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

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/

Fig. 1.

Workflow of SNP selection process.

Fig. 2.

Display LD Bins and selected SNPs as customer tracks in UCSC Genome Browser. (a): The hyper link — “DAS Link” in SNP report Excel spreadsheet. (b): LD bins and selected SNPs are displayed as customer tracks in UCSC genome browser. LD bins have two tracks — the “red” track shows LD bins with multiple SNPs in one bin, the “pink” tracks shows LD bins with a single SNP in one bin. Selected SNPs are displayed in “blue” track under tracks of LD bins.

Fig. 3.

The distribution of selected SNPs and total SNPs in different functional categories.