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GLIDERS--a web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs.
Robert Lawrence1, Aaron G Day-Williams, Richard Mott
1Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. z.r.yang@ex.ac.uk
BMC Bioinformatics
|November 3, 2009
Summary
Researchers developed GLIDERS, a web tool for exploring long-range linkage disequilibrium (LD) patterns across the human genome. This tool helps identify SNP associations and potential mapping issues, improving genetic studies.
Area of Science:
- Genetics
- Bioinformatics
Background:
- Existing tools for examining linkage disequilibrium (LD) patterns primarily focus on nearby alleles.
- There is a lack of accessible tools for investigating LD at longer ranges (>500 kb).
Purpose of the Study:
- To develop a web-based query tool, GLIDERS (Genome-wide LInkage DisEquilibrium Repository and Search engine), for investigating long-range LD patterns.
- To enable retrieval of pairwise associations across the human genome for any SNP genotyped within HapMap phase 2 and 3, irrespective of marker distance.
Main Methods:
- GLIDERS is a user-friendly web tool accepting manual SNP ID entry or file uploads.
- Users can define parameters such as minor allele frequency (MAF), distance limits, r2 values, HapMap populations, and build/release.
- Results are displayed on a single output page with an option for downloadable tab-delimited text files.
Main Results:
- GLIDERS facilitates the retrieval of genome-wide inter-SNP associations.
- The tool enables exploration of LD patterns for numerous SNPs, including those at longer distances.
Conclusions:
- GLIDERS provides a rapid and straightforward method for obtaining genome-wide inter-SNP associations.
- The tool aids in identifying SNPs with long-range LD, potentially highlighting mis-mapping or association signal localization issues.
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