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Updated: Jul 18, 2026
05:01
A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
Published on: July 1, 2020
A tool for selecting SNPs for association studies based on observed linkage disequilibrium patterns.
Francisco M De La Vega1, Hadar I Isaac, Charles R Scafe
1Applied Biosystems, 850 Lincoln Centre Dr., Foster City, CA 94404, USA. delavefm@appliedbiosystems.com
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|November 11, 2006
Summary
SNPbrowser Software aids genetic association studies by selecting optimal single-nucleotide polymorphisms (SNPs) based on linkage disequilibrium (LD). This tool simplifies complex data integration for powerful and cost-effective study designs.
Area of Science:
- Genetics
- Bioinformatics
- Statistical Genetics
Background:
- Genetic association studies require strategic selection of single-nucleotide polymorphisms (SNPs) for statistical power and cost-efficiency.
- Maximizing the probability of linkage disequilibrium (LD) between causative mutations and genotyped markers is crucial for study success.
- Existing methods for SNP selection and data integration are complex and often require disparate database access.
Purpose of the Study:
- To present SNPbrowser Software, a tool designed to facilitate LD-based marker selection for genetic association studies.
- To provide a user-friendly application for integrating complex genetic data and annotations.
- To streamline the process of selecting optimal SNP subsets for genotyping platforms.
Main Methods:
- Development of a stand-alone software application, SNPbrowser.
- Implementation of algorithms for LD-based SNP selection, including haplotype tagging SNP identification.
- Integration of visualization tools for SNPs, gene annotations, power calculations, and LD maps.
- Inclusion of wizards for common SNP selection workflows and screening for genotyping assay compatibility.
Main Results:
- SNPbrowser offers fast query and visualization capabilities for genetic variation data.
- The software supports efficient selection of optimal SNP subsets, such as tagging SNPs.
- SNP screening for TaqMan or SNPlex genotyping platforms is integrated, expediting study setup.
Conclusions:
- SNPbrowser Software simplifies the complex process of designing genetic association studies.
- The tool enhances the probability of success in genetic studies by optimizing SNP selection and assay compatibility.
- Freely available SNPbrowser empowers researchers with efficient data analysis and visualization for genetic research.
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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