RegaDB Gertjan Beheydt Rega Institute Katholieke Universiteit - PowerPoint PPT Presentation

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 managed locally Currently supported organisms: HIV, HCV and HTLV Free and open source software Gertjan Beheydt RegaDB

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

Data So what kind of data can you store in RegaDB? Gertjan Beheydt RegaDB

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

Patient History Graph Gertjan Beheydt RegaDB

Query Tool Gertjan Beheydt RegaDB

Query Tool Gertjan Beheydt RegaDB

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

Analysis Tools Alignment Result Gertjan Beheydt RegaDB

Analysis Tools Drug Resistance Interpretation Gertjan Beheydt RegaDB

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 0.5 1 NNRTI 0 0.25 1 Etravirine 0 0.5 1 PI 0 0.5 1 PI/r 0 0.75 1.5 EI 0 0.25 1 INI 0 0.25 1 Gertjan Beheydt RegaDB

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