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Aoki Y, Röshammar D, Hamrén B, Hooker AC. Model selection and averaging of nonlinear mixed-effect models for robust phase III dose selection. J Pharmacokinet Pharmacodyn 2017; 44:581-597. [PMID: 29103208 PMCID: PMC5686275 DOI: 10.1007/s10928-017-9550-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/14/2017] [Indexed: 11/25/2022]
Abstract
Population model-based (pharmacometric) approaches are widely used for the analyses of phase IIb clinical trial data to increase the accuracy of the dose selection for phase III clinical trials. On the other hand, if the analysis is based on one selected model, model selection bias can potentially spoil the accuracy of the dose selection process. In this paper, four methods that assume a number of pre-defined model structure candidates, for example a set of dose-response shape functions, and then combine or select those candidate models are introduced. The key hypothesis is that by combining both model structure uncertainty and model parameter uncertainty using these methodologies, we can make a more robust model based dose selection decision at the end of a phase IIb clinical trial. These methods are investigated using realistic simulation studies based on the study protocol of an actual phase IIb trial for an oral asthma drug candidate (AZD1981). Based on the simulation study, it is demonstrated that a bootstrap model selection method properly avoids model selection bias and in most cases increases the accuracy of the end of phase IIb decision. Thus, we recommend using this bootstrap model selection method when conducting population model-based decision-making at the end of phase IIb clinical trials.
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Duffull SB, Hooker AC. Assessing robustness of designs for random effects parameters for nonlinear mixed-effects models. J Pharmacokinet Pharmacodyn 2017; 44:611-616. [PMID: 29064062 DOI: 10.1007/s10928-017-9552-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 10/20/2017] [Indexed: 10/18/2022]
Abstract
Optimal designs for nonlinear models are dependent on the choice of parameter values. Various methods have been proposed to provide designs that are robust to uncertainty in the prior choice of parameter values. These methods are generally based on estimating the expectation of the determinant (or a transformation of the determinant) of the information matrix over the prior distribution of the parameter values. For high dimensional models this can be computationally challenging. For nonlinear mixed-effects models the question arises as to the importance of accounting for uncertainty in the prior value of the variances of the random effects parameters. In this work we explore the influence of the variance of the random effects parameters on the optimal design. We find that the method for approximating the expectation and variance of the likelihood is of potential importance for considering the influence of random effects. The most common approximation to the likelihood, based on a first-order Taylor series approximation, yields designs that are relatively insensitive to the prior value of the variance of the random effects parameters and under these conditions it appears to be sufficient to consider uncertainty on the fixed-effects parameters only.
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Strömberg EA, Hooker AC. The effect of using a robust optimality criterion in model based adaptive optimization. J Pharmacokinet Pharmacodyn 2017; 44:317-324. [PMID: 28386710 PMCID: PMC5514236 DOI: 10.1007/s10928-017-9521-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/22/2017] [Indexed: 11/26/2022]
Abstract
Optimizing designs using robust (global) optimality criteria has been shown to be a more flexible approach compared to using local optimality criteria. Additionally, model based adaptive optimal design (MBAOD) may be less sensitive to misspecification in the prior information available at the design stage. In this work, we investigate the influence of using a local (lnD) or a robust (ELD) optimality criterion for a MBAOD of a simulated dose optimization study, for rich and sparse sampling schedules. A stopping criterion for accurate effect prediction is constructed to determine the endpoint of the MBAOD by minimizing the expected uncertainty in the effect response of the typical individual. 50 iterations of the MBAODs were run using the MBAOD R-package, with the concentration from a one-compartment first-order absorption pharmacokinetic model driving the population effect response in a sigmoidal EMAX pharmacodynamics model. The initial cohort consisted of eight individuals in two groups and each additional cohort added two individuals receiving a dose optimized as a discrete covariate. The MBAOD designs using lnD and ELD optimality with misspecified initial model parameters were compared by evaluating the efficiency relative to an lnD-optimal design based on the true parameter values. For the explored example model, the MBAOD using ELD-optimal designs converged quicker to the theoretically optimal lnD-optimal design based on the true parameters for both sampling schedules. Thus, using a robust optimality criterion in MBAODs could reduce the number of adaptations required and improve the practicality of adaptive trials using optimal design.
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Musuamba FT, Manolis E, Holford N, Cheung S, Friberg LE, Ogungbenro K, Posch M, Yates J, Berry S, Thomas N, Corriol-Rohou S, Bornkamp B, Bretz F, Hooker AC, Van der Graaf PH, Standing JF, Hay J, Cole S, Gigante V, Karlsson K, Dumortier T, Benda N, Serone F, Das S, Brochot A, Ehmann F, Hemmings R, Rusten IS. Advanced Methods for Dose and Regimen Finding During Drug Development: Summary of the EMA/EFPIA Workshop on Dose Finding (London 4-5 December 2014). CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2017; 6:418-429. [PMID: 28722322 PMCID: PMC5529745 DOI: 10.1002/psp4.12196] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/27/2017] [Accepted: 03/27/2017] [Indexed: 02/05/2023]
Abstract
Inadequate dose selection for confirmatory trials is currently still one of the most challenging issues in drug development, as illustrated by high rates of late‐stage attritions in clinical development and postmarketing commitments required by regulatory institutions. In an effort to shift the current paradigm in dose and regimen selection and highlight the availability and usefulness of well‐established and regulatory‐acceptable methods, the European Medicines Agency (EMA) in collaboration with the European Federation of Pharmaceutical Industries Association (EFPIA) hosted a multistakeholder workshop on dose finding (London 4–5 December 2014). Some methodologies that could constitute a toolkit for drug developers and regulators were presented. These methods are described in the present report: they include five advanced methods for data analysis (empirical regression models, pharmacometrics models, quantitative systems pharmacology models, MCP‐Mod, and model averaging) and three methods for study design optimization (Fisher information matrix (FIM)‐based methods, clinical trial simulations, and adaptive studies). Pairwise comparisons were also discussed during the workshop; however, mostly for historical reasons. This paper discusses the added value and limitations of these methods as well as challenges for their implementation. Some applications in different therapeutic areas are also summarized, in line with the discussions at the workshop. There was agreement at the workshop on the fact that selection of dose for phase III is an estimation problem and should not be addressed via hypothesis testing. Dose selection for phase III trials should be informed by well‐designed dose‐finding studies; however, the specific choice of method(s) will depend on several aspects and it is not possible to recommend a generalized decision tree. There are many valuable methods available, the methods are not mutually exclusive, and they should be used in conjunction to ensure a scientifically rigorous understanding of the dosing rationale.
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Smith MK, Moodie SL, Bizzotto R, Blaudez E, Borella E, Carrara L, Chan P, Chenel M, Comets E, Gieschke R, Harling K, Harnisch L, Hartung N, Hooker AC, Karlsson MO, Kaye R, Kloft C, Kokash N, Lavielle M, Lestini G, Magni P, Mari A, Mentré F, Muselle C, Nordgren R, Nyberg HB, Parra-Guillén ZP, Pasotti L, Rode-Kristensen N, Sardu ML, Smith GR, Swat MJ, Terranova N, Yngman G, Yvon F, Holford N. Model Description Language (MDL): A Standard for Modeling and Simulation. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2017. [PMID: 28643440 PMCID: PMC5658286 DOI: 10.1002/psp4.12222] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Nguyen THT, Mouksassi M, Holford N, Al‐Huniti N, Freedman I, Hooker AC, John J, Karlsson MO, Mould DR, Pérez Ruixo JJ, Plan EL, Savic R, van Hasselt JGC, Weber B, Zhou C, Comets E, Mentré F. Model Evaluation of Continuous Data Pharmacometric Models: Metrics and Graphics. CPT Pharmacometrics Syst Pharmacol 2017; 6:87-109. [PMID: 27884052 PMCID: PMC5321813 DOI: 10.1002/psp4.12161] [Citation(s) in RCA: 228] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 10/10/2016] [Accepted: 11/09/2016] [Indexed: 12/17/2022] Open
Abstract
This article represents the first in a series of tutorials on model evaluation in nonlinear mixed effect models (NLMEMs), from the International Society of Pharmacometrics (ISoP) Model Evaluation Group. Numerous tools are available for evaluation of NLMEM, with a particular emphasis on visual assessment. This first basic tutorial focuses on presenting graphical evaluation tools of NLMEM for continuous data. It illustrates graphs for correct or misspecified models, discusses their pros and cons, and recalls the definition of metrics used.
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Strömberg EA, Nyberg J, Hooker AC. The effect of Fisher information matrix approximation methods in population optimal design calculations. J Pharmacokinet Pharmacodyn 2016; 43:609-619. [PMID: 27804003 PMCID: PMC5110617 DOI: 10.1007/s10928-016-9499-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/25/2016] [Indexed: 01/04/2023]
Abstract
With the increasing popularity of optimal design in drug development it is important to understand how the approximations and implementations of the Fisher information matrix (FIM) affect the resulting optimal designs. The aim of this work was to investigate the impact on design performance when using two common approximations to the population model and the full or block-diagonal FIM implementations for optimization of sampling points. Sampling schedules for two example experiments based on population models were optimized using the FO and FOCE approximations and the full and block-diagonal FIM implementations. The number of support points was compared between the designs for each example experiment. The performance of these designs based on simulation/estimations was investigated by computing bias of the parameters as well as through the use of an empirical D-criterion confidence interval. Simulations were performed when the design was computed with the true parameter values as well as with misspecified parameter values. The FOCE approximation and the Full FIM implementation yielded designs with more support points and less clustering of sample points than designs optimized with the FO approximation and the block-diagonal implementation. The D-criterion confidence intervals showed no performance differences between the full and block diagonal FIM optimal designs when assuming true parameter values. However, the FO approximated block-reduced FIM designs had higher bias than the other designs. When assuming parameter misspecification in the design evaluation, the FO Full FIM optimal design was superior to the FO block-diagonal FIM design in both of the examples.
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Acharya C, Hooker AC, Türkyılmaz GY, Jönsson S, Karlsson MO. A diagnostic tool for population models using non-compartmental analysis: The ncappc package for R. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2016; 127:83-93. [PMID: 27000291 DOI: 10.1016/j.cmpb.2016.01.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 12/07/2015] [Accepted: 01/07/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND AND OBJECTIVE Non-compartmental analysis (NCA) calculates pharmacokinetic (PK) metrics related to the systemic exposure to a drug following administration, e.g. area under the concentration-time curve and peak concentration. We developed a new package in R, called ncappc, to perform (i) a NCA and (ii) simulation-based posterior predictive checks (ppc) for a population PK (PopPK) model using NCA metrics. METHODS The nca feature of ncappc package estimates the NCA metrics by NCA. The ppc feature of ncappc estimates the NCA metrics from multiple sets of simulated concentration-time data and compares them with those estimated from the observed data. The diagnostic analysis is performed at the population as well as the individual level. The distribution of the simulated population means of each NCA metric is compared with the corresponding observed population mean. The individual level comparison is performed based on the deviation of the mean of any NCA metric based on simulations for an individual from the corresponding NCA metric obtained from the observed data. The ncappc package also reports the normalized prediction distribution error (NPDE) of the simulated NCA metrics for each individual and their distribution within a population. RESULTS The ncappc produces two default outputs depending on the type of analysis performed, i.e., NCA and PopPK diagnosis. The PopPK diagnosis feature of ncappc produces 8 sets of graphical outputs to assess the ability of a population model to simulate the concentration-time profile of a drug and thereby evaluate model adequacy. In addition, tabular outputs are generated showing the values of the NCA metrics estimated from the observed and the simulated data, along with the deviation, NPDE, regression parameters used to estimate the elimination rate constant and the related population statistics. CONCLUSIONS The ncappc package is a versatile and flexible tool-set written in R that successfully estimates NCA metrics from concentration-time data and produces a comprehensive set of graphical and tabular output to summarize the diagnostic results including the model specific outliers. The output is easy to interpret and to use in evaluation of a population PK model. ncappc is freely available on CRAN (http://cran.r-project.org/web/packages/ncappc/index.html/) and GitHub (https://github.com/cacha0227/ncappc/).
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Aoki Y, Sundqvist M, Hooker AC, Gennemark P. PopED lite: An optimal design software for preclinical pharmacokinetic and pharmacodynamic studies. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2016; 127:126-143. [PMID: 27000295 DOI: 10.1016/j.cmpb.2016.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 01/21/2016] [Accepted: 02/02/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND AND OBJECTIVE Optimal experimental design approaches are seldom used in preclinical drug discovery. The objective is to develop an optimal design software tool specifically designed for preclinical applications in order to increase the efficiency of drug discovery in vivo studies. METHODS Several realistic experimental design case studies were collected and many preclinical experimental teams were consulted to determine the design goal of the software tool. The tool obtains an optimized experimental design by solving a constrained optimization problem, where each experimental design is evaluated using some function of the Fisher Information Matrix. The software was implemented in C++ using the Qt framework to assure a responsive user-software interaction through a rich graphical user interface, and at the same time, achieving the desired computational speed. In addition, a discrete global optimization algorithm was developed and implemented. RESULTS The software design goals were simplicity, speed and intuition. Based on these design goals, we have developed the publicly available software PopED lite (http://www.bluetree.me/PopED_lite). Optimization computation was on average, over 14 test problems, 30 times faster in PopED lite compared to an already existing optimal design software tool. PopED lite is now used in real drug discovery projects and a few of these case studies are presented in this paper. CONCLUSIONS PopED lite is designed to be simple, fast and intuitive. Simple, to give many users access to basic optimal design calculations. Fast, to fit a short design-execution cycle and allow interactive experimental design (test one design, discuss proposed design, test another design, etc). Intuitive, so that the input to and output from the software tool can easily be understood by users without knowledge of the theory of optimal design. In this way, PopED lite is highly useful in practice and complements existing tools.
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Ueckert S, Karlsson MO, Hooker AC. Accelerating Monte Carlo power studies through parametric power estimation. J Pharmacokinet Pharmacodyn 2016; 43:223-34. [PMID: 26934878 PMCID: PMC4791488 DOI: 10.1007/s10928-016-9468-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 02/19/2016] [Indexed: 11/30/2022]
Abstract
Estimating the power for a non-linear mixed-effects model-based analysis is challenging due to the lack of a closed form analytic expression. Often, computationally intensive Monte Carlo studies need to be employed to evaluate the power of a planned experiment. This is especially time consuming if full power versus sample size curves are to be obtained. A novel parametric power estimation (PPE) algorithm utilizing the theoretical distribution of the alternative hypothesis is presented in this work. The PPE algorithm estimates the unknown non-centrality parameter in the theoretical distribution from a limited number of Monte Carlo simulation and estimations. The estimated parameter linearly scales with study size allowing a quick generation of the full power versus study size curve. A comparison of the PPE with the classical, purely Monte Carlo-based power estimation (MCPE) algorithm for five diverse pharmacometric models showed an excellent agreement between both algorithms, with a low bias of less than 1.2 % and higher precision for the PPE. The power extrapolated from a specific study size was in a very good agreement with power curves obtained with the MCPE algorithm. PPE represents a promising approach to accelerate the power calculation for non-linear mixed effect models.
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Aoki Y, Nordgren R, Hooker AC. Preconditioning of Nonlinear Mixed Effects Models for Stabilisation of Variance-Covariance Matrix Computations. AAPS JOURNAL 2016; 18:505-18. [PMID: 26857397 DOI: 10.1208/s12248-016-9866-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 01/04/2016] [Indexed: 02/05/2023]
Abstract
As the importance of pharmacometric analysis increases, more and more complex mathematical models are introduced and computational error resulting from computational instability starts to become a bottleneck in the analysis. We propose a preconditioning method for non-linear mixed effects models used in pharmacometric analyses to stabilise the computation of the variance-covariance matrix. Roughly speaking, the method reparameterises the model with a linear combination of the original model parameters so that the Hessian matrix of the likelihood of the reparameterised model becomes close to an identity matrix. This approach will reduce the influence of computational error, for example rounding error, to the final computational result. We present numerical experiments demonstrating that the stabilisation of the computation using the proposed method can recover failed variance-covariance matrix computations, and reveal non-identifiability of the model parameters.
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Kågedal M, Varnäs K, Hooker AC, Karlsson MO. Estimation of drug receptor occupancy when non-displaceable binding differs between brain regions – extending the simplified reference tissue model. Br J Clin Pharmacol 2015; 80:116-27. [PMID: 25406494 PMCID: PMC4500331 DOI: 10.1111/bcp.12558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 10/28/2014] [Indexed: 11/28/2022] Open
Abstract
AIM The simplified reference tissue model (SRTM) is used for estimation of receptor occupancy assuming that the non-displaceable binding in the reference region is identical to the brain regions of interest. The aim of this work was to extend the SRTM to also account for inter-regional differences in non-displaceable concentrations, and to investigate if this model allowed estimation of receptor occupancy using white matter as reference. It was also investigated if an apparent higher affinity in caudate compared with other brain regions, could be better explained by a difference in the extent of non-displaceable binding. METHODS The analysis was based on a PET study in six healthy volunteers using the 5-HT1B receptor radioligand [(11)C]-AZ10419369. The radioligand was given intravenously as a tracer dose alone and following different oral doses of the 5-HT1B receptor antagonist AZD3783. Non-linear mixed effects models were developed where differences between regions in non-specific concentrations were accounted for. The properties of the models were also evaluated by means of simulation studies. RESULTS The estimate (95% CI) of Ki(PL) was 10.2 ng ml(-1) (5.4, 15) and 10.4 ng ml(-1) (8.1, 13.6) based on the extended SRTM with white matter as reference and based on the SRTM using cerebellum as reference, respectively. The estimate (95% CI) of Ki(PL) for caudate relative to other brain regions was 55% (48, 62%). CONCLUSIONS The extended SRTM allows consideration of white matter as reference region when no suitable grey matter region exists. AZD3783 affinity appears to be higher in the caudate compared with other brain regions.
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Swat MJ, Moodie S, Wimalaratne SM, Kristensen NR, Lavielle M, Mari A, Magni P, Smith MK, Bizzotto R, Pasotti L, Mezzalana E, Comets E, Sarr C, Terranova N, Blaudez E, Chan P, Chard J, Chatel K, Chenel M, Edwards D, Franklin C, Giorgino T, Glont M, Girard P, Grenon P, Harling K, Hooker AC, Kaye R, Keizer R, Kloft C, Kok JN, Kokash N, Laibe C, Laveille C, Lestini G, Mentré F, Munafo A, Nordgren R, Nyberg HB, Parra-Guillen ZP, Plan E, Ribba B, Smith G, Trocóniz IF, Yvon F, Milligan PA, Harnisch L, Karlsson M, Hermjakob H, Le Novère N. Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development. CPT Pharmacometrics Syst Pharmacol 2015; 4:316-9. [PMID: 26225259 PMCID: PMC4505825 DOI: 10.1002/psp4.57] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 05/06/2015] [Indexed: 12/02/2022] Open
Abstract
The lack of a common exchange format for mathematical models in pharmacometrics has been a long-standing problem. Such a format has the potential to increase productivity and analysis quality, simplify the handling of complex workflows, ensure reproducibility of research, and facilitate the reuse of existing model resources. Pharmacometrics Markup Language (PharmML), currently under development by the Drug Disease Model Resources (DDMoRe) consortium, is intended to become an exchange standard in pharmacometrics by providing means to encode models, trial designs, and modeling steps.
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Kågedal M, Karlsson MO, Hooker AC. Improved precision of exposure-response relationships by optimal dose-selection. Examples from studies of receptor occupancy using PET and dose finding for neuropathic pain treatment. J Pharmacokinet Pharmacodyn 2015; 42:211-24. [PMID: 25792005 DOI: 10.1007/s10928-015-9410-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 03/03/2015] [Indexed: 11/30/2022]
Abstract
An understanding of the relationship between drug exposure and response is a fundamental basis for any dosing recommendation. We investigate optimal dose-selection for two different types of studies, a receptor occupancy study assessed by positron emission tomography (PET) and a dose-finding study in neuropathic pain treatment. For the PET-study, an inhibitory E-max model describes the relationship between drug exposure and displacement of a radioligand from specific receptors in the brain. The model has a mechanistic basis in the law of mass action and the affinity parameter (Ki PL ) is of primary interest. For optimization of the neuropathic pain study, the model is empirical and the exposure response curve itself is of primary interest. An alternative parameterization of the sigmoid Emax model was therefore used where the plasma concentration corresponding to the minimum relevant efficacy was estimated as a parameter. Optimal design methodology was applied using the D-optimal criterion as well as the Ds-optimal criterion where parameters of interest were defined. For the PET-study it was shown that the precision of Ki PL can be improved by inclusion of brain regions with both high and low receptor density and that the need for high doses is reduced when a brain region with low receptor density is included in the analysis. In the case of the neuropathic pain study it was shown that a Ds-optimal study design using the reparameterized Emax model can improve the precision in the minimum effective dose compared to a D-optimal design.
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Nyberg J, Bazzoli C, Ogungbenro K, Aliev A, Leonov S, Duffull S, Hooker AC, Mentré F. Methods and software tools for design evaluation in population pharmacokinetics-pharmacodynamics studies. Br J Clin Pharmacol 2015; 79:6-17. [PMID: 24548174 PMCID: PMC4294071 DOI: 10.1111/bcp.12352] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 02/09/2014] [Indexed: 11/26/2022] Open
Abstract
Population pharmacokinetic (PK)-pharmacodynamic (PKPD) models are increasingly used in drug development and in academic research; hence, designing efficient studies is an important task. Following the first theoretical work on optimal design for nonlinear mixed-effects models, this research theme has grown rapidly. There are now several different software tools that implement an evaluation of the Fisher information matrix for population PKPD. We compared and evaluated the following five software tools: PFIM, PkStaMp, PopDes, PopED and POPT. The comparisons were performed using two models, a simple-one compartment warfarin PK model and a more complex PKPD model for pegylated interferon, with data on both concentration and response of viral load of hepatitis C virus. The results of the software were compared in terms of the standard error (SE) values of the parameters predicted from the software and the empirical SE values obtained via replicated clinical trial simulation and estimation. For the warfarin PK model and the pegylated interferon PKPD model, all software gave similar results. Interestingly, it was seen, for all software, that the simpler approximation to the Fisher information matrix, using the block diagonal matrix, provided predicted SE values that were closer to the empirical SE values than when the more complicated approximation was used (the full matrix). For most PKPD models, using any of the available software tools will provide meaningful results, avoiding cumbersome simulation and allowing design optimization.
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Marklund M, Strömberg EA, Lærke HN, Knudsen KEB, Kamal-Eldin A, Hooker AC, Landberg R. Simultaneous pharmacokinetic modeling of alkylresorcinols and their main metabolites indicates dual absorption mechanisms and enterohepatic elimination in humans. J Nutr 2014; 144:1674-80. [PMID: 25332465 DOI: 10.3945/jn.114.196220] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Alkylresorcinols have proven to be useful biomarkers of whole-grain wheat and rye intake in many nutritional studies. To improve their utility, more knowledge regarding the fate of alkylresorcinols and their metabolites after consumption is needed. OBJECTIVE The objective of this study was to develop a combined pharmacokinetic model for plasma concentrations of alkylresorcinols and their 2 major metabolites, 3,5-dihydroxybenzoic acid (DHBA) and 3-(3,5-dihydroxyphenyl)-propanoic acid (DHPPA). METHODS The model was established by using plasma samples collected from 3 women and 2 men after a single dose (120 g) of rye bran and validated against fasting plasma concentrations from 8 women and 7 men with controlled rye bran intake (23, 45, or 90 g/d). Alkylresorcinols in the lymph and plasma of a pig fed a single alkylresorcinol dose (1.3 mmol) were quantified to assess absorption. Human ileostomal effluent and pig bile after high and low alkylresorcinol doses were analyzed to evaluate biliary alkylresorcinol metabolite excretion. RESULTS The model contained 2 absorption compartments: 1 that transferred alkylresorcinols directly to the systematic circulation and 1 in which a proportion of absorbed alkylresorcinols was metabolized before reaching the systemic circulation. Plasma concentrations of alkylresorcinols and their metabolites depended on absorption and formation, respectively, and the mean ± SEM terminal elimination half-life of alkylresorcinols (1.9 ± 0.59 h), DHPPA (1.5 ± 0.26 h), and DHBA (1.3 ± 0.22 h) did not differ. The model accurately predicted alkylresorcinol and DHBA concentrations after repeated alkylresorcinol intake but DHPPA concentration was overpredicted, possibly because of poorly modeled enterohepatic circulation. During the 8 h following administration, <2% of the alkylresorcinol dose was recovered in the lymph. DHPPA was identified in both human ileostomal effluent and pig bile, indicating availability of DHPPA for absorption and enterohepatic circulation. CONCLUSION Intact alkylresorcinols have advantages over DHBA and DHPPA as plasma biomarkers for whole-grain wheat and rye intake because of lower susceptibility to factors other than alkylresorcinol intake.
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Steven Ernest C, Nyberg J, Karlsson MO, Hooker AC. Optimal clinical trial design based on a dichotomous Markov-chain mixed-effect sleep model. J Pharmacokinet Pharmacodyn 2014; 41:639-54. [PMID: 25308776 DOI: 10.1007/s10928-014-9391-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 10/03/2014] [Indexed: 11/25/2022]
Abstract
D-optimal designs for discrete-type responses have been derived using generalized linear mixed models, simulation based methods and analytical approximations for computing the fisher information matrix (FIM) of non-linear mixed effect models with homogeneous probabilities over time. In this work, D-optimal designs using an analytical approximation of the FIM for a dichotomous, non-homogeneous, Markov-chain phase advanced sleep non-linear mixed effect model was investigated. The non-linear mixed effect model consisted of transition probabilities of dichotomous sleep data estimated as logistic functions using piecewise linear functions. Theoretical linear and nonlinear dose effects were added to the transition probabilities to modify the probability of being in either sleep stage. D-optimal designs were computed by determining an analytical approximation the FIM for each Markov component (one where the previous state was awake and another where the previous state was asleep). Each Markov component FIM was weighted either equally or by the average probability of response being awake or asleep over the night and summed to derive the total FIM (FIM(total)). The reference designs were placebo, 0.1, 1-, 6-, 10- and 20-mg dosing for a 2- to 6-way crossover study in six dosing groups. Optimized design variables were dose and number of subjects in each dose group. The designs were validated using stochastic simulation/re-estimation (SSE). Contrary to expectations, the predicted parameter uncertainty obtained via FIM(total) was larger than the uncertainty in parameter estimates computed by SSE. Nevertheless, the D-optimal designs decreased the uncertainty of parameter estimates relative to the reference designs. Additionally, the improvement for the D-optimal designs were more pronounced using SSE than predicted via FIM(total). Through the use of an approximate analytic solution and weighting schemes, the FIM(total) for a non-homogeneous, dichotomous Markov-chain phase advanced sleep model was computed and provided more efficient trial designs and increased nonlinear mixed-effects modeling parameter precision.
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Johansson ÅM, Ueckert S, Plan EL, Hooker AC, Karlsson MO. Evaluation of bias, precision, robustness and runtime for estimation methods in NONMEM 7. J Pharmacokinet Pharmacodyn 2014; 41:223-38. [PMID: 24801864 DOI: 10.1007/s10928-014-9359-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/17/2014] [Indexed: 11/26/2022]
Abstract
NONMEM is the most widely used software for population pharmacokinetic (PK)-pharmacodynamic (PD) analyses. The latest version, NONMEM 7 (NM7), includes several sampling-based estimation methods in addition to the classical methods. In this study, performance of the estimation methods available in NM7 was investigated with respect to bias, precision, robustness and runtime for a diverse set of PD models. Simulations of 500 data sets from each PD model were reanalyzed with the available estimation methods to investigate bias and precision. Simulations of 100 data sets were used to investigate robustness by comparing final estimates obtained after estimations starting from the true parameter values and initial estimates randomly generated using the CHAIN feature in NM7. Average estimation time for each algorithm and each model was calculated from the runtimes reported by NM7. The method giving the lowest bias and highest precision across models was importance sampling, closely followed by FOCE/LAPLACE and stochastic approximation expectation-maximization. The methods relative robustness differed between models and no method showed clear superior performance. FOCE/LAPLACE was the method with the shortest runtime for all models, followed by iterative two-stage. The Bayesian Markov Chain Monte Carlo method, used in this study for point estimation, performed worst in all tested metrics.
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Ueckert S, Plan EL, Ito K, Karlsson MO, Corrigan B, Hooker AC. Improved utilization of ADAS-cog assessment data through item response theory based pharmacometric modeling. Pharm Res 2014; 31:2152-65. [PMID: 24595495 PMCID: PMC4153970 DOI: 10.1007/s11095-014-1315-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 01/23/2014] [Indexed: 11/30/2022]
Abstract
PURPOSE This work investigates improved utilization of ADAS-cog data (the primary outcome in Alzheimer's disease (AD) trials of mild and moderate AD) by combining pharmacometric modeling and item response theory (IRT). METHODS A baseline IRT model characterizing the ADAS-cog was built based on data from 2,744 individuals. Pharmacometric methods were used to extend the baseline IRT model to describe longitudinal ADAS-cog scores from an 18-month clinical study with 322 patients. Sensitivity of the ADAS-cog items in different patient populations as well as the power to detect a drug effect in relation to total score based methods were assessed with the IRT based model. RESULTS IRT analysis was able to describe both total and item level baseline ADAS-cog data. Longitudinal data were also well described. Differences in the information content of the item level components could be quantitatively characterized and ranked for mild cognitively impairment and mild AD populations. Based on clinical trial simulations with a theoretical drug effect, the IRT method demonstrated a significantly higher power to detect drug effect compared to the traditional method of analysis. CONCLUSION A combined framework of IRT and pharmacometric modeling permits a more effective and precise analysis than total score based methods and therefore increases the value of ADAS-cog data.
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Marklund M, Strömberg EA, Hooker AC, Hammarlund-Udenaes M, Aman P, Landberg R, Kamal-Eldin A. Chain length of dietary alkylresorcinols affects their in vivo elimination kinetics in rats. J Nutr 2013; 143:1573-8. [PMID: 23946349 DOI: 10.3945/jn.113.178392] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Two phenolic acids, 3,5-dihydroxybenzoic acid (DHBA) and 3-(3,5-dihydroxyphenyl)- propanoic acid (DHPPA), are the major metabolites of cereal alkylresorcinols (ARs). Like their precursors, AR metabolites have been suggested as biomarkers for intake of whole-grain wheat and rye and as such could aid the understanding of diet-disease associations. This study estimated and compared pharmacokinetic parameters of ARs and their metabolites in rats and investigated differences in metabolite formation after ingestion of different AR homologs. Rats were i.v. infused for 30 min with 2, 12, or 23 μmol/kg DHBA or DHPPA or orally given the same amounts of the AR homologs, C17:0 and C25:0. Repeated plasma samples, obtained from rats for 6 h (i.v.) or 36 h (oral), were simultaneously analyzed for ARs and their metabolites by GC-mass spectrometry. Pharmacokinetic parameters were estimated by population-based compartmental modeling and noncompartmental calculation. A 1-compartment model best described C25:0 pharmacokinetics, whereas C17:0 and AR metabolites best fitted 2-compartment models. Combined models for simultaneous prediction of AR and metabolite concentration were more complex, with less reliable estimates of pharmacokinetic parameters. Although the AUC of C17:0 was lower than that of C25:0 (P < 0.05), the total amount and composition of AR metabolites did not differ between rats given C17:0 or C25:0. The elimination half-life of ARs and their metabolites increased with length of the side chain (P-trend < 0.001) and ranged from 1.2 h (DHBA) to 8.8 h (C25:0). The formation of AR metabolites was slower than their elimination, indicating that the rate of AR metabolism and not excretion of DHBA and DHPPA determines their plasma concentrations in rats.
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Kågedal M, Cselényi Z, Nyberg S, Raboisson P, Ståhle L, Stenkrona P, Varnäs K, Halldin C, Hooker AC, Karlsson MO. A positron emission tomography study in healthy volunteers to estimate mGluR5 receptor occupancy of AZD2066 - estimating occupancy in the absence of a reference region. Neuroimage 2013; 82:160-9. [PMID: 23668965 DOI: 10.1016/j.neuroimage.2013.05.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 04/29/2013] [Accepted: 05/06/2013] [Indexed: 11/27/2022] Open
Abstract
AZD2066 is a new chemical entity pharmacologically characterized as a selective, negative allosteric modulator of the metabotropic glutamate receptor subtype 5 (mGluR5). Antagonism of mGluR5 has been implicated in relation to various diseases such as anxiety, depression, and pain disorders. To support translation from preclinical results and previous experiences with this target in man, a positron emission tomography study was performed to estimate the relationship between AZD2066 plasma concentrations and receptor occupancy in the human brain, using the mGluR5 radioligand [(11)C]-ABP688. The study involved PET scans on 4 occasions in 6 healthy volunteers. The radioligand was given as a tracer dose alone and following oral treatment with different doses of AZD2066. The analysis was based on the total volume of distribution derived from each PET-assessment. A non-linear mixed effects model was developed where ten delineated brain regions of interest from all PET scans were included in one simultaneous fit. For comparison the analysis was also performed according to a method described previously by Lassen et al. (1995). The results of the analysis showed that the total volume of distribution decreased with increasing drug concentrations in all regions with an estimated Kipl of 1170 nM. Variability between individuals and occasions in non-displaceable volume of distribution could explain most of the variability in the total volume of distribution. The Lassen approach provided a similar estimate for Kipl, but the variability was exaggerated and difficult to interpret.
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Lledó-García R, Hennig S, Nyberg J, Hooker AC, Karlsson MO. Ethically Attractive Dose-Finding Designs for Drugs With a Narrow Therapeutic Index. J Clin Pharmacol 2013; 52:29-38. [DOI: 10.1177/0091270010390041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Nyberg J, Ueckert S, Strömberg EA, Hennig S, Karlsson MO, Hooker AC. PopED: an extended, parallelized, nonlinear mixed effects models optimal design tool. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2012; 108:789-805. [PMID: 22640817 DOI: 10.1016/j.cmpb.2012.05.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 05/01/2012] [Accepted: 05/03/2012] [Indexed: 06/01/2023]
Abstract
Several developments have facilitated the practical application and increased the general use of optimal design for nonlinear mixed effects models. These developments include new methodology for utilizing advanced pharmacometric models, faster optimization algorithms and user friendly software tools. In this paper we present the extension of the optimal design software PopED, which incorporates many of these recent advances into an easily useable enhanced GUI. Furthermore, we present new solutions to problems related to the design of experiments such as: faster and more robust FIM calculations and optimizations, optimizing over cost/utility functions and diagnostic tools and plots to evaluate design performance. Examples for; (i) Group size optimization and efficiency translation, (ii) Cost/constraint optimization, (iii) Optimizations with different FIM approximations and (iv) optimization with parallel computing demonstrate the new features in PopED and underline the potential use of this tool when designing experiments.
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Nyberg J, Höglund R, Bergstrand M, Karlsson MO, Hooker AC. Serial correlation in optimal design for nonlinear mixed effects models. J Pharmacokinet Pharmacodyn 2012; 39:239-49. [PMID: 22415637 DOI: 10.1007/s10928-012-9245-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 02/26/2012] [Indexed: 10/28/2022]
Abstract
In population modeling two sources of variability are commonly included; inter individual variability and residual variability. Rich sampling optimal design (more samples than model parameters) using these models will often result in a sampling schedule where some measurements are taken at exactly the same time point, thereby maximizing the signal-to-noise ratio. This behavior is a result of not appropriately taking into account error generation mechanisms and is often clinically unappealing and may be avoided by including intrinsic variability, i.e. serially correlated residual errors. In this paper we extend previous work that investigated optimal designs of population models including serial correlation using stochastic differential equations to optimal design with the more robust, and analytic, AR(1) autocorrelation model. Further, we investigate the importance of correlation strength, design criteria and robust designs. Finally, we explore the optimal design properties when estimating parameters with and without serial correlation. In the investigated examples the designs and estimation performance differs significantly when handling serial correlation.
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Välitalo P, Kumpulainen E, Manner M, Kokki M, Lehtonen M, Hooker AC, Ranta VP, Kokki H. Plasma and cerebrospinal fluid pharmacokinetics of naproxen in children. J Clin Pharmacol 2011; 52:1516-26. [PMID: 22067196 DOI: 10.1177/0091270011418658] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The aim of this study was to characterize pediatric pharmacokinetics and central nervous system exposure of naproxen after oral administration. The pharmacokinetics of naproxen was studied in 53 healthy children aged 3 months to 12 years undergoing surgery with spinal anesthesia. Children received preoperatively a single dose of 10 mg/kg oral naproxen suspension. A single cerebrospinal fluid (CSF) sample (n = 52) was collected at the induction of anesthesia, and plasma samples (n = 270) were collected before, during, and after the operation (up to 51 hours after administration). A population pharmacokinetic model was built using the NONMEM software. Naproxen concentrations in plasma were well described by a 2-compartment model. The estimated oral clearance (CL/F) was 0.62 L/h when linearly scaled by weight to 70 kg. The apparent volume of distribution at steady state (Vss/F) was 12.5 L /70 kg. The findings are consistent with previously reported pharmacokinetic parameters for children older than 5 years. Naproxen permeated into the CSF and reached CSF concentrations that were 4 times higher than unbound plasma concentrations. Based on these data, weight can be used as a basis for naproxen dosing in children older than 3 months of age.
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