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. 2009 Jan;37(Database issue):D797-802.
doi: 10.1093/nar/gkn748. Epub 2008 Oct 23.

HGVbaseG2P: a central genetic association database

Gudmundur A Thorisson  1 , Owen Lancaster, Robert C Free, Robert K Hastings, Pallavi Sarmah, Debasis Dash, Samir K Brahmachari, Anthony J Brookes
Affiliations

HGVbaseG2P: a central genetic association database

Gudmundur A Thorisson et al. Nucleic Acids Res. 2009 Jan.

Abstract

The Human Genome Variation database of Genotype to Phenotype information (HGVbaseG2P) is a new central database for summary-level findings produced by human genetic association studies, both large and small. Such a database is needed so that researchers have an easy way to access all the available association study data relevant to their genes, genome regions or diseases of interest. Such a depository will allow true positive signals to be more readily distinguished from false positives (type I error) that fail to consistently replicate. In this paper we describe how HGVbaseG2P has been constructed, and how its data are gathered and organized. We present a range of user-friendly but powerful website tools for searching, browsing and visualizing G2P study findings. HGVbaseG2P is available at http://www.hgvbaseg2p.org.

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Figures

Figure 1.
Figure 1.
Overview data model of HGVbaseG2P. The main subdivisions of data that make up an association report are shown, with further explanation of each component provided in the body text. These components are illustrated sitting on top of a comprehensive ‘Marker’ layer which is pre-built and provides a common foundation that all data submissions are directly connected into.
Figure 2.
Figure 2.
HGVbaseG2P graphical display capabilities. Screenshots are provided that show data from a Type 1 diabetes disease association data set produced by the WTCCC. The histogram alongside each chromosome indicates the number (linear or logarithmic scaling options) of markers per 3 Mbp bin having a P-value that passes a tunable significance threshold. A bin with 20 significant markers is apparent at 9p21. Clicking on this region zooms in to a dynamic image (i.e. scale and position may be tailored to one's preferences) presented in a region-level browser via which the user can access optional tracks for individual marker associations, count of significant markers and P-value of most significant marker within various resolution bins, known genes details and other common annotations.
See this image and copyright information in PMC

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