Genome wide in silico SNP-tumor association analysis

An in silico SNP-tumor association study was performed utilizing tissue library and SNP information available in NCBI's dbEST (release 092002) and dbSNP (build 106).A total of 4865 SNPs were identified which were present at higher allele frequencies in tumor compared to normal tissues. A subset of 327 (6.7%) SNPs induce amino acid changes to the protein coding sequences. This approach identified several SNPs which have been previously associated with carcinogenesis, as well as a number of SNPs that now warrant further investigationThis novel in silico approach can assist in prioritization of genes and SNPs in the effort to elucidate the genetic mechanisms underlying the development of cancer.Expressed Sequence Tags (ESTs) are single-pass, partial sequences of cDNA clones derived from a vast number of disease and normal tissues [1]. ESTs have been used extensively for gene discovery and transcript mapping of genes from a wide number of organisms, including human and mouse [1,2]. ESTs have also been used for SNP identification [3-5], gene expression analysis and transcriptome analysis [6,7]. Currently there are more than 4 millions human ESTs in GenBank dbEST database and the number is still growing.Susceptibility to common, complex diseases is in part genetically determined [8-11], although the genetic contribution might vary greatly depending on the diseases. Single nucleotide polymorphisms (SNPs) are the most common genetic variation in the human genome, and the number of SNPs identified experimentally is growing tremendously. Currently, dbSNP (build 106) contains more than 2.7 million unique SNPs. These data provides a vital resource to study the role of specific sequence alterations on disease susceptibility as well as drug resistance/sensitivity. In recent years SNPs have been favored as more tractable genotypic markers [12]. As genetic markers, SNPs have several advantages over microsatellites sequence repeats, including abundance (one every 750–1000 bp) [13],