RegaDB: Community-driven data management and analysis for infectious diseases

Authors: Alcantara LC, Assel M, Ayouba A, Beheydt G, Boucher C, Camacho RJ, Carvalho AP, Cavaco-Silva J, De Bel A, De Munter P, De Oliveira T, Deforche K, Ferreira F, Grossman Z, Imbrechts S, Kaiser R, Lacor P, Lapadula G, Libin P, Otelea D, Paraschiv S, Peeters M, Ruelle J, Sloot P, Snoeck J, Theys K, Torti C, Van Laethem K, Van Wijngaerden E, Vandamme AM, Wesner S, Zazzi M
Journal: Bioinformatics
Link: http://www.ncbi.nlm.nih.gov/pubmed/23645815

RegaDB is a free and open source data management and analysis environment for infectious diseases. RegaDB allows clinicians to store, manage and analyse patient data, including viral genetic sequences. Moreover, RegaDB provides researchers with a mechanism to collect data in a uniform format and offers them a canvas to make newly developed bioinformatics tools available to clinicians and virologists through a user friendly interface.
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Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort

Authors: Abecasis AB, Assel M, Bartha I, Luca AD, Müller V, Paredes R, Rosi A, Schülter E, Sloot PMA, Sönner-borg A, Svärd J, Torti C, van de Vijver DC, Van Laethem K, Vandamme AM, Zazzi M
Publication Year: 2013
Journal: BMC Infectious Diseases
Link: http://www.biomedcentral.com/1471-2334/13/537/

Superinfection with drug resistant HIV strains could potentially contribute to compromised therapy in patients initially infected with drug-sensitive virus and receiving antiretroviral therapy. To investigate the importance of this potential route to drug resistance, we developed a bioinformatics pipeline to detect superinfection from routinely collected genotyping data, and assessed whether superinfection contributed to increased drug resistance in a large European cohort of viremic, drug treated patients.
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Clinical Evaluation of Rega 8: An Updated Genotypic Interpretation System That Significantly Predicts HIV-Therapy Response

Authors: Camacho R, Clotet B, De Luca A, Geretti AM, Grossman Z, Kaiser R, Prosperi M, Schmit JC, Sönnerborg A, Torti C, Van Wijngaerden E, Vercauteren J, Zazzi M, Beheydt G, Imbrechts S, Libin P, Vandamme AM, Van Laethem K
Journal: PLoS One
Link: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0061436

Clinically evaluating genotypic interpretation systems is essential to provide optimal guidance in designing potent individualized HIV-regimens. This study aimed at investigating the ability of the latest Rega algorithm to predict virological response on a short and longer period.
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HIV-1 subtype is an independent predictor of reverse transcriptase mutation k65r in HIV-1 patients treated with combination antiretroviral therapy including tenofovir

Authors: Abecasis AB, Camacho RJ, Clotet B, De Luca A, Grossman Z, Schülter E, Snoeck J, Sönnerborg A, Struck D, Theys K, Torti C, Vandamme AM, Vercauteren J, Zazzi M
Journal: Antimicrobial Agents and Chemotherapy
Link: http://www.ncbi.nlm.nih.gov/pubmed/23183438

Subtype-dependent selection of HIV-1 reverse transcriptase resistance mutation K65R was previously observed in cell culture and small clinical investigations. We compared K65R prevalence across subtypes A, B, C, F, G, and CRF02_AG separately in a cohort of 3,076 patients on combination therapy including tenofovir. K65R selection was significantly higher in HIV-1 subtype C. This could not be explained by clinical and demographic factors in multivariate analysis, suggesting subtype sequence-specific K65R pathways.
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RegaDB: Community-driven data management and analysis for infectious diseases

Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort

Clinical Evaluation of Rega 8: An Updated Genotypic Interpretation System That Significantly Predicts HIV-Therapy Response

HIV-1 subtype is an independent predictor of reverse transcriptase mutation k65r in HIV-1 patients treated with combination antiretroviral therapy including tenofovir

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