WGAViewer: Software for genomic annotation of whole genome association studies
WGAViewer: Software for genomic annotation of whole genome association studies
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DOI：
10.1101/gr.071571.107
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发表时间：
2008-04-01
期刊：
影响因子：
7
通讯作者：
Goldstein, David B.
中科院分区：
文献类型：
--
作者：
Ge, Dongliang;Zhang, Kunlin;Goldstein, David B.
为了满足对后全基因组关联(WGA)注释框架的迫切需要，我们开发了WGAViewer，这是一套Java软件工具，提供了一个用户友好的界面来自动注释、可视化和解释从WGA研究中出现的一组P值。最有价值的是，它可以用来以自动的方式突出可能的功能机制，例如，通过直接或间接地暗示与基因表达有明显联系的多态，并帮助产生关于所观察到的关联的可能生物学基础的假设。然后，这些易于解释的图表可以用来识别似乎最有可能与生物相关的关联，并选择可能需要重新测序的基因组区域，以寻找候选的因果变异。在这份报告中，我们使用了我们最近完成的关于无症状设定点期间宿主控制HIV-1病毒载量的研究作为该软件的启发式注释及其在成功的WGA项目中的贡献作用的例证。
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.