High throughput screening for splice variant cDNAs

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DESCRIPTION (provided by applicant): The catalog of human splice variant mRNAs is believed to be far from complete with many undiscovered isoforms likely to play an important role in health and disease. The current practice of hunting for splice variants by screening cDNA libraries 1 at a time is both time consuming and expensive. Higher throughput and more cost-effective methods of screening would be helpful in accelerating this important enterprise. The goal of this proposed work is to develop a consumable research tool that enables rapid and cost- effective screening for splice variant cDNAs. The Library Sampler will be comprised of 15 high-quality cDNA libraries representing 28 human cancer cell lines and 34 human tissues. To evaluate the utility of the Library Sampler, it will be screened by PCR for the known splice variants of 10 genes implicated in various cancers. It is expected that full-length clones representing 70-80% of known isoforms will be identified along with clones representing many novel isoforms. In Phase II, the Library Sampler will be optimized, product application data generated, and a large-scale manufacturing process developed. Relevance to public health: In October 2004 the International Human Genome Sequencing Consortium reduced the estimated number of human protein-coding genes to only 20,000-25,000 genes, a surprisingly low number for our species, suggesting that gene regulation is far more important than gene number. It is well known that most of our genes produce more than 1 protein by alternative splicing of the primary transcript of the gene but the indentification of all these isoforms is far from complete. The Library Sampler provides a powerful research tool to identify these splice isoforms from a broad range of normal tissues and cancer cell lines, and because many splice isoforms have been associated with human genetic diseases, their discovery offers new potentials for the development of clinical biomarkers and molecular diagnostic testing.