D., and Albertson, D. G. (2005) Comparative genomic hybridization. Annu Rev Genomics Hum Genet 6, 331–354.
Herman, J. G., and Baylin, S. B. (2003) Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med 349, 2042–2054.
Wold, B., and Myers, R. M. (2008) Sequence census methods for functional genomics. Nat Methods 5, 19–21.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Pollack, J.R. (2009). Introduction. In: Pollack, J. (eds) Microarray Analysis of the Physical Genome. Methods in Molecular Biology™, vol 556. Humana Press. https://doi.org/10.1007/978-1-60327-192-9_1
Download citation
DOI: https://doi.org/10.1007/978-1-60327-192-9_1
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-60327-191-2
Online ISBN: 978-1-60327-192-9
eBook Packages: Springer Protocols