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research article

WGAViewer: software for genomic annotation of whole genome association studies

Ge, Dongliang
•
Zhang, Kunlin
•
Need, Anna C.
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2008
Genome research

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.

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Type
research article
DOI
10.1101/gr.071571.107
Author(s)
Ge, Dongliang
Zhang, Kunlin
Need, Anna C.
Martin, Olivier
Fellay, Jacques  
Urban, Thomas J.
Telenti, Amalio
Goldstein, David B.
Date Issued

2008

Publisher

Cold Spring Harbor Laboratory Press

Published in
Genome research
Volume

18

Issue

4

Start page

640

End page

3

Subjects

Genomics

•

Polymorphism, Single Nucleotide

•

Software

Editorial or Peer reviewed

REVIEWED

Written at

OTHER

EPFL units
UPFELLAY  
Available on Infoscience
April 11, 2011
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/66278
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