Development of a cross-European virtual sample repository and HIV resistance database

Details

Serval ID
serval:BIB_F35F46F6497C
Type
Inproceedings: an article in a conference proceedings.
Publication sub-type
Abstract (Abstract): shot summary in a article that contain essentials elements presented during a scientific conference, lecture or from a poster.
Collection
Publications
Institution
Title
Development of a cross-European virtual sample repository and HIV resistance database
Title of the conference
International Workshop on HIV and Hepatitis Virus Drug Resistance and Curative Strategies
Author(s)
Kjaer J., Kristensen D.K., Beheydt G., Imbrechts S., Rickenbach M., Fanti I., Incardona F., Vandamme A.M.
Address
Los Cabos, Mexico, June 7-11, 2011
ISBN
1359-6535
Publication state
Published
Issued date
2011
Peer-reviewed
Oui
Volume
16
Series
Antiviral therapy
Pages
A106
Language
english
Notes
Publication type : Meeting Abstract
Abstract
BACKGROUND: Several European HIV observational data bases have, over the last decade, accumulated a substantial number of resistance test results and developed large sample repositories, There is a need to link these efforts together, We here describe the development of such a novel tool that allows to bind these data bases together in a distributed fashion for which the control and data remains with the cohorts rather than classic data mergers.METHODS: As proof-of-concept we entered two basic queries into the tool: available resistance tests and available samples. We asked for patients still alive after 1998-01-01, and between 180 and 195 cm of height, and how many samples or resistance tests there would be available for these patients, The queries were uploaded with the tool to a central web server from which each participating cohort downloaded the queries with the tool and ran them against their database, The numbers gathered were then submitted back to the server and we could accumulate the number of available samples and resistance tests.RESULTS: We obtained the following results from the cohorts on available samples/resistance test: EuResist: not availableI11,194; EuroSIDA: 20,71611,992; ICONA: 3,751/500; Rega: 302/302; SHCS: 53,78311,485, In total, 78,552 samples and 15,473 resistance tests were available amongst these five cohorts. Once these data items have been identified, it is trivial to generate lists of relevant samples that would be usefuI for ultra deep sequencing in addition to the already available resistance tests, Saon the tool will include small analysis packages that allow each cohort to pull a report on their cohort profile and also survey emerging resistance trends in their own cohort,CONCLUSIONS: We plan on providing this tool to all cohorts within the Collaborative HIV and Anti-HIV Drug Resistance Network (CHAIN) and will provide the tool free of charge to others for any non-commercial use, The potential of this tool is to ease collaborations, that is, in projects requiring data to speed up identification of novel resistance mutations by increasing the number of observations across multiple cohorts instead of awaiting single cohorts or studies to reach the critical number needed to address such issues.
Keywords
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Web of science
Create date
23/09/2011 16:12
Last modification date
20/08/2019 17:20
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