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Access to the GSID HIV Data Browser
GSID made this valuable resource available to the HIV vaccine research community from 2009 to 2012, but due to termination of financial support for the Browser, GSID discontinued public access. |
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In 2004, GSID established a specimen repository with more than 300,000 tubes of serological material, over 1.2 million electronic pages of clinical information and volumes of other scientific data generated during and after the conduct of the VaxGen trials.
Knowing that we cannot tackle HIV alone, we developed the web-accessible GSID HIV Data Browser containing clinical and viral sequence information related to the HIV infected subjects who participated in the VaxGen trials. The GSID HIV Data Browser was developed in collaboration with the Genome Bioinformatics Group at the University of California, Santa Cruz (UCGBG), which is a cross-departmental team within the Center of Biomolecular Sciences and Engineering (CBSE). Under the guidance of Jim Kent and the late Fan Hsu, UCGBG developed a relational database containing the significant clinical data and sequence information pertaining to the infected subjects participating in the VAX003 and VAX004 Phase III clinical trials.
The specimens and data have been used by a number of HIV vaccine collaborators for further in-depth analysis. A list of publications can be found here.
The GSID HIV Data Browser contains three main “view” pages:
Subject View Page
This view allows the user to capture all of the available information for individual subjects identified by a blinded subject identification number. As was required during the conduct of the trial, both GSID and UCGBG will continue to blind the information contained in the database to ensure volunteer (subject) confidentiality and privacy. A filter control page is available to allow the user to set search parameters to retrieve and display information. The database includes the following demographic and clinical information (a summary of the data is available in PDF format here):
• Age
• Race
• Gender
• Risk group
• Geographic location
• Weight
• Immunization status: vaccine or placebo recipient
• Estimated study days of infection
• CD4 counts
• Viral load measurements
Table View Page
This view allows users to construct tables containing selected information from multiple subjects. In this view, users have the ability to sort, display information broadly or based upon data specific criteria and output the text in tab delineated format. Additionally, the user is able to retrieve associated DNA or protein sequences from this view.
Sequence View Page
Sequence view contains tools which allow for sequences to be aligned with each other, with reference sequences or with consensus sequences. The database contains three sequences per infected subject, as well as phylogenetic and positive selection analysis data. The primary alignment tool included in this view is called BLAT.
Additional Resources
