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Open Access Genome database

SNPTrackTM : an integrated bioinformatics system for genetic association studies

Joshua Xu1, Reagan Kelly1, Guangxu Zhou1, Steven A Turner1, Don Ding1, Stephen C Harris2, Huixiao Hong2, Hong Fang1* and Weida Tong2*

Author Affiliations

1 ICF International at NCTR, 3900 NCTR Rd, Jefferson, AR, 72079, USA

2 Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA

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Human Genomics 2012, 6:5  doi:10.1186/1479-7364-6-5

Published: 5 July 2012

Abstract

A genetic association study is a complicated process that involves collecting phenotypic data, generating genotypic data, analyzing associations between genotypic and phenotypic data, and interpreting genetic biomarkers identified. SNPTrack is an integrated bioinformatics system developed by the US Food and Drug Administration (FDA) to support the review and analysis of pharmacogenetics data resulting from FDA research or submitted by sponsors. The system integrates data management, analysis, and interpretation in a single platform for genetic association studies. Specifically, it stores genotyping data and single-nucleotide polymorphism (SNP) annotations along with study design data in an Oracle database. It also integrates popular genetic analysis tools, such as PLINK and Haploview. SNPTrack provides genetic analysis capabilities and captures analysis results in its database as SNP lists that can be cross-linked for biological interpretation to gene/protein annotations, Gene Ontology, and pathway analysis data. With SNPTrack, users can do the entire stream of bioinformatics jobs for genetic association studies. SNPTrack is freely available to the public at http://www.fda.gov/ScienceResearch/BioinformaticsTools/SNPTrack/default.htm webcite.