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Discordance between Etravirine Phenotype and Genotype-based Predicted Phenotype for Subtype C HIV-1 from First-line Antiretroviral Therapy Failures in South Africa

Kevin D. McCormick, Kerri J. Penrose, Chanson J. Brumme, Richard Harrigan, Raquel V Viana, John W. Mellors, Urvi M. Parikh, Carole L. Wallis
2020 Antimicrobial Agents and Chemotherapy  
Modifications to genotypic algorithms are needed to improve the prediction of ETR resistance for HIV-1 subtype C.  ...  Genotypic resistance test-interpretation systems can predict ETR resistance; however, genotype-based algorithms are derived primarily from HIV-1 subtype B and may not accurately predict resistance in non-B  ...  However, the accuracy of genotypic drug resistance algorithms in predicting ETR resistance in subtype C HIV-1 is uncertain.  ... 
doi:10.1128/aac.02101-19 pmid:32071061 pmcid:PMC7179637 fatcat:rm4glfxjibad3dssla5a4mvgca

Predicting HIV-1 Protease and Reverse Transcriptase Drug Resistance Using Fuzzy Cognitive Maps [chapter]

Isel Grau, Gonzalo Nápoles, María M. García
2013 Lecture Notes in Computer Science  
For this reason, it is important to study the resistance mechanisms of the HIV proteins in order to make a better use of existing drugs and design new ones.  ...  In the last ten years, numerous statistical and machine learning approaches were applied for predicting drug resistance from protein genome information.  ...  In general, the resistance testing of an observed mutation can be performed by two main approaches: the genotypic and the phenotypic tests.  ... 
doi:10.1007/978-3-642-41827-3_24 fatcat:mx3o6a3ub5dj7ej6rmxxfxrexa

Predictive Value of HIV‐1 Genotypic Resistance Test Interpretation Algorithms

Soo‐Yon Rhee, W. Jeffrey Fessel, Tommy F. Liu, Natalia M. Marlowe, Charles M. Rowland, Richard A. Rode, Anne‐Mieke Vandamme, Kristel Van Laethem, Françoise Brun‐Vezinet, Vincent Calvez, Jonathan Taylor, Leo Hurley (+2 others)
2009 Journal of Infectious Diseases  
Interpreting human immunodeficienc virus type 1 (HIV-1) genotypic drug-resistance test results is challenging for clinicians treating HIV-1-infected patients.  ...  Retrospective studies have shown that the presence of human immunodeficienc virus type 1 (HIV-1) drug resistance before the start of a new antiretroviral (ARV) regimen is an independent predictor of the  ...  .001 DISCUSSION Rationale for genotypic drug-resistance interpretation algorithms. Genotypic drug-resistance testing is part of the standard care of HIV-1-infected patients.  ... 
doi:10.1086/600073 pmid:19552527 pmcid:PMC4774893 fatcat:7wrlzcimvfec3de6o3xsmq72d4

Similar predictions of etravirine sensitivity regardless of genotypic testing method used: comparison of available scoring systems

Johan Vingerhoets, Steven Nijs, Lotke Tambuyzer, Annemie Hoogstoel, David Anderson, Gaston Picchio
2012 Antiviral Therapy  
and virco®TYPE HIV-1 (predicted fold change based on genotype).  ...  As such, phenotypic interpretations, and in their absence all genotypic scoring systems investigated, may be used to reliably predict the activity of etravirine.  ...  All authors contributed to the study design and analysis of results, and reviewed the drafts for clinical accuracy and intellectual content. SN and AH performed all statistical analyses.  ... 
doi:10.3851/imp2275 pmid:22869341 fatcat:tuhjq3p27fcuvjqq2mhglgaqfm

HIV-GRADE: A Publicly Available, Rules-Based Drug Resistance Interpretation Algorithm Integrating Bioinformatic Knowledge

Martin Obermeier, Alejandro Pironti, Thomas Berg, Patrick Braun, Martin Däumer, Josef Eberle, Robert Ehret, Rolf Kaiser, Niels Kleinkauf, Klaus Korn, Claudia Kücherer, Harm Müller (+5 others)
2012 Intervirology  
tion system (geno2pheno [resistance] ). HIV-GRADE presents the option of seeing the rules and results of other drug resistance algorithms for a given sequence simultaneously.  ...  Results: As the developed online tool allows easy Abstract Background: Genotypic drug resistance testing provides essential information for guiding treatment in HIV-infected patients.  ...  On the much smaller data set for DRV coefficients of determination were 0.36 for HIV-GRADE, 0.33 for ANRS and 0.32 for Stanford HIVdb. REGA algorithm was not tested using this data set.  ... 
doi:10.1159/000331999 pmid:22286877 fatcat:k3qrqvnvtnctnivk5pcivp4vtq

Scoring Methods for Building Genotypic Scores: An Application to Didanosine Resistance in a Large Derivation Set

Allal Houssaini, Lambert Assoumou, Veronica Miller, Vincent Calvez, Anne-Geneviève Marcelin, Philippe Flandre, Nicolas Sluis-Cremer
2013 PLoS ONE  
This approach could be used for building scores of genotypic resistance to other antiretroviral drugs.  ...  Several attempts have been made to determine HIV-1 resistance from genotype resistance testing.  ...  Such scoring strategies have not been extensively used for building algorithms for predicting HIV-1 resistance to antiretrovirals.  ... 
doi:10.1371/journal.pone.0059014 pmid:23555613 pmcid:PMC3605419 fatcat:sugbl6tgpndovk3fokuambtqae

Fuzzy-multidimensional deep learning for efficient prediction of patient response to antiretroviral therapy

Moses E. Ekpenyong, Philip I. Etebong, Tenderwealth C. Jackson
2019 Heliyon  
DNN classification results for both databases showed best performance metrics for the Levenberg-Marquardt algorithm when compared with the resilient backpropagation algorithm, with improved drug pattern  ...  predictions for experiment with MDS.  ...  Acknowledgements We acknowledge the anonymous reviewers for their invaluable comments that have contributed to improving the quality of this paper.  ... 
doi:10.1016/j.heliyon.2019.e02080 pmid:31372545 pmcid:PMC6656963 fatcat:kurxnqspu5h6tiwn46vq4dwsg4

HIV Resistance Prediction to Reverse Transcriptase Inhibitors: Focus on Open Data

Olga Tarasova, Vladimir Poroikov
2018 Molecules  
The experimental data stored in the databases of HIV sequences can be used for development of methods that are able to predict HIV resistance based on amino acid or nucleotide sequences.  ...  HIV reverse transcriptase (RT) is an important target for HIV treatment. RT inhibitors targeting early stages of the virus-host interaction are of great interest for researchers.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules23040956 pmid:29671808 fatcat:c2dniltpszgd3jlzmkjdkv3pqq

Probabilistic Neural Network for Predicting Resistance to HIV-Protease Inhibitor Nelfinavir

Letícia Martins Raposo, Mônica Barcellos Arruda, Rodrigo de Moraes Brindeiro, Flavio Fonseca Nobre
2014 Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms  
The development of models to predict drug resistance is already recognized as useful for helping the decision making process regarding the best therapy for each individual HIV+.  ...  Resistance to antiretroviral drugs has been a major obstacle for a long-lasting treatment of HIV infected patients.  ...  The use of tests that identify HIV drug resistance is recommended as an important monitoring tool in clinical practice.  ... 
doi:10.5220/0004735900170023 dblp:conf/biostec/RaposoABN14 fatcat:rbnvxra3xndxpefts53n6vgnca

HIV susceptibility to amprenavir: phenotype-based versus rules-based interpretations

L. Scudeller
2003 Journal of Antimicrobial Chemotherapy  
However, our results indicate that a number of mutations may have an impact on APV resistance, but that they are missed by current interpretation algorithms and this merits further investigations.  ...  Objectives: The objective was to study genotypic correlates of discordant interpretations of amprenavir (APV) resistance between a rules-based algorithm and either recombinant phenotype or virtual phenotype  ...  This work has been presented in part at the 1st European Drug Resistance Workshop, Luxembourg  ... 
doi:10.1093/jac/dkg456 pmid:14563897 fatcat:zc7tqmnrubb3jloxlxdddnmemy

A Randomised Trial Comparing Genotypic and Virtual Phenotypic Interpretation of HIV Drug Resistance: The CREST Study

Gillian Hales, Chris Birch, Suzanne Crowe, Cassy Workman, Jennifer F Hoy, Matthew G Law, Anthony D Kelleher, Douglas Lincoln, Sean Emery
2006 PLoS Clinical Trials  
Objectives: The aim of this study was to compare the efficacy of different HIV drug resistance test reports (genotype and virtual phenotype) in patients who were changing their antiretroviral therapy (  ...  Outcome Measures: Patient groups were compared for patterns of ART selection and surrogate outcomes (plasma viral load and CD4 counts) on an intention-to-treat basis over a 48-week period.  ...  ACKNOWLEDGMENTS We are extremely grateful to the patients for their participation.  ... 
doi:10.1371/journal.pctr.0010018 pmid:16878178 pmcid:PMC1523224 fatcat:obwkxhahxzexfpbebs3ipqnpj4

Improving the prediction of virological response to tipranavir: the development and validation of a tipranavir-weighted mutation score

Jonathan M Schapiro, Joseph Scherer, Charles A Boucher, John D Baxter, Clemens Tilke, Carlo F Perno, Franco Maggiolo, Maria M Santoro, David B Hall
2010 Antiviral Therapy  
Almost all testing is population genotypic-based, for reasons of availability and cost.  ...  Guidance documents recommend resistance testing for HIV type-1 (HIV-1) patients whenever changes in antiretroviral regimen are being considered as a result of virological failure [1] [2] [3] .  ...  JB is a consultant to Boehringer Ingelheim and is on the speakers' bureau for Pfizer, Boehringer Ingelheim and Tibotec. JS, CT and DH are full-time employees of Boehringer Ingelheim.  ... 
doi:10.3851/imp1670 pmid:21041916 fatcat:rvsea32ut5av7f4njib7tiqwey

Predicting Bevirimat resistance of HIV-1 from genotype

Dominik Heider, Jens Verheyen, Daniel Hoffmann
2010 BMC Bioinformatics  
We have investigated a set of p24/p2 sequences of HIV-1 of known phenotypic resistance to BVM to test whether BVM resistance can be predicted from sequence, and to identify possible molecular mechanisms  ...  of BVM resistance in HIV-1.  ...  Nikolaj Dybowski for the assistance and helpful discussions. We also thank Dr. Nelly Morellet (Universitè Paris-Descartes, Paris, France) for the p24/p2 structural model.  ... 
doi:10.1186/1471-2105-11-37 pmid:20089140 pmcid:PMC3224585 fatcat:ebyznqeq4jddvbnpveqn6yeiqe

Personalized HIV therapy to control drug resistance

Thomas Lengauer, Nico Pfeifer, Rolf Kaiser
2014 Drug Discovery Today : Technologies  
In the past decade, computer-based support for therapy selection, which assesses the level of viral resistance against drugs has become a mainstay for HIV patients.  ...  The therapy of HIV patients is characterized by both the high genomic diversity of the virus population harbored by the patient and a substantial volume of therapy options.  ...  This work has been conducted in the context of the MASTER/HIV-HEP Project (funded by German Ministry of Health) and the EUCOHIV Project (  ... 
doi:10.1016/j.ddtec.2014.02.004 pmid:24847654 fatcat:7fwlle3khbdhlki3pkka7v45f4

Performance of HIV-1 Drug Resistance Testing at Low-Level Viremia and Its Ability to Predict Future Virologic Outcomes and Viral Evolution in Treatment-Naive Individuals

A. Gonzalez-Serna, J. E. Min, C. Woods, D. Chan, V. D. Lima, J. S. G. Montaner, P. R. Harrigan, L. C. Swenson
2014 Clinical Infectious Diseases  
A genotypic sensitivity score (GSS) was calculated based on therapy and resistance testing results by genotyping, and stratified according to number of active drugs. Results.  ...  Here, we assess the ability to perform resistance testing by genotyping at LLV and whether it is predictive of future virologic outcomes in patients beginning ART. Methods.  ...  We thank Liliana Barrios and Emily Anderson from the Drug Treatment program; all the staff from the British Columbia Centre for Excellence in HIV/AIDS for their assistance and commitment to maintaining  ... 
doi:10.1093/cid/ciu019 pmid:24429436 pmcid:PMC3967823 fatcat:2bgytckpxngnthv5bimxgzh3qy
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