WGAViewer
WGAViewer is a suite of JAVA software tools that provides a user-friendly interface to annotate, visualize, and help interpret the full set of P values emerging from a whole genome association (WGA) study. The program uses the latest available genomic databases to annotate the SNPs and their associated P values in the context of predicted gene structure and SNP function (1) , association with gene expression (2), evidence of recent selection (3), and results from other association studies. HapMap (4) data is used to identify non-genotyped polymorphisms that associate with the phenotype of interest through linkage disequilibrium (LD) with genotyped variants. The easily interpretable diagrams can be used to identify the associations that seem most likely to be biologically relevant, and to select genomic regions that may need to be resequenced in a search for candidate causal variants.
A recently completed study (5) in Duke IGSP Center for Population Genomics & Pharmacogenetics on host control of HIV-1 viral load during the asymptomatic set point period has utilized this software. A separate paper describing the WGAViewer software is being published in Genome Research (6).
WGAViewer is being developed by Dongliang Ge and David Goldstein at Duke IGSP Center for Population Genomics & Pharmacogenetics, with the support of Kunlin Zhang, Olivier Martin, and Amalio Telenti at University of Lausanne, Switzerland. WGAViewer is supported by the Center for HIV-AIDS Vaccine Immunology (CHAVI) and the Duke Institute for Genome Sciences & Policy (IGSP).
A JAVA environment (free access from http://www.java.com/en/download/index.jsp) no earlier than version 1.5.07 is required to use this software.
References
(1) Hubbard TJ, Aken BL, Beal K, et al. Ensembl 2007. Nucleic Acids Res 35, D610-7 (2007).
(2) Stranger BE, Forrest MS, Dunning M, et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315, 848-53 (2007).
(3) Voight BF, Kudaravalli S, Wen X & Pritchard JK. A map of recent positive selection in the human genome. PLoS Biol 4, e72 (2006).
(4) The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-320 (2005).
(5) Fellay J, Shianna KV, Ge D, et al. Identification of Major Determinants of the Host Control of HIV-1 through a Whole-Genome Association Study. Science 317(5840), 944-7 (2007).
(6) Ge D, Zhang D, Need AC, Martin O, Fellay J, Telenti A, Goldstein DB. WGAViewer: A Software for Genomic Annotation of Whole Genome Association Studies. Genome Res 18(4), 640-3 (2008).
To subscribe to the WGAViewer mailing list, or change your existing subscription, send an email to Dr. Dongliang Ge: d.ge@duke.edu