GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis.

Published

Journal Article

Genome-wide association studies are beginning to elucidate how our genetic differences contribute to susceptibility and severity of disease. While computational tools have previously been developed to support various aspects of genome-wide association studies, there is currently a need for informatics solutions that facilitate the integration of data from multiple sources.Here we present GWAS Analyzer, a database driven web-based tool that integrates genotype and phenotype data, association analysis results and genomic annotations from multiple public resources. GWAS Analyzer contains features for browsing these interrelated data, exploring phenotypic values by family or genotype, and filtering association results based on multiple criteria. The utility of the tool has been demonstrated by a genome-wide association study of human in vitro susceptibility to bacterial infection. GWAS Analyzer facilitated management of large sets of phenotype and genotype data, analysis of phenotypic variation and heritability, and most importantly, generation of a refined set of candidate single nucleotide polymorphisms (SNPs). The tool revealed a SNP that was experimentally validated to be associated with increased cell death among Salmonella infected HapMap cell lines.

Full Text

Duke Authors

Cited Authors

  • Fong, C; Ko, DC; Wasnick, M; Radey, M; Miller, SI; Brittnacher, M

Published Date

  • February 2010

Published In

Volume / Issue

  • 26 / 4

Start / End Page

  • 560 - 564

PubMed ID

  • 20053839

Pubmed Central ID

  • 20053839

Electronic International Standard Serial Number (EISSN)

  • 1367-4811

International Standard Serial Number (ISSN)

  • 1367-4803

Digital Object Identifier (DOI)

  • 10.1093/bioinformatics/btp714

Language

  • eng