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Bing A, Hu Y, Prague M, Hill AL, Li JZ, Bosch RJ, De Gruttola V, Wang R. Comparison of empirical and dynamic models for HIV viral load rebound after treatment interruption. STATISTICAL COMMUNICATIONS IN INFECTIOUS DISEASES 2020; 12:20190021. [PMID: 34158910 PMCID: PMC8216669 DOI: 10.1515/scid-2019-0021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVE To compare empirical and mechanistic modeling approaches for describing HIV-1 RNA viral load trajectories after antiretroviral treatment interruption and for identifying factors that predict features of viral rebound process. METHODS We apply and compare two modeling approaches in analysis of data from 346 participants in six AIDS Clinical Trial Group studies. From each separate analysis, we identify predictors for viral set points and delay in rebound. Our empirical model postulates a parametric functional form whose parameters represent different features of the viral rebound process, such as rate of rise and viral load set point. The viral dynamics model augments standard HIV dynamics models-a class of mathematical models based on differential equations describing biological mechanisms-by including reactivation of latently infected cells and adaptive immune response. We use Monolix, which makes use of a Stochastic Approximation of the Expectation-Maximization algorithm, to fit non-linear mixed effects models incorporating observations that were below the assay limit of quantification. RESULTS Among the 346 participants, the median age at treatment interruption was 42. Ninety-three percent of participants were male and sixty-five percent, white non-Hispanic. Both models provided a reasonable fit to the data and can accommodate atypical viral load trajectories. The median set points obtained from two approaches were similar: 4.44 log10 copies/mL from the empirical model and 4.59 log10 copies/mL from the viral dynamics model. Both models revealed that higher nadir CD4 cell counts and ART initiation during acute/recent phase were associated with lower viral set points and identified receiving a non-nucleoside reverse transcriptase inhibitor (NNRTI)-based pre-ATI regimen as a predictor for a delay in rebound. CONCLUSION Although based on different sets of assumptions, both models lead to similar conclusions regarding features of viral rebound process.
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Affiliation(s)
- Ante Bing
- Department of Mathematics and Statistics, Boston University, Boston, MA, 02215, USA
| | - Yuchen Hu
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Melanie Prague
- University of Bordeaux, Inria Bordeaux Sud-Ouest, Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR 1219, F-33000 Bordeaux, France
| | - Alison L Hill
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston MA 02215, USA
| | - Ronald J Bosch
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Victor De Gruttola
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Rui Wang
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
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Commenges D. Dealing with death when studying disease or physiological marker: the stochastic system approach to causality. LIFETIME DATA ANALYSIS 2019; 25:381-405. [PMID: 30448970 DOI: 10.1007/s10985-018-9454-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 11/12/2018] [Indexed: 06/09/2023]
Abstract
The stochastic system approach to causality is applied to situations where the risk of death is not negligible. This approach grounds causality on physical laws, distinguishes system and observation and represents the system by multivariate stochastic processes. The particular role of death is highlighted, and it is shown that local influences must be defined on the random horizon of time of death. We particularly study the problem of estimating the effect of a factor V on a process of interest Y, taking death into account. We unify the cases where Y is a counting process (describing an event) and the case where Y is quantitative; we examine the case of observations in continuous and discrete time and we study the issue of whether the mechanism leading to incomplete data can be ignored. Finally, we give an example of a situation where we are interested in estimating the effect of a factor (blood pressure) on cognitive ability in elderly.
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Villain L, Commenges D, Pasin C, Prague M, Thiébaut R. Adaptive protocols based on predictions from a mechanistic model of the effect of IL7 on CD4 counts. Stat Med 2018; 38:221-235. [PMID: 30259533 DOI: 10.1002/sim.7957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 07/05/2018] [Accepted: 08/18/2018] [Indexed: 12/16/2022]
Abstract
In human immunodeficiency virus-infected patients, antiretroviral therapy suppresses the viral replication, which is followed in most patients by a restoration of CD4+ T cells pool. For patients who fail to do so, repeated injections of exogenous interleukin 7 (IL7) are experimented. The IL7 is a cytokine that is involved in the T cell homeostasis and the INSPIRE study has shown that injections of IL7 induced a proliferation of CD4+ T cells. Phase I/II INSPIRE 2 and 3 studies have evaluated a protocol in which a first cycle of three IL7 injections is followed by a new cycle at each visit when the patient has less than 550 CD4 cells/μL. Restoration of the CD4 concentration has been demonstrated, but the long-term best adaptive protocol is yet to be determined. A mechanistic model of the evolution of CD4 after IL7 injections has been developed, which is based on a system of ordinary differential equations and includes random effects. Based on the estimation of this model, we use a Bayesian approach to forecast the dynamics of CD4 in new patients. We propose four prediction-based adaptive protocols of injections to minimize the time spent under 500 CD4 cells/μL for each patient, without increasing the number of injections received too much. We show that our protocols significantly reduce the time spent under 500 CD4 over a period of two years, without increasing the number of injections. These protocols have the potential to increase the efficiency of this therapy.
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Affiliation(s)
- Laura Villain
- University of Bordeaux, Inserm, Bordeaux, Population Health Research Center, Team SISTM, Bordeaux, France.,INRIA Bordeaux Sud Ouest, Talence, France.,Vaccine Research Institute (VRI), Hôpital Henri Mondor, Créteil, France
| | - Daniel Commenges
- University of Bordeaux, Inserm, Bordeaux, Population Health Research Center, Team SISTM, Bordeaux, France.,INRIA Bordeaux Sud Ouest, Talence, France.,Vaccine Research Institute (VRI), Hôpital Henri Mondor, Créteil, France
| | - Chloé Pasin
- University of Bordeaux, Inserm, Bordeaux, Population Health Research Center, Team SISTM, Bordeaux, France.,INRIA Bordeaux Sud Ouest, Talence, France.,Vaccine Research Institute (VRI), Hôpital Henri Mondor, Créteil, France
| | - Mélanie Prague
- University of Bordeaux, Inserm, Bordeaux, Population Health Research Center, Team SISTM, Bordeaux, France.,INRIA Bordeaux Sud Ouest, Talence, France.,Vaccine Research Institute (VRI), Hôpital Henri Mondor, Créteil, France
| | - Rodolphe Thiébaut
- University of Bordeaux, Inserm, Bordeaux, Population Health Research Center, Team SISTM, Bordeaux, France.,INRIA Bordeaux Sud Ouest, Talence, France.,Vaccine Research Institute (VRI), Hôpital Henri Mondor, Créteil, France
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4
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Jarne A, Commenges D, Villain L, Prague M, Lévy Y, Thiébaut R. Modeling $\mathrm{CD4}^{+}$ T cells dynamics in HIV-infected patients receiving repeated cycles of exogenous Interleukin 7. Ann Appl Stat 2017. [DOI: 10.1214/17-aoas1047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Desmée S, Mentré F, Veyrat-Follet C, Sébastien B, Guedj J. Nonlinear joint models for individual dynamic prediction of risk of death using Hamiltonian Monte Carlo: application to metastatic prostate cancer. BMC Med Res Methodol 2017; 17:105. [PMID: 28716060 PMCID: PMC5513366 DOI: 10.1186/s12874-017-0382-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/30/2017] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Joint models of longitudinal and time-to-event data are increasingly used to perform individual dynamic prediction of a risk of event. However the difficulty to perform inference in nonlinear models and to calculate the distribution of individual parameters has long limited this approach to linear mixed-effect models for the longitudinal part. Here we use a Bayesian algorithm and a nonlinear joint model to calculate individual dynamic predictions. We apply this approach to predict the risk of death in metastatic castration-resistant prostate cancer (mCRPC) patients with frequent Prostate-Specific Antigen (PSA) measurements. METHODS A joint model is built using a large population of 400 mCRPC patients where PSA kinetics is described by a biexponential function and the hazard function is a PSA-dependent function. Using Hamiltonian Monte Carlo algorithm implemented in Stan software and the estimated population parameters in this population as priors, the a posteriori distribution of the hazard function is computed for a new patient knowing his PSA measurements until a given landmark time. Time-dependent area under the ROC curve (AUC) and Brier score are derived to assess discrimination and calibration of the model predictions, first on 200 simulated patients and then on 196 real patients that are not included to build the model. RESULTS Satisfying coverage probabilities of Monte Carlo prediction intervals are obtained for longitudinal and hazard functions. Individual dynamic predictions provide good predictive performances for landmark times larger than 12 months and horizon time of up to 18 months for both simulated and real data. CONCLUSIONS As nonlinear joint models can characterize the kinetics of biomarkers and their link with a time-to-event, this approach could be useful to improve patient's follow-up and the early detection of most at risk patients.
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Affiliation(s)
- Solène Desmée
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, 16, rue Henri Huchard, Paris, 75018 France
| | - France Mentré
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, 16, rue Henri Huchard, Paris, 75018 France
| | | | | | - Jérémie Guedj
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, 16, rue Henri Huchard, Paris, 75018 France
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Prague M, Commenges D, Gran JM, Ledergerber B, Young J, Furrer H, Thiébaut R. Dynamic models for estimating the effect of HAART on CD4 in observational studies: Application to the Aquitaine Cohort and the Swiss HIV Cohort Study. Biometrics 2016; 73:294-304. [PMID: 27461460 DOI: 10.1111/biom.12564] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 05/01/2016] [Accepted: 06/01/2016] [Indexed: 11/29/2022]
Abstract
Highly active antiretroviral therapy (HAART) has proved efficient in increasing CD4 counts in many randomized clinical trials. Because randomized trials have some limitations (e.g., short duration, highly selected subjects), it is interesting to assess the effect of treatments using observational studies. This is challenging because treatment is started preferentially in subjects with severe conditions. This general problem had been treated using Marginal Structural Models (MSM) relying on the counterfactual formulation. Another approach to causality is based on dynamical models. We present three discrete-time dynamic models based on linear increments models (LIM): the first one based on one difference equation for CD4 counts, the second with an equilibrium point, and the third based on a system of two difference equations, which allows jointly modeling CD4 counts and viral load. We also consider continuous-time models based on ordinary differential equations with non-linear mixed effects (ODE-NLME). These mechanistic models allow incorporating biological knowledge when available, which leads to increased statistical evidence for detecting treatment effect. Because inference in ODE-NLME is numerically challenging and requires specific methods and softwares, LIM are a valuable intermediary option in terms of consistency, precision, and complexity. We compare the different approaches in simulation and in illustration on the ANRS CO3 Aquitaine Cohort and the Swiss HIV Cohort Study.
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Affiliation(s)
- Mélanie Prague
- Harvard T.H. Chan School of Public Health, Biostatistics Department, Boston, U.S.A
| | - Daniel Commenges
- University of Bordeaux, ISPED, F-33000 Bordeaux, France.,INSERM, U1219 Bordeaux Population Health Research Centre, F-33000, Bordeaux, France.,INRIA (SISTM) Centre Recherche Bordeaux Sud-Ouest, University of Bordeaux, Talence, France
| | - Jon Michael Gran
- Oslo Center for Biostatistics and Epidemiology, Oslo University Hospital and University of Oslo, Norway
| | - Bruno Ledergerber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, Switzerland
| | - Jim Young
- Basel Institute for Clinical Epidemiology and Biostatistics, University Hospital of Basel, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases Bern University Hospital, University of Bern, Switzerland
| | - Rodolphe Thiébaut
- University of Bordeaux, ISPED, F-33000 Bordeaux, France.,INSERM, U1219 Bordeaux Population Health Research Centre, F-33000, Bordeaux, France.,INRIA (SISTM) Centre Recherche Bordeaux Sud-Ouest, University of Bordeaux, Talence, France
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Commenges D, Gégout-Petit A. The stochastic system approach for estimating dynamic treatments effect. LIFETIME DATA ANALYSIS 2015; 21:561-578. [PMID: 25665819 DOI: 10.1007/s10985-015-9322-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 01/28/2015] [Indexed: 06/04/2023]
Abstract
The problem of assessing the effect of a treatment on a marker in observational studies raises the difficulty that attribution of the treatment may depend on the observed marker values. As an example, we focus on the analysis of the effect of a HAART on CD4 counts, where attribution of the treatment may depend on the observed marker values. This problem has been treated using marginal structural models relying on the counterfactual/potential response formalism. Another approach to causality is based on dynamical models, and causal influence has been formalized in the framework of the Doob-Meyer decomposition of stochastic processes. Causal inference however needs assumptions that we detail in this paper and we call this approach to causality the "stochastic system" approach. First we treat this problem in discrete time, then in continuous time. This approach allows incorporating biological knowledge naturally. When working in continuous time, the mechanistic approach involves distinguishing the model for the system and the model for the observations. Indeed, biological systems live in continuous time, and mechanisms can be expressed in the form of a system of differential equations, while observations are taken at discrete times. Inference in mechanistic models is challenging, particularly from a numerical point of view, but these models can yield much richer and reliable results.
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Affiliation(s)
| | - Anne Gégout-Petit
- Institut Elie Cartan, UMR CNRS 7502, Univ. de Lorraine, Nancy, France.
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8
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Thiébaut R, Prague M, Commenges D. [Mathematical dynamical models for personalized medicine]. Med Sci (Paris) 2014; 30 Spec No 2:23-6. [PMID: 25407454 DOI: 10.1051/medsci/201430s205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
One of the necessary conditions to perform any personalized medicine is to obtain good individual predictions. In addition to the numerous markers available (omics data), the methods used to analyze the data are very important too. We are presenting an example of mathematical dynamical mechanistic model that could be used for adapting the antiretroviral treatment in patients infected by the human immunodeficiency virus. The interest of this type of approach is to build a model based on biological knowledge about the interaction between markers and therefore to allow for a better predictive power.
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Affiliation(s)
- Rodolphe Thiébaut
- Inserm U897, INRIA SISTM (statistics in systems biology and translational medicine), université de Bordeaux, ISPED (institut de santé publique, d'épidémiologie et de développement), CHU de Bordeaux, unité de soutien méthodologique à la recherche clinique et épidémiologique, Bordeaux, France; institut de recherche vaccinale (Labex) UPEC, Créteil, France
| | - Mélanie Prague
- Inserm U897, INRIA SISTM (statistics in systems biology and translational medicine), université de Bordeaux, ISPED (institut de santé publique, d'épidémiologie et de développement), CHU de Bordeaux, unité de soutien méthodologique à la recherche clinique et épidémiologique, Bordeaux, France; institut de recherche vaccinale (Labex) UPEC, Créteil, France
| | - Daniel Commenges
- Inserm U897, INRIA SISTM (statistics in systems biology and translational medicine), université de Bordeaux, ISPED (institut de santé publique, d'épidémiologie et de développement), CHU de Bordeaux, unité de soutien méthodologique à la recherche clinique et épidémiologique, Bordeaux, France; institut de recherche vaccinale (Labex) UPEC, Créteil, France
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9
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Barker CIS, Germovsek E, Hoare RL, Lestner JM, Lewis J, Standing JF. Pharmacokinetic/pharmacodynamic modelling approaches in paediatric infectious diseases and immunology. Adv Drug Deliv Rev 2014; 73:127-39. [PMID: 24440429 PMCID: PMC4076844 DOI: 10.1016/j.addr.2014.01.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 12/09/2013] [Accepted: 01/11/2014] [Indexed: 02/02/2023]
Abstract
Pharmacokinetic/pharmacodynamic (PKPD) modelling is used to describe and quantify dose-concentration-effect relationships. Within paediatric studies in infectious diseases and immunology these methods are often applied to developing guidance on appropriate dosing. In this paper, an introduction to the field of PKPD modelling is given, followed by a review of the PKPD studies that have been undertaken in paediatric infectious diseases and immunology. The main focus is on identifying the methodological approaches used to define the PKPD relationship in these studies. The major findings were that most studies of infectious diseases have developed a PK model and then used simulations to define a dose recommendation based on a pre-defined PD target, which may have been defined in adults or in vitro. For immunological studies much of the modelling has focused on either PK or PD, and since multiple drugs are usually used, delineating the relative contributions of each is challenging. The use of dynamical modelling of in vitro antibacterial studies, and paediatric HIV mechanistic PD models linked with the PK of all drugs, are emerging methods that should enhance PKPD-based recommendations in the future.
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Affiliation(s)
- Charlotte I S Barker
- Paediatric Infectious Diseases Research Group, Division of Clinical Sciences, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK; Infectious Diseases and Microbiology Unit, University College London, Institute of Child Health, London WC1N 1EH, UK
| | - Eva Germovsek
- Infectious Diseases and Microbiology Unit, University College London, Institute of Child Health, London WC1N 1EH, UK
| | - Rollo L Hoare
- Infectious Diseases and Microbiology Unit, University College London, Institute of Child Health, London WC1N 1EH, UK; CoMPLEX, University College London, Physics Building, Gower Street, London WC1E 6BT, UK
| | - Jodi M Lestner
- Paediatric Infectious Diseases Research Group, Division of Clinical Sciences, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK; Faculty of Medicine, Imperial College London, London, UK
| | - Joanna Lewis
- Infectious Diseases and Microbiology Unit, University College London, Institute of Child Health, London WC1N 1EH, UK; CoMPLEX, University College London, Physics Building, Gower Street, London WC1E 6BT, UK
| | - Joseph F Standing
- Infectious Diseases and Microbiology Unit, University College London, Institute of Child Health, London WC1N 1EH, UK; CoMPLEX, University College London, Physics Building, Gower Street, London WC1E 6BT, UK.
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Aalen OO, Røysland K, Gran JM, Kouyos R, Lange T. Can we believe the DAGs? A comment on the relationship between causal DAGs and mechanisms. Stat Methods Med Res 2014; 25:2294-2314. [PMID: 24463886 PMCID: PMC5051601 DOI: 10.1177/0962280213520436] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Directed acyclic graphs (DAGs) play a large role in the modern approach to causal inference. DAGs describe the relationship between measurements taken at various discrete times including the effect of interventions. The causal mechanisms, on the other hand, would naturally be assumed to be a continuous process operating over time in a cause–effect fashion. How does such immediate causation, that is causation occurring over very short time intervals, relate to DAGs constructed from discrete observations? We introduce a time-continuous model and simulate discrete observations in order to judge the relationship between the DAG and the immediate causal model. We find that there is no clear relationship; indeed the Bayesian network described by the DAG may not relate to the causal model. Typically, discrete observations of a process will obscure the conditional dependencies that are represented in the underlying mechanistic model of the process. It is therefore doubtful whether DAGs are always suited to describe causal relationships unless time is explicitly considered in the model. We relate the issues to mechanistic modeling by using the concept of local (in)dependence. An example using data from the Swiss HIV Cohort Study is presented.
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Affiliation(s)
- O O Aalen
- Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - K Røysland
- Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - J M Gran
- Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - R Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - T Lange
- Department of Biostatistics, University of Copenhagen, Copenhagen K, Denmark
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Prague M, Commenges D, Guedj J, Drylewicz J, Thiébaut R. NIMROD: a program for inference via a normal approximation of the posterior in models with random effects based on ordinary differential equations. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2013; 111:447-458. [PMID: 23764196 DOI: 10.1016/j.cmpb.2013.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 03/04/2013] [Accepted: 04/23/2013] [Indexed: 06/02/2023]
Abstract
Models based on ordinary differential equations (ODE) are widespread tools for describing dynamical systems. In biomedical sciences, data from each subject can be sparse making difficult to precisely estimate individual parameters by standard non-linear regression but information can often be gained from between-subjects variability. This makes natural the use of mixed-effects models to estimate population parameters. Although the maximum likelihood approach is a valuable option, identifiability issues favour Bayesian approaches which can incorporate prior knowledge in a flexible way. However, the combination of difficulties coming from the ODE system and from the presence of random effects raises a major numerical challenge. Computations can be simplified by making a normal approximation of the posterior to find the maximum of the posterior distribution (MAP). Here we present the NIMROD program (normal approximation inference in models with random effects based on ordinary differential equations) devoted to the MAP estimation in ODE models. We describe the specific implemented features such as convergence criteria and an approximation of the leave-one-out cross-validation to assess the model quality of fit. In pharmacokinetics models, first, we evaluate the properties of this algorithm and compare it with FOCE and MCMC algorithms in simulations. Then, we illustrate NIMROD use on Amprenavir pharmacokinetics data from the PUZZLE clinical trial in HIV infected patients.
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Affiliation(s)
- Mélanie Prague
- Univ. Bordeaux, ISPED, Centre INSERM U897-Epidemiologie-Biostatistique, F-33000 Bordeaux, France.
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12
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Prague M, Commenges D, Thiébaut R. Dynamical models of biomarkers and clinical progression for personalized medicine: the HIV context. Adv Drug Deliv Rev 2013; 65:954-65. [PMID: 23603207 DOI: 10.1016/j.addr.2013.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 02/15/2013] [Accepted: 04/10/2013] [Indexed: 01/11/2023]
Abstract
Mechanistic models, based on ordinary differential equation systems, can exhibit very good predictive abilities that will be useful to build treatment monitoring strategies. In this review, we present the potential and the limitations of such models for guiding treatment (monitoring and optimizing) in HIV-infected patients. In the context of antiretroviral therapy, several biological processes should be considered in addition to the interaction between viruses and the host immune system: the mechanisms of action of the drugs, their pharmacokinetics and pharmacodynamics, as well as the viral and host characteristics. Another important aspect to take into account is clinical progression, although its implementation in such modelling approaches is not easy. Finally, the control theory and the use of intrinsic properties of mechanistic models make them very relevant for dynamic treatment adaptation. Their implementation would nevertheless require their evaluation through clinical trials.
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