Monday, 23 May 2005 - 11:20 AM

This presentation is part of: Bioinformatics

Identification of tumor associated SNPs based on EST analysis

Wei Ding1, Mitch Kostich2, Luquan Wang3, Ping Qiu1, Jonathan Greene1, and Marco Hernandez1. (1) Schering-Plough Research Institute, Kenilworth, NJ, (2) Environmental Protection Agency, Cincinnati, OH, (3) GenScript Corporate, Piscataway, NJ

Carcinogenesis occurs, at least in part, due to the accumulation of mutations in critical genes that control the mechanisms of cell proliferation, differentiation and death. Expressed Sequence Tags (ESTs) are derived from cDNA libraries generated from a vast number of normal and disease tissues. By statistical analysis of human ESTs, we detected 176,207 candidate Single Nucleotide Polymorphisms (SNPs). We manually curated and catalogued EST cDNA tissue libraries into non-tumor libraries and tumor libraries and examined the association between individual SNPs and tumor tissues. A total of 5152 SNPs were identified which were present at higher allele frequencies in tumor compared to normal tissues. A subset of 1955 (37.9%) SNPs induce amino acid changes to the protein coding sequences. This approach identified many SNPs which have been previously associated with carcinogenesis, as well as a number of SNPs that now warrant further investigation. This genome-wide in silico approach can assist in detection of tumor associated SNPs and help to elucidate the genetic mechanisms underlying the development of cancer

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