Universal Probe Reagents for Detection and Quantitation of RNA Splicing

The number of genes in the genome of higher organisms is relatively small; however, the protein complexity arising from these genes has been shown to be much higher. In part, this is due to alternative splice variants that are created during the processing of gene transcripts. The formation of gene splice variants has implications for human disease (for example, in cancer susceptibility) and also for medical diagnostics, drug development, and bioengineering. However, there are hundreds of thousands of exons for each higher organism, which imposes a technical problem of generating millions of exon-specific detection reagents. This project will advance gene splice variant detection and quantitation by utilizing a small library of a few thousand universal-probe reagents and universal-probe microarrays, sufficient to analyze any gene from any organism. In Phase I, efficient assay designs and analysis software were developed, and accurate exon detection was demonstrated on 11 genes. Accurate exon detection was also demonstrated on pools of 10 cDNA clones representing 10 distinct genes. Over 300 cDNA clones (~1Mb of DNA) from 6 human tissues were efficiently analyzed using this new splice variant analysis method. Phase II will develop fully functional prototypes and user-friendly protocols, and perform end-user-directed testing of: (1) pre-made probe pools for human genes; (2) on-demand probe pools for gene mixes and genes from other organisms; and (3) a universal set of labeled probe pools for multiplex detection of DNA clones or amplicons longer than 100 bp. The technical goal is to provide novel or improved chips, probe reagents, assay kits, and software, underlying all three products. Commercial Applications and other Benefits as described by the awardee: Pre-made or easy made-on-demand-labeled gene probe cocktails, combined with universal 6-mer microarrays, would have many research and diagnostic applications, including fundamental studies of gene expression control, organism development and evolution, understanding disease susceptibility and progression such as in cancer, drug development for gene expression control, and agricultural and industrial research. An additional benefit involves the isolation of rare and complex splice variants for protein expression, without an expensive long gene synthesis process