Software and Instrumentation to Identify Cancer Genes

Garner, Harold

Abstract

The ability to rapidly re-sequence a genomic region or to determine the differential expression profile of a large number of genes that are potentially implicated in cancer development will be extremely valuable for the cancer researcher. There is a tremendous amount of DNA sequence information being generated by the CGAP and human genome programs, more than can be effectively analyzed and then represented in contemporary 'chip' style re- sequencing or expression arrays. This severely limits the number of clinical samples that can be thoroughly inspected. We propose to construct dedicated arrays which have immediately reconfigurable gene sequences identified and designed by computer. This phased innovation award will answer the following questions: 1) Can the array design software, Digital Optical Chemistry (DOC) chip manufacturing device, the MAGNA/HIC readout device, and analysis/gene network software be constructed and ruggedized for routine analysis of cancer samples to differentiate cancer non-cancer cells and their progression by gene expression profiling and chip based resequencing? 2) Can the customizable arrays made possible by the DOC approach be continuously expanded and improved as new genomic data is amassed to generate chips dedicated to analysis of different cancer cell types? 3) Can candidate cDNA sequences (CGAP) and larger genomic regions identified by computer analysis such as Virtual Expression Array calculations be re-sequenced to identify informative gross variations down to SNPs in cancer patient populations to identify new oncogenes or tumor suppressor genes? The specific aims of this program are: 1) To develop bioinformatics tools for the identification and ellucidation of candidate cancer related genes including software for the design, readout and analysis of gene expression and re-sequencing arrays; 2) to develop and complete a Digital Optical Chemistry (DOC) array fabrication unit capable of synthesis of at least 100,000 custom oligonucleotide array members on a single chip with the capability of rapidly constructing chips with different arrays every 2 hours; 3) to develop and construct a custom DOC readout system by modifying/replicating an in-house developed hyperspectral imaging microscope; and 4) the integration of the entire system of software and hardware for the design, fabrication, and data analysis of DNA microarray chips and their subsequent testing on clinical samples relevant for cancer research. The testing of the integrated system for use in mutation detection, SNP discovery, allelotyping, and expression analysis will progress to use archival and prospectively collected cells from biopsies and fine needle aspirates that have been purified with the new laser capture microdissection system. This will integrate our system with current major technologies to produce a tool that should be widely available in translational and clinical trials cancer research.