Automated fluorescent differential display for cancer gene profiling

• Published in: Methods in molecular biology (Clifton, N.J.) Vol. 576; p. 99
• Main Authors: Meade, Jonathan D, Cho, Yong-jig, Shester, Blake R, Walden, Jamie C, Guo, Zhen, Liang, Peng
• Format: Journal Article
• Language: English
• Published: United States 01.01.2010
• Subjects: Automation; Cloning, Molecular; DNA, Complementary - metabolism; Electrophoresis, Capillary; Fluorescence; Fluorescent Dyes - pharmacology; Gene Expression Profiling - methods; Gene Expression Regulation, Neoplastic; Genes, p53; Humans; Molecular Biology - methods; Neoplasms - metabolism; Polymerase Chain Reaction
• ISSN: 1940-6029
• DOI: 10.1007/978-1-59745-545-9_7

Since its invention in 1992, differential display (DD) has become the most commonly used technique for identifying differentially expressed genes because of its many advantages over competing technologies such as DNA microarray, serial analysis of gene expression (SAGE), and subtractive hybridization. A large number of these publications have been in the field of cancer, specifically on p53 target genes. Despite the great impact of the method on biomedical research, there had been a lack of automation of DD technology to increase its throughput and accuracy for systematic gene expression analysis. Many previous DD work has taken a "shotgun" approach of identifying one gene at a time, with a limited number of polymerase chain reactions (PCRs) set up manually, giving DD a low-tech and low-throughput image. We have optimized the DD process with a platform that incorporates fluorescent digital readout, automated liquid handling, and large-format gels capable of running entire 96-well plates. The resulting streamlined fluorescent DD (FDD) technology offers an unprecedented accuracy, sensitivity, and throughput in comprehensive and quantitative analysis of gene expression. These major improvements will allow researchers to find differentially expressed genes of interest, both known and novel, quickly and easily.