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Bioinformatics Advance Access published online on September 22, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti682
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received September 8, 2005
Accepted September 18, 2005

Article

SNPselector: a web tool for selecting SNPs for genetic association studies

Hong Xu 1*, Simon G. Gregory 1, Elizabeth R. Hauser 1, Judith E. Stenger 1, Margaret A. Pericak-Vance 1, Jeffery M. Vance 1, Stephan Züchner 1, and Michael A. Hauser 1

1 The Duke Center for Human Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA

* To whom correspondence should be addressed.
Hong Xu, E-mail: hong.xu{at}duke.edu


  Abstract

Summary: 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.

Availability: SNPselector is freely available at http://primer.duhs.duke.edu/.


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