Representational Difference Analysis of Gene Expression

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.