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

BMC Bioinformatics. 2009 Oct 31;10:367. doi: 10.1186/1471-2105-10-367.

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 >or= 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Genetic
  • Genome*
  • Genome-Wide Association Study / methods*
  • Humans
  • Internet
  • Linkage Disequilibrium / genetics*
  • Polymorphism, Single Nucleotide*
  • Search Engine / methods*
  • Software*
  • User-Computer Interface