WGAViewer: Software for genomic annotation of whole genome association studies: Figure 1.

Abstract

To meet the immediate need for a framework of post-whole genome association (WGA) annotation, we have developed WGAViewer, a suite of JAVA software tools that provides a user-friendly interface to automatically annotate, visualize, and interpret the set of P-values emerging from a WGA study. Most valuably, it can be used to highlight possible functional mechanisms in an automatic manner, for example, by directly or indirectly implicating a polymorphism with an apparent link to gene expression, and help to generate hypotheses concerning the possible biological bases of observed associations. The easily interpretable diagrams can then 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. In this report, we used our recently completed study on host control of HIV-1 viral load during the asymptomatic set point period as an illustration for the heuristic annotation of this software and its contributive role in a successful WGA project.

Genetic Variants in Major Histocompatibility Complex-Linked Genes Associate With Pediatric Liver Transplant Rejection

“…Significant repression of the first HLA DOA exon among Rejectors in our study supports this view. Decreased HLA-DOA gene expression is also seen with increasing numbers of the risk allele of rs9296068 for both Caucasian and Yoruba populations in public databases (28).…”

Replication of genetic associations with plasma lipoprotein traits in a multiethnic sample

“…Since genotype data is unaffected, linkage disequilibrium between SNPs remains throughout permutations. Results of association and permutation were displayed using WGAViewer (16).…”

Genome-wide association study of recurrent major depressive disorder in two European case–control cohorts

“…The gene annotation was performed according to National Center for Biotechnology Information dbSNP through the use of WGAViewer software. 40 The gene list was submitted to the Ingenuity Pathway Analysis tool (Ingenuity Systems, Mountain View, CA, USA; https://analysis.ingenuity. com/pa/login/login.jsp), a system with a web-based interface providing computational algorithms to functionally analyse large datasets and identify or generate gene/protein networks that are formed by the genes of interest.…”