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PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping
Lucía Conde1, Juan M Vaquerizas, Carles Ferrer-Costa
1Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain.
Nucleic Acids Research
|June 28, 2005
Summary
PupasView is a new web tool that helps researchers select single nucleotide polymorphisms (SNPs) with potential phenotypic effects. It integrates functional and population data to identify SNPs for genotyping, aiding in multifactorial disorder studies.
Area of Science:
- Genetics
- Bioinformatics
- Computational Biology
Background:
- Single nucleotide polymorphisms (SNPs) are crucial in understanding genetic variations and their impact on phenotypes.
- Identifying functional SNPs is essential for genetic association studies, particularly for complex multifactorial disorders.
- Existing tools often lack comprehensive integration of functional and population data for SNP selection.
Purpose of the Study:
- To develop and present PupasView, a novel web tool for selecting single nucleotide polymorphisms (SNPs) with potential phenotypic effects.
- To provide an interactive environment integrating functional information and population frequency data for SNP selection.
- To offer a resource that considers both translational and transcriptional levels of SNP-mediated phenotypic effects.
Main Methods:
- PupasView utilizes sequential filtering of functional information and population frequency data over linkage disequilibrium parameters.
- The tool incorporates data on SNPs affecting conserved gene processing regions (intron/exon boundaries, exonic splicing enhancers).
- It retrieves SNPs impacting predicted transcription factor binding sites and amino acid changes with calculated pathological effects, using Ensembl genome mapping.
Main Results:
- PupasView is the first resource to integrate phenotypic effects of SNPs at both translational and transcriptional levels.
- The tool provides a curated list of SNPs optimal for genotyping based on integrated functional and population data.
- It identifies SNPs potentially affecting gene function, protein structure, and regulatory elements.
Conclusions:
- PupasView facilitates the selection of functional SNPs, enhancing the sensitivity of gene identification in multifactorial disorder studies.
- The web tool offers a valuable resource for researchers investigating the genetic basis of complex diseases.
- By integrating diverse data types, PupasView streamlines the process of identifying disease-associated SNPs.