RISK/TOX CHIP PROGRAM

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DESCRIPTION: (Applicant's abstract) We will develop the instrumentation, the techniques and the DNA microarray technology to enable very large scale analysis of inherited genetic variation, on as many as 50 genes at a time. We refer to such testing as population-wide "allele signature" analysis. Below we list the specific aims of the research plan. SA 1. We will optimize DNA microarray fabrication so that it can supply up to 1,000,000 microarrays per year for allele signature analysis. We focus our development and testing on a panel of approximately 100 alleles chosen with reference to their importance in chemical toxicology and environmental carcinogenesis of the lung. We refer to this as the "Risk-fox Chip." SA 2. We will develop procedures and automated workstations which can extract DNA and perform the requisite microarray hybridization, detection and data analysis on up 950,000 blood samples per year. The workstations will be based upon the use of a Beckman robot, coupled to a Sagian robot arm and will exploit recent advances made in the theory of nucleic acid extraction and highly multiplex DNA amplification. SA 3 & SA 4. First, traditional methods will be used to measure the genotype of a set of about 100 DNA samples from blood, for each of the 100 alleles on the Risk-Tox Chip. These standardized DNA samples will be then used to validate the performance of the Risk-tox Chip, and to test the approaches chosen for automated sample preparation, hybridization and detection. Secondly, the high throughput automation procedures and the quality of the DNA microarray product will be validated on a twenty-fold larger set of blood samples which will have been archived by the National Center for Toxicological Research and by M.D. Anderson Cancer Center. Special emphasis will be placed on development of the informatics required for organization of very large-scale blood and DNA sample archives and the mathematical methods required to evaluate the predictive power of an allele signature in the very large scale, population based applications which we envision.