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Detection of novel HIV-1 drug resistance mutations by support vector analysis of deep sequence data and experimental validation

https://doi.org/10.1101/804781
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Antiretroviral Treatment of Adult HIV Infection
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Antiretroviral Treatment of Adult HIV Infection
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Support vector machines for predicting HIV protease cleavage sites in protein
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Comparative Protein Modelling by Satisfaction of Spatial Restraints
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Pattern classification with missing data: a review
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Selection of diverse and clinically relevant integrase inhibitor-resistant human immunodeficiency virus type 1 mutants
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In vitro resistance selections using elvitegravir, raltegravir, and two metabolites of elvitegravir M1 and M4
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The development of novel HIV integrase inhibitors and the problem of drug resistance
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HIV-1 genotypic drug resistance testing: digging deep, reaching wide?
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Support vector machines: Development of QSAR models for predicting anti-HIV-1 activity of TIBO derivatives
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Antiretroviral Therapy
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Primary mutations selected in vitro with raltegravir confer large fold changes in susceptibility to first-generation integrase inhibitors, but minor fold changes to inhibitors with second-generation resistance profiles
inferredcites →https://doi.org/10.1016/j.virusres.2016.12.008openalex-snapshot
Promises and pitfalls of Illumina sequencing for HIV resistance genotyping
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Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing
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Tracking a century of global expansion and evolution of HIV to drive understanding and to combat disease
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Efficacy and safety of raltegravir for treatment of HIV for 5 years in the BENCHMRK studies: final results of two randomised, placebo-controlled trials
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Dolutegravir for first-line antiretroviral therapy in low-income and middle-income countries: uncertainties and opportunities for implementation and research
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An Introduction to Support Vector Machines and Other Kernel-based Learning Methods
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Mapping Features of HIV-1 Integrase Near Selected Sites on Viral and Target DNA Molecules in an Active Enzyme−DNA Complex by Photo-Cross-Linking
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C-Terminal Domain of Integrase Binds between the Two Active Sites
inferredcites →https://doi.org/10.1038/365671a0openalex-snapshot
Quantitative detection of HIV-1 drug resistance mutations by automated DNA sequencing
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.2109openalex-snapshot
jModelTest 2: more models, new heuristics and parallel computing
inferredcites →https://doi.org/10.1073/pnas.150220297openalex-snapshot
Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: A model for viral DNA binding
inferredcites →https://doi.org/10.1086/503914openalex-snapshot
Web Resources for HIV Type 1 Genotypic-Resistance Test Interpretation
inferredcites →https://doi.org/10.1086/505356openalex-snapshot
Rationale and Uses of a Public HIV Drug‐Resistance Database
inferredcites →https://doi.org/10.1086/598502openalex-snapshot
Effect of HIV‐1 Subtype on Virologic and Immunologic Response to Starting Highly Active Antiretroviral Therapy
inferredcites →https://doi.org/10.1086/650002openalex-snapshot
Long‐Term Efficacy and Safety of Raltegravir Combined with Optimized Background Therapy in Treatment‐Experienced Patients with Drug‐Resistant HIV Infection: Week 96 Results of the BENCHMRK 1 and 2 Phase III Trials
inferredcites →https://doi.org/10.1089/aid.2012.0338openalex-snapshot
Comparison of Population and 454 “Deep” Sequence Analysis for HIV Type 1 Tropism Versus the Original Trofile Assay in Non-B Subtypes
inferredcites →https://doi.org/10.1089/aid.2017.0205openalex-snapshot
Absence of HIV-1 Drug Resistance Mutations Supports the Use of Dolutegravir in Uganda
inferredcites →https://doi.org/10.1093/bfgp/elt008openalex-snapshot
Explaining microbial phenotypes on a genomic scale: GWAS for microbes
inferredcites →https://doi.org/10.1093/bioinformatics/btp286openalex-snapshot
penalizedSVM: a R-package for feature selection SVM classification
inferredcites →https://doi.org/10.1093/bioinformatics/bts373openalex-snapshot
Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btu531openalex-snapshot
AliView: a fast and lightweight alignment viewer and editor for large datasets
inferredcites →https://doi.org/10.1093/bioinformatics/btu535openalex-snapshot
gCUP: rapid GPU-based HIV-1 co-receptor usage prediction for next-generation sequencing
inferredcites →https://doi.org/10.1093/infdis/jir025openalex-snapshot
HIV-1 Integrase Inhibitor Resistance and Its Clinical Implications
inferredcites →https://doi.org/10.1093/jac/dkp423openalex-snapshot
Integrase variability and susceptibility to HIV integrase inhibitors: impact of subtypes, antiretroviral experience and duration of HIV infection
inferredcites →https://doi.org/10.1093/jac/dkq099openalex-snapshot
HIV-1 resistance patterns to integrase inhibitors in antiretroviral-experienced patients with virological failure on raltegravir-containing regimens
inferredcites →https://doi.org/10.1093/jac/dkr389openalex-snapshot
The HIV-1 integrase G118R mutation confers raltegravir resistance to the CRF02_AG HIV-1 subtype
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkw336openalex-snapshot
3Drefine: an interactive web server for efficient protein structure refinement
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1097/00002030-200301030-00001openalex-snapshot
A V106M mutation in HIV-1 clade C viruses exposed to efavirenz confers cross-resistance to non-nucleoside reverse transcriptase inhibitors
inferredcites →https://doi.org/10.1097/01.aids.0000247564.73009.bcopenalex-snapshot
Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004
inferredcites →https://doi.org/10.1097/qad.0b013e3283610ec7openalex-snapshot
Treatment failure and drug resistance is more frequent in HIV-1 subtype D versus subtype A-infected Ugandans over a 10-year study period
inferredcites →https://doi.org/10.1097/qai.0b013e3181c9c967openalex-snapshot
Long-Term Efficacy and Safety of the HIV Integrase Inhibitor Raltegravir in Patients With Limited Treatment Options in a Phase II Study
inferredcites →https://doi.org/10.1097/qai.0b013e3181e9a87aopenalex-snapshot
Effect of Raltegravir Resistance Mutations in HIV-1 Integrase on Viral Fitness
inferredcites →https://doi.org/10.1128/aac.00038-16openalex-snapshot
Low-Frequency Drug Resistance in HIV-Infected Ugandans on Antiretroviral Treatment Is Associated with Regimen Failure
inferredcites →https://doi.org/10.1128/aac.01075-09openalex-snapshot
Impact of Y143 HIV-1 Integrase Mutations on Resistance to Raltegravir In Vitro and In Vivo
inferredcites →https://doi.org/10.1128/aac.01228-07openalex-snapshot
Mutations Associated with Failure of Raltegravir Treatment Affect Integrase Sensitivity to the Inhibitor In Vitro
inferredcites →https://doi.org/10.1128/aac.01490-15openalex-snapshot
HIV Drug Resistance Testing by High-Multiplex “Wide” Sequencing on the MiSeq Instrument
inferredcites →https://doi.org/10.1128/aac.01733-09openalex-snapshot
Cross-Resistance Profile Determination of Two Second-Generation HIV-1 Integrase Inhibitors Using a Panel of Recombinant Viruses Derived from Raltegravir-Treated Clinical Isolates
inferredcites →https://doi.org/10.1128/aac.02710-13openalex-snapshot
Sensitive Deep-Sequencing-Based HIV-1 Genotyping Assay To Simultaneously Determine Susceptibility to Protease, Reverse Transcriptase, Integrase, and Maturation Inhibitors, as Well as HIV-1 Coreceptor Tropism
inferredcites →https://doi.org/10.1128/jcm.37.7.2291-2296.1999openalex-snapshot
Worldwide Evaluation of DNA Sequencing Approaches for Identification of Drug Resistance Mutations in the Human Immunodeficiency Virus Type 1 Reverse Transcriptase
inferredcites →https://doi.org/10.1128/jvi.00470-08openalex-snapshot
Resistance Mutations in Human Immunodeficiency Virus Type 1 Integrase Selected with Elvitegravir Confer Reduced Susceptibility to a Wide Range of Integrase Inhibitors
inferredcites →https://doi.org/10.1128/jvi.00495-16openalex-snapshot
HIV-1 Protease, Reverse Transcriptase, and Integrase Variation
inferredcites →https://doi.org/10.1128/jvi.01168-09openalex-snapshot
Loss of Raltegravir Susceptibility by Human Immunodeficiency Virus Type 1 Is Conferred via Multiple Nonoverlapping Genetic Pathways
inferredcites →https://doi.org/10.1128/jvi.02005-10openalex-snapshot
Confirmation of Putative HIV-1 Group P in Cameroon
inferredcites →https://doi.org/10.1128/jvi.06618-11openalex-snapshot
Substitutions at Amino Acid Positions 143, 148, and 155 of HIV-1 Integrase Define Distinct Genetic Barriers to Raltegravir Resistance In Vivo
inferredcites →https://doi.org/10.1128/jvi.66.4.2232-2239.1992openalex-snapshot
Detection of replication-competent and pseudotyped human immunodeficiency virus with a sensitive cell line on the basis of activation of an integrated beta-galactosidase gene
inferredcites →https://doi.org/10.1128/jvi.71.10.7478-7487.1997openalex-snapshot
Coreceptor usage of primary human immunodeficiency virus type 1 isolates varies according to biological phenotype
inferredcites →https://doi.org/10.1128/mbio.00922-17openalex-snapshot
Mutations Located outside the Integrase Gene Can Confer Resistance to HIV-1 Integrase Strand Transfer Inhibitors
inferredcites →https://doi.org/10.1177/135965350501000206openalex-snapshot
Impact of Human Immunodeficiency Virus Type 1 Subtype on First-Line Antiretroviral Therapy Effectiveness
inferredcites →https://doi.org/10.1177/135965350701200411openalex-snapshot
Natural Polymorphism of the HIV-1 Integrase Gene and Mutations associated with Integrase Inhibitor Resistance
inferredcites →https://doi.org/10.1186/1471-2105-12-138openalex-snapshot
Elastic SCAD as a novel penalization method for SVM classification tasks in high-dimensional data
inferredcites →https://doi.org/10.1186/1742-4690-5-74openalex-snapshot
Natural variation of HIV-1 group M integrase: Implications for a new class of antiretroviral inhibitors
inferredcites →https://doi.org/10.1186/1758-2652-13-4openalex-snapshot
Impact of HIV‐1 viral subtype on disease progression and response to antiretroviral therapy
inferredcites →https://doi.org/10.1186/s12859-016-0976-yopenalex-snapshot
Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data
inferredcites →https://doi.org/10.1186/s12981-019-0218-2openalex-snapshot
First-line HIV treatment failures in non-B subtypes and recombinants: a cross-sectional analysis of multiple populations in Uganda
inferredcites →https://doi.org/10.1186/s40249-017-0377-0openalex-snapshot
Sensitive detection of HIV-1 resistance to Zidovudine and impact on treatment outcomes in low- to middle-income countries
inferredcites →https://doi.org/10.1201/9780429340512openalex-snapshot
Principles of Biostatistics
inferredcites →https://doi.org/10.1371/journal.pcbi.1000581openalex-snapshot
An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1
inferredcites →https://doi.org/10.1371/journal.pcbi.1003254openalex-snapshot
Feature Selection Methods for Identifying Genetic Determinants of Host Species in RNA Viruses
inferredcites →https://doi.org/10.1371/journal.pmed.0050158openalex-snapshot
Minority HIV-1 Drug Resistance Mutations Are Present in Antiretroviral Treatment–Naïve Populations and Associate with Reduced Treatment Efficacy
inferredcites →https://doi.org/10.1371/journal.pone.0099508openalex-snapshot
“Deep” Sequencing Accuracy and Reproducibility Using Roche/454 Technology for Inferring Co-Receptor Usage in HIV-1
inferredcites →https://doi.org/10.1371/journal.pone.0163746openalex-snapshot
Genome-Wide Association Study of HIV Whole Genome Sequences Validated using Drug Resistance
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.18637/jss.v045.i03openalex-snapshot
mice: Multivariate Imputation by Chained Equations inR
inferredcites →https://doi.org/10.2144/000113119openalex-snapshot
A Novel Yeast-Based Recombination Method to Clone and Propagate Diverse HIV-1 Isolates
inferredcites →https://doi.org/10.2174/1568026043388547openalex-snapshot
Structure and Function of HIV-1 Integrase
inferredcites →https://doi.org/10.3390/v1030713openalex-snapshot
HIV-1 Integrase-DNA Recognition Mechanisms
inferredcites →https://doi.org/10.5167/uzh-122257openalex-snapshot
2015 update of the drug resistance mutations in HIV-1
inferredcites →https://doi.org/10.7448/ias.17.1.18944openalex-snapshot
Do HIV‐1 non‐B subtypes differentially impact resistance mutations and clinical disease progression in treated populations? Evidence from a systematic review
inferredcites →https://doi.org/10.7554/elife.11282openalex-snapshot
Population genomics of intrapatient HIV-1 evolution

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inferred← citeshttps://doi.org/10.1186/s12864-026-13243-3openalex-snapshot
Machine learning identifies potential accessory resistance-associated mutations in HIV-1 integrase
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