Bioinformatics · 2008 · 1.4K citations · 8 references
Life SciencesBioinformaticsGeneticsGenomic Data AnalysisGenomicsStatistical GeneticsGene MappingGenetic Fine-mappingGenome-wide Association StudiesGenotype-phenotype Association AnalysisLinkage DisequilibriumVariant AnalysisFine-mapping Of Genetic AssociationsGenome-wide Association InterpretationGenome-wide Association MappingGenome-wide Association Study Fine-mappingLinkage Disequilibrium AnalysisLinkage Disequilibrium MappingLinkage Disequilibrium PatternsSingle-nucleotide Polymorphisms
The interpretation of genome‑wide association results is confounded by linkage disequilibrium between nearby alleles. We have developed a flexible bioinformatics query tool for SNPs to identify and annotate nearby SNPs in linkage disequilibrium (proxies) based on HapMap. The SNAP server provides flexible queries and graphical plots of proxy SNPs derived from HapMap, enabling users to visualize linkage disequilibrium patterns and delineate genomic regions for fine‑mapping. The tool successfully generates visualizations of proxy SNPs, aiding interpretation of GWAS results and guiding fine‑mapping experiment design. The SNAP server is available at http://www.broad.mit.edu/mpg/snap/ and can be contacted at debakker@broad.mit.edu.
Abstract Summary: The interpretation of genome-wide association results is confounded by linkage disequilibrium between nearby alleles. We have developed a flexible bioinformatics query tool for single-nucleotide polymorphisms (SNPs) to identify and to annotate nearby SNPs in linkage disequilibrium (proxies) based on HapMap. By offering functionality to generate graphical plots for these data, the SNAP server will facilitate interpretation and comparison of genome-wide association study results, and the design of fine-mapping experiments (by delineating genomic regions harboring associated variants and their proxies). Availability: SNAP server is available at http://www.broad.mit.edu/mpg/snap/. Contact: debakker@broad.mit.edu
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