FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization

Area of Science:

• Genetics
• Bioinformatics
• Computational Biology

Background:

• Prioritizing single nucleotide polymorphisms (SNPs) by phenotypic risk is essential for genetic association studies.
• Assessing SNP risk necessitates integrating data from diverse biological databases and analytical tools.

Purpose of the Study:

• To develop and present FASTSNP, a web server for efficient identification and prioritization of high-risk SNPs.
• To provide up-to-date functional effect information for SNP prioritization.

Main Methods:

• FASTSNP utilizes web wrapper agents to extract real-time functional effect data from 11 external web servers.
• The system is designed for extensibility through the addition of more web wrapper agents.
• Validation involved analyzing 1569 SNPs from the SNP500Cancer database.

Main Results:

• FASTSNP successfully prioritized SNPs based on phenotypic risk and putative functional effects.
• Validated results showed high-risk SNPs with low minor allele frequencies, consistent with selective pressure on functional polymorphisms.
• The tool facilitated the discovery of a novel promoter polymorphism.

Conclusions:

• FASTSNP offers an efficient and up-to-date solution for SNP prioritization in genetic association studies.
• The web server's dynamic data retrieval and extendable architecture enhance its utility.
• FASTSNP aids in identifying functionally significant SNPs and potential disease associations.