RegaDB Gertjan Beheydt Rega Institute Katholieke Universiteit - - PowerPoint PPT Presentation

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RegaDB Gertjan Beheydt Rega Institute Katholieke Universiteit Leuven April 23, 2010 Gertjan Beheydt RegaDB RegaDB A Viral Data Management and Analysis Environment A database system Integration of tools for sequence analysis Installed and

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RegaDB

Gertjan Beheydt

Rega Institute Katholieke Universiteit Leuven

April 23, 2010

Gertjan Beheydt RegaDB

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RegaDB

A Viral Data Management and Analysis Environment

A database system Integration of tools for sequence analysis Installed and managed locally Currently supported organisms: HIV, HCV and HTLV Free and open source software

Gertjan Beheydt RegaDB

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Motivation

Organization of data. Provide tools so data can be used as information source. Clinical practice as well as in research. A local database managed by the research center or clinic itself ⇒ An export mechanism to exchange data. Sensitive data is automatically anonymized while exporting.

Gertjan Beheydt RegaDB

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Data

So what kind of data can you store in RegaDB?

Gertjan Beheydt RegaDB

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Data

So what kind of data can you store in RegaDB? Patient information (gender, birth date, country of origin, . . . ) Events (therapy failure, AIDS defining illness, . . . ) Test results (VL, CD4 count, resistance tests, seroconversion test, . . . ) Therapy information Viral isolates

Gertjan Beheydt RegaDB

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Patient History Graph

Gertjan Beheydt RegaDB

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Query Tool

Gertjan Beheydt RegaDB

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Query Tool

Gertjan Beheydt RegaDB

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Analysis Tools

Alignment

Codon-correct nucleotide sequence alignment Aligns against 5 reference sequences (HIV-1, HIV-2A, HIV-2B, HTLV-1 and HCV-1) Frame-shift detection and correction

Gertjan Beheydt RegaDB

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Analysis Tools

Alignment Result

Gertjan Beheydt RegaDB

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Analysis Tools

Drug Resistance Interpretation

Gertjan Beheydt RegaDB

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Rega algorithm

For HIV-1 and HIV-2 http://regaweb.med.kuleuven.be/software/rega algorithm/ (PDF & XML) Updated ± twice a year Drug (class) Resistant Intermediate Resistant Susceptible NRTI 0.5 1 NNRTI 0.25 1 Etravirine 0.5 1 PI 0.5 1 PI/r 0.75 1.5 EI 0.25 1 INI 0.25 1

Gertjan Beheydt RegaDB

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Acknowledgements

Rega Institute, Katholieke Universiteit Leuven

Anne-Mieke Vandamme Kristel Van Laethem Li Guangdi Stijn Imbrechts Raphael Sangeda Kristof Theys Jurgen Vercauteren

MyBioData Biomedical IT solutions

Koen Deforche Pieter Libin

The research leading to the results has received funding from the European Community’s Seventh Framework Programme (FP7/2007-2013) under the project ”Collaborative HIV and Anti-HIV Drug Resistance Network (CHAIN)” - grant agreement n 223131 Gertjan Beheydt RegaDB