FastSNP

FastSNP prioritizes single nucleotide polymorphisms (SNPs) by assessing phenotypic risk and predicted functional effects to support association studies and identification of functional variants.

Key Features:

• Phenotypic Risk-Based Prioritization: Prioritizes SNPs by evaluating phenotypic risks and predicted functional effects for use in association studies.
• Integration of Heterogeneous Biological Databases: Aggregates annotations by accessing data from 11 external web servers.
• Real-Time Data Extraction: Extracts functional effect information in real time at query time using web wrapper agents.
• Extendability: Supports deployment of additional web wrapper agents to incorporate new data sources.
• Validation through Empirical Analysis: Validated using 1569 SNPs from the SNP500Cancer database, showing that SNPs with high predicted risks tend to have low minor allele frequencies.
• Discovery of Promoter Polymorphisms: Facilitated discovery of novel promoter polymorphisms over a two-year period of use.

Scientific Applications:

• Association studies: Prioritizes candidate SNPs to link genetic variation with specific traits or diseases.
• Genomics and personalized medicine: Narrows candidate variants for disease prediction, prevention, and treatment.
• Functional variant identification: Identifies SNPs with putative functional effects for experimental follow-up.

Methodology:

Performs real-time data extraction from multiple external databases via web wrapper agents, integrates annotations from 11 external web servers, and prioritizes SNPs by evaluating phenotypic risk and predicted functional effects; validation compared predicted risks to minor allele frequencies using 1569 SNPs from the SNP500Cancer database.