CORE--GENE DISCOVERY BIOINFORMATICS

DESCRIPTION (provided by applicant): The Gene Discovery/Bioinformatics Core (GDBC) of this Specialized Program of Research Excellence (SPORE) provides a program to analyze public and private genomic data related to prostate and to supply leads to the other SPORE projects of interesting genes that would be utilized to accomplish their goals as well as to facilitate discovery of novel prostate genes that would be useful for diagnosis or therapy. With the human genome project close to completion, and sequence information pouring into databases from many other projects (e.g. CGAP) genomic data is becoming one of the most valuable resources for cancer projects. The GDBC aims to analyze and utilize this information in order to be a resource of interesting leads to genes for all the other SPORE projects. More specifically, the GDBC will analyze the Expressed Sequence Tags (ESTs) that derive from high quality cDNA libraries produced from normal and tumor prostate cells. This analysis, in conjunction with data from micro-array gene expression profiling, will provide diagnostic markers for Project x, and candidates for immune therapy and Gene therapy (Project y, z). Analysis of the sequences derived from the human genome project and in conjunction with data from cDNA libraries and expression profiling of micro-arrays can aid the Prognostic Marker Projects. This goal will be achieved by analyzing the information in the Expressed Sequence Tag (EST) database which contains more than two million partial sequences of cDNA clones from cDNA libraries extracted from different human organs or cell types. About 70,000 ESTs are derived from normal prostate, prostate cancer, and prostate cell-lines. By comparing these ESTs with each other using computer algorithms, we can group ESTs in clusters that correspond to distinct genes, estimate the level of expression of genes, and define their expression patterns in different tissues or cell types. Similarly, we will obtain differential expression levels of genes in cancer vs. normal prostate tissue. Such genes can be markers for diagnosis or predictors for the aggressiveness of the disease. We will also select clusters corresponding to genes that express in prostate but not in any essential tissues and can be used as targets for immunotherapy.