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Kuo NIH, Garcia F, Sönnerborg A, Böhm M, Kaiser R, Zazzi M, Polizzotto M, Jorm L, Barbieri S. Generating synthetic clinical data that capture class imbalanced distributions with generative adversarial networks: Example using antiretroviral therapy for HIV. J Biomed Inform 2023; 144:104436. [PMID: 37451495 DOI: 10.1016/j.jbi.2023.104436] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/24/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
OBJECTIVE Clinical data's confidential nature often limits the development of machine learning models in healthcare. Generative adversarial networks (GANs) can synthesise realistic datasets, but suffer from mode collapse, resulting in low diversity and bias towards majority demographics and common clinical practices. This work proposes an extension to the classic GAN framework that includes a variational autoencoder (VAE) and an external memory mechanism to overcome these limitations and generate synthetic data accurately describing imbalanced class distributions commonly found in clinical variables. METHODS The proposed method generated a synthetic dataset related to antiretroviral therapy for human immunodeficiency virus (ART for HIV). We evaluated it based on five metrics: (1) accurately representing imbalanced class distribution; (2) the realism of the individual variables; (3) the realism among variables; (4) patient disclosure risk; and (5) the utility of the generated dataset for developing downstream machine learning models. RESULTS The proposed method overcomes the issue of mode collapse and generates a synthetic dataset that accurately describes imbalanced class distributions commonly found in clinical variables. The generated data has a patient disclosure risk of 0.095%, lower than the 9% threshold stated by Health Canada and the European Medicines Agency, making it suitable for distribution to the research community with high security. The generated data also has high utility, indicating the potential of the proposed method to enable the development of downstream machine learning algorithms for healthcare applications using synthetic data. CONCLUSION Our proposed extension to the classic GAN framework, which includes a VAE and an external memory mechanism, represents a promising approach towards generating synthetic data that accurately describe imbalanced class distributions commonly found in clinical variables. This method overcomes the limitations of GANs and creates more realistic datasets with higher patient cohort diversity, facilitating the development of downstream machine learning algorithms for healthcare applications.
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Affiliation(s)
- Nicholas I-Hsien Kuo
- Centre for Big Data Research in Health, the University of New South Wales, Sydney, Australia.
| | - Federico Garcia
- Instituto de Investigación Ibs.Granada, Spain; Hospital Universitario San Cecilio, Spain; CIBER de Enfermedades Infecciosas, Spain
| | | | | | - Rolf Kaiser
- Uniklinik Köln, Universität zu Köln, Germany
| | | | | | - Louisa Jorm
- Centre for Big Data Research in Health, the University of New South Wales, Sydney, Australia
| | - Sebastiano Barbieri
- Centre for Big Data Research in Health, the University of New South Wales, Sydney, Australia
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Kuo NIH, Polizzotto MN, Finfer S, Garcia F, Sönnerborg A, Zazzi M, Böhm M, Kaiser R, Jorm L, Barbieri S. The Health Gym: synthetic health-related datasets for the development of reinforcement learning algorithms. Sci Data 2022; 9:693. [PMID: 36369205 PMCID: PMC9652426 DOI: 10.1038/s41597-022-01784-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
In recent years, the machine learning research community has benefited tremendously from the availability of openly accessible benchmark datasets. Clinical data are usually not openly available due to their confidential nature. This has hampered the development of reproducible and generalisable machine learning applications in health care. Here we introduce the Health Gym - a growing collection of highly realistic synthetic medical datasets that can be freely accessed to prototype, evaluate, and compare machine learning algorithms, with a specific focus on reinforcement learning. The three synthetic datasets described in this paper present patient cohorts with acute hypotension and sepsis in the intensive care unit, and people with human immunodeficiency virus (HIV) receiving antiretroviral therapy. The datasets were created using a novel generative adversarial network (GAN). The distributions of variables, and correlations between variables and trends in variables over time in the synthetic datasets mirror those in the real datasets. Furthermore, the risk of sensitive information disclosure associated with the public distribution of the synthetic datasets is estimated to be very low.
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Affiliation(s)
- Nicholas I-Hsien Kuo
- Centre for Big Data Research in Health, University of New South Wales, Sydney, Australia.
| | | | - Simon Finfer
- The George Institute for Global Health, Sydney, Australia
- University of New South Wales, Sydney, Australia
- Imperial College London, London, United Kingdom
| | | | | | | | - Michael Böhm
- Uniklinik Köln, Universität zu Köln, Cologne, Germany
| | - Rolf Kaiser
- Uniklinik Köln, Universität zu Köln, Cologne, Germany
| | - Louisa Jorm
- Centre for Big Data Research in Health, University of New South Wales, Sydney, Australia
| | - Sebastiano Barbieri
- Centre for Big Data Research in Health, University of New South Wales, Sydney, Australia
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Mu Y, Kodidela S, Wang Y, Kumar S, Cory TJ. The dawn of precision medicine in HIV: state of the art of pharmacotherapy. Expert Opin Pharmacother 2018; 19:1581-1595. [PMID: 30234392 DOI: 10.1080/14656566.2018.1515916] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Combination antiretroviral therapy (ART) reduces viral load to under the limit of detection, successfully decreasing HIV-related morbidity and mortality. Due to viral mutations, complex drug combinations and different patient response, there is an increasing demand for individualized treatment options for patients. AREAS COVERED This review first summarizes the pharmacokinetic and pharmacodynamic profile of clinical first-line drugs, which serves as guidance for antiretroviral precision medicine. Factors which have influential effects on drug efficacy and thus precision medicine are discussed: patients' pharmacogenetic information, virus mutations, comorbidities, and immune recovery. Furthermore, strategies to improve the application of precision medicine are discussed. EXPERT OPINION Precision medicine for ART requires comprehensive information on the drug, virus, and clinical data from the patients. The clinically available genetic tests are a good starting point. To better apply precision medicine, deeper knowledge of drug concentrations, HIV reservoirs, and efficacy associated genes, such as polymorphisms of drug transporters and metabolizing enzymes, are required. With advanced computer-based prediction systems which integrate more comprehensive information on pharmacokinetics, pharmacodynamics, pharmacogenomics, and the clinically relevant information of the patients, precision medicine will lead to better treatment choices and improved disease outcomes.
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Affiliation(s)
- Ying Mu
- a Department of Clinical Pharmacy and Translational Science , University of Tennessee Health Science Center College of Pharmacy , Memphis , USA
| | - Sunitha Kodidela
- b Department of Pharmaceutical Science , University of Tennessee Health Science Center College of Pharmacy , Memphis , USA
| | - Yujie Wang
- b Department of Pharmaceutical Science , University of Tennessee Health Science Center College of Pharmacy , Memphis , USA
| | - Santosh Kumar
- b Department of Pharmaceutical Science , University of Tennessee Health Science Center College of Pharmacy , Memphis , USA
| | - Theodore J Cory
- a Department of Clinical Pharmacy and Translational Science , University of Tennessee Health Science Center College of Pharmacy , Memphis , USA
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Parbhoo S, Bogojeska J, Zazzi M, Roth V, Doshi-Velez F. Combining Kernel and Model Based Learning for HIV Therapy Selection. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2017; 2017:239-248. [PMID: 28815137 PMCID: PMC5543338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We present a mixture-of-experts approach for HIV therapy selection. The heterogeneity in patient data makes it difficult for one particular model to succeed at providing suitable therapy predictions for all patients. An appropriate means for addressing this heterogeneity is through combining kernel and model-based techniques. These methods capture different kinds of information: kernel-based methods are able to identify clusters of similar patients, and work well when modelling the viral response for these groups. In contrast, model-based methods capture the sequential process of decision making, and are able to find simpler, yet accurate patterns in response for patients outside these groups. We take advantage of this information by proposing a mixture-of-experts model that automatically selects between the methods in order to assign the most appropriate therapy choice to an individual. Overall, we verify that therapy combinations proposed using this approach significantly outperform previous methods.
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Affiliation(s)
- Sonali Parbhoo
- University of Basel, Department of Mathematics and Computer Science, Switzerland
| | | | - Maurizio Zazzi
- University of Siena, Department of Medical Biotechnology, Italy
| | - Volker Roth
- University of Basel, Department of Mathematics and Computer Science, Switzerland
| | - Finale Doshi-Velez
- Harvard University, John A. Paulsen School of Engineering and Applied Sciences, Cambridge, MA
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Pironti A, Pfeifer N, Walter H, Jensen BEO, Zazzi M, Gomes P, Kaiser R, Lengauer T. Using drug exposure for predicting drug resistance - A data-driven genotypic interpretation tool. PLoS One 2017; 12:e0174992. [PMID: 28394945 PMCID: PMC5386274 DOI: 10.1371/journal.pone.0174992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/17/2017] [Indexed: 01/31/2023] Open
Abstract
Antiretroviral treatment history and past HIV-1 genotypes have been shown to be useful predictors for the success of antiretroviral therapy. However, this information may be unavailable or inaccurate, particularly for patients with multiple treatment lines often attending different clinics. We trained statistical models for predicting drug exposure from current HIV-1 genotype. These models were trained on 63,742 HIV-1 nucleotide sequences derived from patients with known therapeutic history, and on 6,836 genotype-phenotype pairs (GPPs). The mean performance regarding prediction of drug exposure on two test sets was 0.78 and 0.76 (ROC-AUC), respectively. The mean correlation to phenotypic resistance in GPPs was 0.51 (PhenoSense) and 0.46 (Antivirogram). Performance on prediction of therapy-success on two test sets based on genetic susceptibility scores was 0.71 and 0.63 (ROC-AUC), respectively. Compared to geno2pheno[resistance], our novel models display a similar or superior performance. Our models are freely available on the internet via www.geno2pheno.org. They can be used for inferring which drug compounds have previously been used by an HIV-1-infected patient, for predicting drug resistance, and for selecting an optimal antiretroviral therapy. Our data-driven models can be periodically retrained without expert intervention as clinical HIV-1 databases are updated and therefore reduce our dependency on hard-to-obtain GPPs.
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Affiliation(s)
- Alejandro Pironti
- Department of Computational Biology and Applied Algorithmics, Max-Planck-Institut für Informatik, Saarbrücken, Germany
- * E-mail:
| | - Nico Pfeifer
- Department of Computational Biology and Applied Algorithmics, Max-Planck-Institut für Informatik, Saarbrücken, Germany
| | - Hauke Walter
- Medizinisches Infektiologiezentrum Berlin, Berlin, Germany
- Medizinisches Labor Stendal, Stendal, Germany
| | - Björn-Erik O. Jensen
- Clinic for Gastroenterology, Hepatology, and Infectiology, University Clinic of Düsseldorf, Düsseldorf, Germany
| | - Maurizio Zazzi
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Perpétua Gomes
- Laboratorio de Biologia Molecular, LMCBM, SPC, HEM - Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
- Centro de Investigacao Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciencias da Saude Sul, Caparica, Portugal
| | - Rolf Kaiser
- Institute for Virology, University Clinic of Cologne, Cologne, Germany
| | - Thomas Lengauer
- Department of Computational Biology and Applied Algorithmics, Max-Planck-Institut für Informatik, Saarbrücken, Germany
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6
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Saladini F, Vicenti I. Role of phenotypic investigation in the era of routine genotypic HIV-1 drug resistance testing. Future Virol 2016. [DOI: 10.2217/fvl-2016-0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The emergence of drug resistance can seriously compromise HIV type-1 therapy and decrease therapeutic options. Resistance testing is highly recommended to guide treatment decisions and drug activity can be accurately predicted in the clinical setting through genotypic assays. While phenotypic systems are not suitable for monitoring drug resistance in routine laboratory practice, genotyping can misclassify unusual or complex mutational patterns, particularly with recently approved antivirals. In addition, phenotypic assays remain fundamental for characterizing candidate antiretroviral compounds. This review aims to discuss how phenotypic assays contributed to and still play a role in understanding the mechanisms of resistance of both licensed and investigational HIV type-1 inhibitors.
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Affiliation(s)
- Francesco Saladini
- Department of Medical Biotechnologies, University of Siena Italy, Policlinico Le Scotte, Viale Bracci 16 53100 Siena, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena Italy, Policlinico Le Scotte, Viale Bracci 16 53100 Siena, Italy
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Montazeri H, Günthard HF, Yang WL, Kouyos R, Beerenwinkel N. Estimating the dynamics and dependencies of accumulating mutations with applications to HIV drug resistance. Biostatistics 2015; 16:713-26. [PMID: 25979750 DOI: 10.1093/biostatistics/kxv019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 03/13/2015] [Indexed: 12/14/2022] Open
Abstract
We introduce a new model called the observed time conjunctive Bayesian network (OT-CBN) that describes the accumulation of genetic events (mutations) under partial temporal ordering constraints. Unlike other CBN models, the OT-CBN model uses sampling time points of genotypes in addition to genotypes themselves to estimate model parameters. We developed an expectation-maximization algorithm to obtain approximate maximum likelihood estimates by accounting for this additional information. In a simulation study, we show that the OT-CBN model outperforms the continuous time CBN (CT-CBN) (Beerenwinkel and Sullivant, 2009. Markov models for accumulating mutations. Biometrika 96: (3), 645-661), which does not take into account individual sampling times for parameter estimation. We also show superiority of the OT-CBN model on several datasets of HIV drug resistance mutations extracted from the Swiss HIV Cohort Study database.
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Affiliation(s)
- Hesam Montazeri
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland and SIB Swiss Institute of Bioinformatics, Basel 4058, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland Institute of Medical Virology, University of Zurich, Zurich 8057, Switzerland
| | - Wan-Lin Yang
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland Institute of Medical Virology, University of Zurich, Zurich 8057, Switzerland
| | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland Institute of Medical Virology, University of Zurich, Zurich 8057, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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Lengauer T, Pfeifer N, Kaiser R. Personalized HIV therapy to control drug resistance. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 11:57-64. [PMID: 24847654 DOI: 10.1016/j.ddtec.2014.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
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. The virus population is unique for each patient and time point. The large number of therapy options makes it difficult to select an optimal or near optimal therapy, especially with therapy-experienced patients. 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. We discuss the properties of available systems and the perspectives of the field.
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Revell AD, Wang D, Wood R, Morrow C, Tempelman H, Hamers R, Alvarez-Uria G, Streinu-Cercel A, Ene L, Wensing A, Reiss P, van Sighem AI, Nelson M, Emery S, Montaner JSG, Lane HC, Larder BA. An update to the HIV-TRePS system: the development of new computational models that do not require a genotype to predict HIV treatment outcomes. J Antimicrob Chemother 2013; 69:1104-10. [PMID: 24275116 DOI: 10.1093/jac/dkt447] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The optimal individualized selection of antiretroviral drugs in resource-limited settings is challenging because of the limited availability of drugs and genotyping. Here we describe the development of the latest computational models to predict the response to combination antiretroviral therapy without a genotype, for potential use in such settings. METHODS Random forest models were trained to predict the probability of a virological response to therapy (<50 copies HIV RNA/mL) following virological failure using the following data from 22,567 treatment-change episodes including 1090 from southern Africa: baseline viral load and CD4 cell count, treatment history, drugs in the new regimen, time to follow-up and follow-up viral load. The models were assessed during cross-validation and with an independent global test set of 1000 cases including 100 from southern Africa. The models' accuracy [area under the receiver-operating characteristic curve (AUC)] was evaluated and compared with genotyping using rules-based interpretation systems for those cases with genotypes available. RESULTS The models achieved AUCs of 0.79-0.84 (mean 0.82) during cross-validation, 0.80 with the global test set and 0.78 with the southern African subset. The AUCs were significantly lower (0.56-0.57) for genotyping. CONCLUSIONS The models predicted virological response to HIV therapy without a genotype as accurately as previous models that included a genotype. They were accurate for cases from southern Africa and significantly more accurate than genotyping. These models will be accessible via the online treatment support tool HIV-TRePS and have the potential to help optimize antiretroviral therapy in resource-limited settings where genotyping is not generally available.
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Affiliation(s)
- Andrew D Revell
- HIV Resistance Response Database Initiative (RDI), London, UK
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10
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Masso M, Vaisman II. Sequence and structure based models of HIV-1 protease and reverse transcriptase drug resistance. BMC Genomics 2013; 14 Suppl 4:S3. [PMID: 24268064 PMCID: PMC3849442 DOI: 10.1186/1471-2164-14-s4-s3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Successful management of chronic human immunodeficiency virus type 1 (HIV-1) infection with a cocktail of antiretroviral medications can be negatively affected by the presence of drug resistant mutations in the viral targets. These targets include the HIV-1 protease (PR) and reverse transcriptase (RT) proteins, for which a number of inhibitors are available on the market and routinely prescribed. Protein mutational patterns are associated with varying degrees of resistance to their respective inhibitors, with extremes that can range from continued susceptibility to cross-resistance across all drugs. RESULTS Here we implement statistical learning algorithms to develop structure- and sequence-based models for systematically predicting the effects of mutations in the PR and RT proteins on resistance to each of eight and eleven inhibitors, respectively. Employing a four-body statistical potential, mutant proteins are represented as feature vectors whose components quantify relative environmental perturbations at amino acid residue positions in the respective target structures upon mutation. Two approaches are implemented in developing sequence-based models, based on use of either relative frequencies or counts of n-grams, to generate vectors for representing mutant proteins. To the best of our knowledge, this is the first reported study on structure- and sequence-based predictive models of HIV-1 PR and RT drug resistance developed by implementing a four-body statistical potential and n-grams, respectively, to generate mutant attribute vectors. Performance of the learning methods is evaluated on the basis of tenfold cross-validation, using previously assayed and publicly available in vitro data relating mutational patterns in the targets to quantified inhibitor susceptibility changes. CONCLUSION Overall performance results are competitive with those of a previously published study utilizing a sequence-based strategy, while our structure- and sequence-based models provide orthogonal and complementary prediction methodologies, respectively. In a novel application, we describe a technique for identifying every possible pair of RT inhibitors as either potentially effective together as part of a cocktail, or a combination that is to be avoided.
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Revell AD, Wang D, Wood R, Morrow C, Tempelman H, Hamers RL, Alvarez-Uria G, Streinu-Cercel A, Ene L, Wensing AMJ, DeWolf F, Nelson M, Montaner JS, Lane HC, Larder BA. Computational models can predict response to HIV therapy without a genotype and may reduce treatment failure in different resource-limited settings. J Antimicrob Chemother 2013; 68:1406-14. [PMID: 23485767 DOI: 10.1093/jac/dkt041] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Genotypic HIV drug-resistance testing is typically 60%-65% predictive of response to combination antiretroviral therapy (ART) and is valuable for guiding treatment changes. Genotyping is unavailable in many resource-limited settings (RLSs). We aimed to develop models that can predict response to ART without a genotype and evaluated their potential as a treatment support tool in RLSs. METHODS Random forest models were trained to predict the probability of response to ART (≤400 copies HIV RNA/mL) using the following data from 14 891 treatment change episodes (TCEs) after virological failure, from well-resourced countries: viral load and CD4 count prior to treatment change, treatment history, drugs in the new regimen, time to follow-up and follow-up viral load. Models were assessed by cross-validation during development, with an independent set of 800 cases from well-resourced countries, plus 231 cases from Southern Africa, 206 from India and 375 from Romania. The area under the receiver operating characteristic curve (AUC) was the main outcome measure. RESULTS The models achieved an AUC of 0.74-0.81 during cross-validation and 0.76-0.77 with the 800 test TCEs. They achieved AUCs of 0.58-0.65 (Southern Africa), 0.63 (India) and 0.70 (Romania). Models were more accurate for data from the well-resourced countries than for cases from Southern Africa and India (P < 0.001), but not Romania. The models identified alternative, available drug regimens predicted to result in virological response for 94% of virological failures in Southern Africa, 99% of those in India and 93% of those in Romania. CONCLUSIONS We developed computational models that predict virological response to ART without a genotype with comparable accuracy to genotyping with rule-based interpretation. These models have the potential to help optimize antiretroviral therapy for patients in RLSs where genotyping is not generally available.
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Affiliation(s)
- A D Revell
- The HIV Resistance Response Database Initiative (RDI), London, UK
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Svärd J, Sönnerborg A. Optimizing background therapy in treatment-experienced HIV-1 patients by rules-based algorithms and bioinformatics. Future Virol 2012. [DOI: 10.2217/fvl.12.66] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In HIV-1-infected patients with extensive drug resistance, the optimization of background antiretroviral therapy is essential when changing drugs after treatment failure. The genotypic sensitivity score (GSS) and phenotypic sensitivity score (PSS), determined by rules-based algorithms, are employed to predict which drugs to select in a background therapy in order to receive the best treatment response when a new drug will be used, both in investigational trials of new agents and in clinical care. However, the outcome of the GSS/PSS approach for the purpose of assessing antiretroviral efficacy in patients with multiresistance has become more problematic, despite improvements such as drug potency weighting and adding information on treatment history. Bioinformatics-based methods are more recent attractive alternatives that have demonstrated equal or better precision compared with rules-based algorithms. This review aims to discuss the usefulness of GSS/PSS and bioinformatics, respectively, for the optimization of anti-HIV background therapy in heavily treatment-experienced patients.
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Affiliation(s)
- Jenny Svärd
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sönnerborg
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
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Lengauer T. Bioinformatical assistance of selecting anti-HIV therapies: where do we stand? Intervirology 2012; 55:108-12. [PMID: 22286878 DOI: 10.1159/000332000] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In this opinion statement, we give a critical synopsis of the state-of-the-art of bioinformatic HIV resistance analysis and point out what we consider to be challenges and perspectives.
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Oette M, Schülter E, Rosen-Zvi M, Peres Y, Zazzi M, Sönnerborg A, Struck D, Altmann A, Kaiser R. Efficacy of antiretroviral therapy switch in HIV-infected patients: a 10-year analysis of the EuResist Cohort. Intervirology 2012; 55:160-6. [PMID: 22286887 DOI: 10.1159/000332018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Highly active antiretroviral therapy (HAART) has been shown to be effective in many recent trials. However, there is limited data on time trends of HAART efficacy after treatment change. METHODS Data from different European cohorts were compiled within the EuResist Project. The efficacy of HAART defined by suppression of viral replication at 24 weeks after therapy switch was analyzed considering previous treatment modifications from 1999 to 2008. RESULTS Altogether, 12,323 treatment change episodes in 7,342 patients were included in the analysis. In 1999, HAART after treatment switch was effective in 38.0% of the patients who had previously undergone 1-5 therapies. This figure rose to 85.0% in 2008. In patients with more than 5 previous therapies, efficacy rose from 23.9 to 76.2% in the same time period. In patients with detectable viral load at therapy switch, the efficacy rose from 23.3 to 66.7% with 1-5 previous treatments and from 14.4 to 55.6% with more than 5 previous treatments. CONCLUSION The results of this large cohort show that the outcome of HAART switch has improved considerably over the last years. This result was particularly observed in the context after viral rebound. Thus, changing HAART is no longer associated with a high risk of treatment failure.
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Affiliation(s)
- Mark Oette
- Clinic for General Medicine, Gastroenterology and Infectious Diseases, Augustinerinnen Hospital, Cologne, Germany.
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Zazzi M, Incardona F, Rosen-Zvi M, Prosperi M, Lengauer T, Altmann A, Sonnerborg A, Lavee T, Schülter E, Kaiser R. Predicting Response to Antiretroviral Treatment by Machine Learning: The EuResist Project. Intervirology 2012; 55:123-7. [DOI: 10.1159/000332008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Cozzi-Lepri A, Prosperi MCF, Kjær J, Dunn D, Paredes R, Sabin CA, Lundgren JD, Phillips AN, Pillay D. Can linear regression modeling help clinicians in the interpretation of genotypic resistance data? An application to derive a lopinavir-score. PLoS One 2011; 6:e25665. [PMID: 22110581 PMCID: PMC3217925 DOI: 10.1371/journal.pone.0025665] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 09/07/2011] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The question of whether a score for a specific antiretroviral (e.g. lopinavir/r in this analysis) that improves prediction of viral load response given by existing expert-based interpretation systems (IS) could be derived from analyzing the correlation between genotypic data and virological response using statistical methods remains largely unanswered. METHODS AND FINDINGS We used the data of the patients from the UK Collaborative HIV Cohort (UK CHIC) Study for whom genotypic data were stored in the UK HIV Drug Resistance Database (UK HDRD) to construct a training/validation dataset of treatment change episodes (TCE). We used the average square error (ASE) on a 10-fold cross-validation and on a test dataset (the EuroSIDA TCE database) to compare the performance of a newly derived lopinavir/r score with that of the 3 most widely used expert-based interpretation rules (ANRS, HIVDB and Rega). Our analysis identified mutations V82A, I54V, K20I and I62V, which were associated with reduced viral response and mutations I15V and V91S which determined lopinavir/r hypersensitivity. All models performed equally well (ASE on test ranging between 1.1 and 1.3, p = 0.34). CONCLUSIONS We fully explored the potential of linear regression to construct a simple predictive model for lopinavir/r-based TCE. Although, the performance of our proposed score was similar to that of already existing IS, previously unrecognized lopinavir/r-associated mutations were identified. The analysis illustrates an approach of validation of expert-based IS that could be used in the future for other antiretrovirals and in other settings outside HIV research.
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Affiliation(s)
- Alessandro Cozzi-Lepri
- Department of Infection and Population Health, Division of Population Health, UCL Medical School, Royal Free Campus, London, United Kingdom.
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Abstract
PURPOSE OF REVIEW Genotypic resistance testing has become part of routine clinical management of HIV-infected patients. Focussing on observational studies, this review looks at recent advances in this area. RECENT FINDINGS Translation of the nucleotide sequence generated by the resistance test into clinically useful information remains a major challenge. A recent key development is the availability of therapy optimization tools to predict regimens that are most likely to achieve virological suppression. Standard genotypic resistance testing only examines protease and part of reverse transcriptase; as drugs are licensed to further targets, it has become necessary to expand the repertoire for testing. Traditionally, genotypic testing has not been attempted at viral loads less than 1000 copies/ml, but recent studies indicate that major mutations are often detected at much lower levels. Similarly, various methods have been developed for the detection of minority variants including allele-specific PCR, single-genome sequencing, and ultra-deep sequencing. SUMMARY The technology and interpretation of genotypic resistance tests is in a phase of rapid development. It remains uncertain which of these developments will become part of routine clinical practice.
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