Abstract
The technique of representational difference analysis (RDA) allows the selective amplification of DNA fragments that differ greatly in abundance between two samples. The method was originally developed by Lisitsyn and co-workers for detecting differences between complex genomes (1), and has been used to identify genomic deletions (including putative tumor suppressor genes), genomic amplifications, genetic polymorphisms, and viral insertions (2). RDA was later adapted for application to cDNA by Hubank and Schatz (3), and like other techniques for the comparative analysis of gene expression, including microarray hybridization (4), differential display (5), and serial analysis of gene expression (6), RDA has been used to identify genes deregulated in cancers and cancer cell lines (7–9). Some major advantages of RDA relative to other approaches include the potential for identifying novel or rare transcripts that differ greatly in expression between two samples.
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References
Lisitsyn, N., Lisitsyn, N., and Wigler, M. (1993) Cloning the differences between two complex genomes. Science 259, 946–951.
Lisitsyn, N. A. (1995) Representational difference analysis: finding the differences between genomes. Trends Genet. 11, 303–307.
Hubank, M. and Schatz, D. G. (1994) Identifying differences in mRNA expression by representational difference analysis of cDNA. Nucleic Acids Res. 22, 5640–5648.
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.
Liang, P. and Pardee, A. B. (1995) Recent advances in differential display. Curr. Opin. Immunol. 7, 274–280.
Velculescu, V. E., Zhang, L., Vogelstein, B., and Kinzler, K. W. (1995) Serial analysis of gene expression. Science 270, 484–487.
Ismail, R. S., Baldwin, R. L., Fang, J., et al. (2000) Differential gene expression between normal and tumor-derived ovarian epithelial cells. Cancer Res. 60, 6744–6749.
Graveel, C. R., Jatkoe, T., Madore, S. J., Holt, A. L., and Farnham, P. J. (2001) Expression profiling and identification of novel genes in hepatocellular carcinomas. Oncogene 20, 2704–2712.
Welford, S. M., Gregg, J., Chen, E., et al. (1998) Detection of differentially expressed genes in primary tumor tissues using representational differences analysis coupled to microarray hybridization. Nucleic Acids Res. 26, 3059–3065.
Hubank, M. and Schatz, D. G. (1999) cDNA representational difference analysis: a sensitive and flexible method for identification of differentially expressed genes. Meth. Enzymol. 303, 325–349.
O’Neill, M. J. and Sinclair, A. H. (1997) Isolation of rare transcripts by representational difference analysis. Nucleic Acids Res. 25, 2681–2682.
Pastorian, K., Hawel, L., and Byus, C. V. (2000) Optimization of cDNA representational difference analysis for the identification of differentially expressed mRNAs. Anal. Biochem. 283, 89–98.
Geng, M., Wallrapp, C., Muller-Pillasch, F, Frohme, M., Hoheisel, J. D., and Gress, T. M. (1998) Isolation of differentially expressed genes by combining representational difference analysis (RDA) and cDNA library arrays. Biotechniques 25, 434–438.
Kim, S., Zeller, K., Dang, C. V., Sandgren, E. P., and Lee, L. A. (2001) A strategy to identify differentially expressed genes using representational difference analysis and cDNA arrays. Anal. Biochem. 288, 141–148.
Wallrapp, C., Muller-Pillasch, F., Micha, A., et al. (1999) Strategies for the detection of disease genes in pancreatic cancer. Ann. N.Y. Acad. Sci. 880, 122–146.
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Bugni, J.M., Drinkwater, N.R. (2003). Representational Difference Analysis of Gene Expression. In: El-Deiry, W.S. (eds) Tumor Suppressor Genes. Methods in Molecular Biology™, vol 222. Humana Press, Totowa, NJ. https://doi.org/10.1385/1-59259-328-3:385
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DOI: https://doi.org/10.1385/1-59259-328-3:385
Publisher Name: Humana Press, Totowa, NJ
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