Open AccessSNPselector: a web tool for selecting SNPs for genetic association studies
Author(s) -
Hong Xu,
Simon G. Gregory,
Elizabeth R. Hauser,
Judith E. Stenger,
Margaret A. PericakVance,
Jeffery M. Vance,
Stephan Züchner,
Michael A. Hauser
Publication year - 2005
Publication title -
bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.599
H-Index - 390
eISSN - 1367-4811
pISSN - 1367-4803
DOI - 10.1093/bioinformatics/bti682
Subject(s) - single nucleotide polymorphism , ensembl , snp genotyping , linkage disequilibrium , snp , tag snp , computational biology , genotyping , genetic association , genetics , computer science , dbsnp , linkage (software) , biology , genomics , gene , genotype , genome
Single nucleotide polymorphisms (SNPs) are commonly used for association studies to find genes responsible for complex genetic diseases. With the recent advance of SNP technology, researchers are able to assay thousands of SNPs in a single experiment. But the process of manually choosing thousands of genotyping SNPs for tens or hundreds of genes is time consuming. We have developed a web-based program, SNPselector, to automate the process. SNPselector takes a list of gene names or a list of genomic regions as input and searches the Ensembl genes or genomic regions for available SNPs. It prioritizes these SNPs on their tagging for linkage disequilibrium, SNP allele frequencies and source, function, regulatory potential and repeat status. SNPselector outputs result in compressed Excel spreadsheet files for review by the user.
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