Project 1 of the CREATE Pharmacogenetic Research Network is focused on the identification of polymorphism in members of the pathways regulating drug activity. In this project, we propose to survey the 43 candidate genes fully, identifying DNA sequence variations from the promoters to the 3'-untranslated regions, encompassing all the exons plus the exon/intron boundaries. We will do so by the most cost effective and efficient approach developed by our group; namely, comparative pooled DNA sequencing of a moderate number of individuals (n=100). In addition, we will use a computational biology approach to evaluate the variants identified and predict which variants are most likely to be of functional importance. Specifically, we propose the following aims: 1: Design and validate PCR assays for the 5' regulatory region, exons, and 3' untranslated regions for 43 candidate genes. 2: Sequence and analyze all PCR fragment from pooled DNA samples 3: Deposit all variant to dbSNP. : Provide computational prediction of functional significance of variants found. 5: Develop an iterative algorithm for incorporation of biological data into prediction ov variant function. With these approaches, we will not only identify a comprehensive panel of gene-associated variants for the pharmacogenetic community, but also provide a framework to select the most promising variants (as predicted by computational approach) for analysis in the other project of this network.
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