GLIDERS - A web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs

doi:10.1186/1471-2105-10-367

BMC Bioinformatics

Volume 10

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Lawrence R
Day-Williams AG
Mott R
Broxholme J
Cardon LR
Zeggini E

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GLIDERS - A web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs

Robert Lawrence¹^,2 , Aaron G Day-Williams² , Richard Mott¹ , John Broxholme¹ , Lon R Cardon³^,4 and Eleftheria Zeggini¹^,2

¹Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK

²Wellcome Trust Sanger Institute, Hinxton, UK

³Fred Hutchinson Cancer Research Center, Seattle, Washington, USA

⁴GlaxoSmithKline, King of Prussia, Pennsylvania, USA

author email corresponding author email

BMC Bioinformatics 2009, 10:367doi:10.1186/1471-2105-10-367


Published:	31 October 2009

Abstract

Background

A number of tools for the examination of linkage disequilibrium (LD) patterns between nearby alleles exist, but none are available for quickly and easily investigating LD at longer ranges (>500 kb). We have developed a web-based query tool (GLIDERS: Genome-wide LInkage DisEquilibrium Repository and Search engine) that enables the retrieval of pairwise associations with r²≥ 0.3 across the human genome for any SNP genotyped within HapMap phase 2 and 3, regardless of distance between the markers.

Description

GLIDERS is an easy to use web tool that only requires the user to enter rs numbers of SNPs they want to retrieve genome-wide LD for (both nearby and long-range). The intuitive web interface handles both manual entry of SNP IDs as well as allowing users to upload files of SNP IDs. The user can limit the resulting inter SNP associations with easy to use menu options. These include MAF limit (5-45%), distance limits between SNPs (minimum and maximum), r²(0.3 to 1), HapMap population sample (CEU, YRI and JPT+CHB combined) and HapMap build/release. All resulting genome-wide inter-SNP associations are displayed on a single output page, which has a link to a downloadable tab delimited text file.

Conclusion

GLIDERS is a quick and easy way to retrieve genome-wide inter-SNP associations and to explore LD patterns for any number of SNPs of interest. GLIDERS can be useful in identifying SNPs with long-range LD. This can highlight mis-mapping or other potential association signal localisation problems.