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

Publication ,  Journal Article
Fong, C; Ko, DC; Wasnick, M; Radey, M; Miller, SI; Brittnacher, M
Published in: Bioinformatics
February 15, 2010

MOTIVATION: 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. RESULTS: 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.

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Published In

Bioinformatics

DOI

EISSN

1367-4811

Publication Date

February 15, 2010

Volume

26

Issue

4

Start / End Page

560 / 564

Location

England

Related Subject Headings

  • Software
  • Polymorphism, Single Nucleotide
  • Phenotype
  • Genotype
  • Genome-Wide Association Study
  • Genome
  • Databases, Genetic
  • Computational Biology
  • Bioinformatics
  • 49 Mathematical sciences
 

Citation

APA
Chicago
ICMJE
MLA
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Fong, C., Ko, D. C., Wasnick, M., Radey, M., Miller, S. I., & Brittnacher, M. (2010). GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis. Bioinformatics, 26(4), 560–564. https://doi.org/10.1093/bioinformatics/btp714
Fong, Christine, Dennis C. Ko, Michael Wasnick, Matthew Radey, Samuel I. Miller, and Mitchell Brittnacher. “GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis.Bioinformatics 26, no. 4 (February 15, 2010): 560–64. https://doi.org/10.1093/bioinformatics/btp714.
Fong C, Ko DC, Wasnick M, Radey M, Miller SI, Brittnacher M. GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis. Bioinformatics. 2010 Feb 15;26(4):560–4.
Fong, Christine, et al. “GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis.Bioinformatics, vol. 26, no. 4, Feb. 2010, pp. 560–64. Pubmed, doi:10.1093/bioinformatics/btp714.
Fong C, Ko DC, Wasnick M, Radey M, Miller SI, Brittnacher M. GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis. Bioinformatics. 2010 Feb 15;26(4):560–564.

Published In

Bioinformatics

DOI

EISSN

1367-4811

Publication Date

February 15, 2010

Volume

26

Issue

4

Start / End Page

560 / 564

Location

England

Related Subject Headings

  • Software
  • Polymorphism, Single Nucleotide
  • Phenotype
  • Genotype
  • Genome-Wide Association Study
  • Genome
  • Databases, Genetic
  • Computational Biology
  • Bioinformatics
  • 49 Mathematical sciences