| 1. |
- Ueckert, Sebastian, 1983-, et al.
(författare)
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Challenges and potential of optimal design in late phase clinical trials through application in Alzheimer’s disease
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Optimal design is a methodology that can be a valuable tool for the planning of clinical studies. Current applications however, are largely limited to early phases of the drug development process. The increasing complexity in late phase trials is a major reason why optimal design is not applied at these stages. This work uses the example of Alzheimer's disease to investigate challenges and potential of applying optimal design in late phase clinical trials.Information from several sources was used to construct a disease progression model for Alzheimer's disease. The resulting model was used to optimize the study design of an Alzheimer's trial for three distinct metrics: maximal information, minimal number of samples and maximal power to detect a drug effect. Challenges encountered and addressed during the implementation included covariates, dropout and clinical constraints.Depending on the optimization criterion used, the optimal designs had 35% a higher efficiency, needed 33% fewer samples to obtain the same amount of information or required 70% fewer individuals to achieve 80% power compared to the reference design.Optimal design can improve the design and therefore reduce the costs of late phase trials. Several tools and techniques have been identified to address the main challenges connected to this application.
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| 2. |
- Acharya, Chayan, et al.
(författare)
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A diagnostic tool for population models using non-compartmental analysis : The ncappc package for R
- 2016
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 127, s. 83-93
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Tidskriftsartikel (refereegranskat)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://crantoprojectorg/web/packages/ncappc/index.html/) and GitHub (https://github.comicacha0227/ncappc/).
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| 3. |
- Aoki, Yasunori, 1982-, et al.
(författare)
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Model selection and averaging of nonlinear mixed-effect models for robust phase III dose selection
- 2017
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Ingår i: Journal of Pharmacokinetics and Pharmacodynamics. - : Springer Science and Business Media LLC. - 1567-567X .- 1573-8744. ; 44:6, s. 581-597
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Tidskriftsartikel (refereegranskat)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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| 4. |
- Aoki, Yasunori, 1982-, et al.
(författare)
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PopED lite : an optimal design software for preclinical pharmacokinetic and pharmacodynamic studies
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Optimal experimental design approaches are seldom used in pre-clinical drug discovery. Main reasons for this lack of use are that available software tools require relatively high insight in optimal design theory, and that the design-execution cycle of in vivo experiments is short, making time-consuming optimizations infeasible. We present the publicly available software PopED lite in order to increase the use of optimal design in pre-clinical drug discovery. PopED lite is designed to be simple, fast and intuitive. Simple, to give many users access to basic optimal design calculations. Fast, to fit the 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 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. Key functionality of PopED lite is demonstrated by three case studies from real drug discovery projects.
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| 5. |
- Aoki, Yasunori, et al.
(författare)
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PopED lite: an optimal design software for preclinical pharmacokinetic and pharmacodynamic studies
- 2016
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 127, s. 126-143
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Tidskriftsartikel (refereegranskat)abstract
- Background and ObjectiveOptimal 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.MethodsSeveral 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.ResultsThe 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.ConclusionsPopED 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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| 6. |
- Aoki, Yasunori, et al.
(författare)
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Preconditioning of Nonlinear Mixed Effects Models for Stabilisation of Variance-Covariance Matrix Computations
- 2016
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Ingår i: AAPS Journal. - : Springer Science and Business Media LLC. - 1550-7416. ; 18:2, s. 505-518
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Tidskriftsartikel (refereegranskat)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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| 7. |
- Bauer, Robert J., et al.
(författare)
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Tutorial for $DESIGN in NONMEM : Clinical trial evaluation and optimization
- 2021
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Ingår i: CPT. - : John Wiley & Sons. - 2163-8306. ; 10:12, s. 1452-1465
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Tidskriftsartikel (refereegranskat)abstract
- This NONMEM tutorial shows how to evaluate and optimize clinical trial designs, using algorithms developed in design software, such as PopED and PFIM 4.0. Parameter precision and model parameter estimability is obtained by assessing the Fisher Information Matrix (FIM), providing expected model parameter uncertainty. Model parameter identifiability may be uncovered by very large standard errors or inability to invert an FIM. Because evaluation of FIM is more efficient than clinical trial simulation, more designs can be investigated, and the design of a clinical trial can be optimized. This tutorial provides simple and complex pharmacokinetic/pharmacodynamic examples on obtaining optimal sample times, doses, or best division of subjects among design groups. Robust design techniques accounting for likely variability among subjects are also shown. A design evaluator and optimizer within NONMEM allows any control stream first developed for trial design exploration to be subsequently used for estimation of parameters of simulated or clinical data, without transferring the model to another software. Conversely, a model developed in NONMEM could be used for design optimization. In addition, the $DESIGN feature can be used on any model file and dataset combination to retrospectively evaluate the model parameter uncertainty one would expect given that the model generated the data, particularly if outliers of the actual data prevent a reasonable assessment of the variance-covariance. The NONMEM trial design feature is suitable for standard continuous data, whereas more elaborate trial designs or with noncontinuous data-types can still be accomplished in optimal design dedicated software like PopED and PFIM.
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| 8. |
- Bergstrand, Martin, 1977-, et al.
(författare)
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Prediction-Corrected Visual Predictive Checks for Diagnosing Nonlinear Mixed-Effects Models
- 2011
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Ingår i: AAPS Journal. - : Springer Science and Business Media LLC. - 1550-7416. ; 13:2, s. 143-151
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Tidskriftsartikel (refereegranskat)abstract
- Informative diagnostic tools are vital to the development of useful mixed-effects models. The Visual Predictive Check (VPC) is a popular tool for evaluating the performance of population PK and PKPD models. Ideally, a VPC will diagnose both the fixed and random effects in a mixed-effects model. In many cases, this can be done by comparing different percentiles of the observed data to percentiles of simulated data, generally grouped together within bins of an independent variable. However, the diagnostic value of a VPC can be hampered by binning across a large variability in dose and/or influential covariates. VPCs can also be misleading if applied to data following adaptive designs such as dose adjustments. The prediction-corrected VPC (pcVPC) offers a solution to these problems while retaining the visual interpretation of the traditional VPC. In a pcVPC, the variability coming from binning across independent variables is removed by normalizing the observed and simulated dependent variable based on the typical population prediction for the median independent variable in the bin. The principal benefit with the pcVPC has been explored by application to both simulated and real examples of PK and PKPD models. The investigated examples demonstrate that pcVPCs have an enhanced ability to diagnose model misspecification especially with respect to random effects models in a range of situations. The pcVPC was in contrast to traditional VPCs shown to be readily applicable to data from studies with a priori and/or a posteriori dose adaptations.
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| 9. |
- Bizzotto, Roberto, et al.
(författare)
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Multinomial Logistic Functions in Markov Chain Models of Sleep Architecture : Internal and External Validation and Covariate Analysis
- 2011
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Ingår i: AAPS Journal. - : Springer Science and Business Media LLC. - 1550-7416. ; 13:3, s. 445-463
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Tidskriftsartikel (refereegranskat)abstract
- Mixed-effect Markov chain models have been recently proposed to characterize the time course of transition probabilities between sleep stages in insomniac patients. The most recent one, based on multinomial logistic functions, was used as a base to develop a final model combining the strengths of the existing ones. This final model was validated on placebo data applying also new diagnostic methods and then used for the inclusion of potential age, gender, and BMI effects. Internal validation was performed through simplified posterior predictive check (sPPC), visual predictive check (VPC) for categorical data, and new visual methods based on stochastic simulation and estimation and called visual estimation check (VEC). External validation mainly relied on the evaluation of the objective function value and sPPC. Covariate effects were identified through stepwise covariate modeling within NONMEM VI. New model features were introduced in the model, providing significant sPPC improvements. Outcomes from VPC, VEC, and external validation were generally very good. Age, gender, and BMI were found to be statistically significant covariates, but their inclusion did not improve substantially the model's predictive performance. In summary, an improved model for sleep internal architecture has been developed and suitably validated in insomniac patients treated with placebo. Thereafter, covariate effects have been included into the final model.
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| 10. |
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| 11. |
- Bjugård Nyberg, Henrik, 1984-
(författare)
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Garnishing the smorgasbord of pharmacometric methods
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The smorgasbord of methods that we use within the field of pharmacometrics has developed steadily over several decades and is now a well-laid-out buffet. This thesis adds some garnish to the table in the form of small improvements to the handling of certain problems.The first problem tackled by the thesis was the challenge of saddle points and local non-identifiability when estimating pharmacometric model parameters. Substituting the common method of randomly perturbing the initial parameter estimates with one saddle-reset step enhances the accuracy of maximum likelihood estimates by overcoming saddle points parameter values, a common issue in nonlinear mixed-effects models. This algorithm, as implemented in the NONMEM software, was applied to various identifiable and nonidentifiable pharmacometric models, showing improved performance over traditional methods.Part of the thesis was dedicated to the development of a paediatric pharmacokinetic model for ethionamide, a drug used in treating multidrug-resistant tuberculosis. The resulting model was then used to simulate drug exposure under different dosing regimens, a new dosing regimen for children was proposed. The developed model, and therefore the proposed paediatric dosing regimen, considers factors like maturation of pharmacokinetic pathways and, administration by nasogastric tube, and concurrent rifampicin treatment. The regimen, with some modifications, was adopted in the 2022 update to the World Health Organization operational handbook on tuberculosis.Finally, the thesis explored novel model-integrated evidence (MIE) approaches for bioequivalence (BE) determination. Such methods could offer more robust alternatives to standard BE approached using non-compartmental analysis (NCA). Model-based methods have been shown to be advantageous in sparse data situations, such as is found in studies of ophthalmic formulations, but have suffered from inflated type I error rates. MIE BE approaches using a single model or using model averaging were presented and shown to control type I error at the nominal level while demonstrating increased power in bioequivalence determination.
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| 12. |
- Bjugård Nyberg, Henrik, 1984-, et al.
(författare)
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Population Pharmacokinetics and Dosing of Ethionamide in Children with Tuberculosis
- 2020
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Ingår i: Antimicrobial Agents and Chemotherapy. - : American Society for Microbiology. - 0066-4804 .- 1098-6596. ; 64:3
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Tidskriftsartikel (refereegranskat)abstract
- Ethionamide has proven efficacy against both drug-susceptible and some drug-resistant strains of Mycobacterium tuberculosis. Limited information on its pharmacokinetics in children is available, and current doses are extrapolated from weight-based adult doses. Pediatric doses based on more robust evidence are expected to improve antituberculosis treatment, especially in small children. In this analysis, ethionamide concentrations in children from 2 observational clinical studies conducted in Cape Town, South Africa, were pooled. All children received ethionamide once daily at a weight-based dose of approximately 20 mg/kg of body weight (range, 10.4 to 25.3 mg/kg) in combination with other first- or second-line antituberculosis medications and with antiretroviral therapy in cases of HIV coinfection. Pharmacokinetic parameters were estimated using nonlinear mixed-effects modeling. The MDR-PK1 study contributed data for 110 children on treatment for multidrug-resistant tuberculosis, while the DATiC study contributed data for 9 children treated for drug-susceptible tuberculosis. The median age of the children in the studies combined was 2.6 years (range, 0.23 to 15 years), and the median weight was 12.5 kg (range, 2.5 to 66 kg). A one-compartment, transit absorption model with first-order elimination best described ethionamide pharmacokinetics in children. Allometric scaling of clearance (typical value, 8.88 liters/h), the volume of distribution (typical value, 21.4 liters), and maturation of clearance and absorption improved the model fit. HIV coinfection decreased the ethionamide bioavailability by 22%, rifampin coadministration increased clearance by 16%, and ethionamide administration by use of a nasogastric tube increased the rate, but the not extent, of absorption. The developed model was used to predict pediatric doses achieving the same drug exposure achieved in 50- to 70-kg adults receiving 750-mg once-daily dosing. Based on model predictions, we recommend a weight-banded pediatric dosing scheme using scored 125-mg tablets.
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| 13. |
- Bjugård Nyberg, Henrik, et al.
(författare)
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Saddle-Reset for Robust Parameter Estimation and Identifiability Analysis of Nonlinear Mixed Effects Models
- 2020
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Ingår i: AAPS Journal. - : Springer Science and Business Media LLC. - 1550-7416. ; 22:4
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Tidskriftsartikel (refereegranskat)abstract
- Parameter estimation of a nonlinear model based on maximizing the likelihood using gradient-based numerical optimization methods can often fail due to premature termination of the optimization algorithm. One reason for such failure is that these numerical optimization methods cannot distinguish between the minimum, maximum, and a saddle point; hence, the parameters found by these optimization algorithms can possibly be in any of these three stationary points on the likelihood surface. We have found that for maximization of the likelihood for nonlinear mixed effects models used in pharmaceutical development, the optimization algorithm Broyden-Fletcher-Goldfarb-Shanno (BFGS) often terminates in saddle points, and we propose an algorithm, saddle-reset, to avoid the termination at saddle points, based on the second partial derivative test. In this algorithm, we use the approximated Hessian matrix at the point where BFGS terminates, perturb the point in the direction of the eigenvector associated with the lowest eigenvalue, and restart the BFGS algorithm. We have implemented this algorithm in industry standard software for nonlinear mixed effects modeling (NONMEM, version 7.4 and up) and showed that it can be used to avoid termination of parameter estimation at saddle points, as well as unveil practical parameter non-identifiability. We demonstrate this using four published pharmacometric models and two models specifically designed to be practically non-identifiable.
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| 14. |
- Brekkan, Ari, et al.
(författare)
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A Population Pharmacokinetic-Pharmacodynamic Model of Pegfilgrastim
- 2018
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Ingår i: AAPS Journal. - : SPRINGER. - 1550-7416. ; 20:5
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Tidskriftsartikel (refereegranskat)abstract
- Neutropenia and febrile neutropenia (FN) are serious side effects of cytotoxic chemotherapy which may be alleviated with the administration of recombinant granulocyte colony-stimulating factor (GCSF) derivatives, such as pegfilgrastim (PG) which increases absolute neutrophil count (ANC). In this work, a population pharmacokinetic-pharmacodynamic (PKPD) model was developed based on data obtained from healthy volunteers receiving multiple administrations of PG. The developed model was a bidirectional PKPD model, where PG stimulated the proliferation, maturation, and margination of neutrophils and where circulating neutrophils in turn increased the elimination of PG. Simulations from the developed model show disproportionate changes in response with changes in dose. A dose increase of 10% from the 6 mg therapeutic dose taken as a reference leads to area under the curve (AUC) increases of similar to 50 and similar to 5% for PK and PD, respectively. A full random effects covariate model showed that little of the parameter variability could be explained by sex, age, body size, and race. As a consequence, little of the secondary parameter variability (C-max and AUC of PG and ANC) could be explained by these covariates.
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| 15. |
- Brekkan, Ari, et al.
(författare)
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Reduced and optimized trial designs for drugs described by a target mediated drug disposition model
- 2018
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Ingår i: Journal of Pharmacokinetics and Pharmacodynamics. - : SPRINGER/PLENUM PUBLISHERS. - 1567-567X .- 1573-8744. ; 45:4, s. 637-647
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Tidskriftsartikel (refereegranskat)abstract
- Monoclonal antibodies against soluble targets are often rich and include the sampling of multiple analytes over a lengthy period of time. Predictive models built on data obtained in such studies can be useful in all drug development phases. If adequate model predictions can be maintained with a reduced design (e.g. fewer samples or shorter duration) the use of such designs may be advocated. The effect of reducing and optimizing a rich design based on a published study for Omalizumab (OMA) was evaluated as an example. OMA pharmacokinetics were characterized using a target-mediated drug disposition model considering the binding of OMA to free IgE and the subsequent formation of an OMA-IgE complex. The performance of the reduced and optimized designs was evaluated with respect to: efficiency, parameter uncertainty and predictions of free target. It was possible to reduce the number of samples in the study by 30% while still maintaining an efficiency of almost 90%. A reduction in sampling duration by two-thirds resulted in an efficiency of 75%. Omission of any analyte measurement or a reduction of the number of dose levels was detrimental to the efficiency of the designs (efficiency ae 51%). However, other metrics were, in some cases, relatively unaffected, showing that multiple metrics may be needed to obtain balanced assessments of design performance.
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| 16. |
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| 17. |
- Chasseloup, Estelle
(författare)
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Methods for handling model misspecification in pharmacometric model-based approaches for the analysis of longitudinal clinical trial data
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Pharmacometrics model-based analyses proved to be increasingly useful in drug discovery and development. This usefulness was made evident by the formalisation of the model-integrated drug discovery and development framework (MID3). The overall objective of this thesis was to assess and improve the robustness of longitudinal pharmacometric-model-based approaches toward model misspecification. IMA is a new approach using mixture models to test for a drug effect. It was presented and assessed together with other approaches, including model averaging, in the context of controlled balanced two-armed parallel trials. The assessment (type I error, power, and accuracy) carried out over real and simulated data demonstrated problems with the existing method, caused by model misspecification and selection bias, and the robustness of IMA towards these issues. In the same context another novel approach presented and assessed among the alternatives, rcLRT, also showed robustness and good performance. IMA was generalised to unbalanced designs and dose-response scenarios where it confirmed its good performance. A new extension of the visual predictive checks diagnostic tool to the specific case of mixture models was presented. It was able to diagnose the mixture proportion aspect, enabling the diagnostic of model misspecification in that aspect. PACS is a new approach balancing data information and prior information in the selection process between correlated covariates, in which the prior was introduced as a penalty to the objective function. PACS was able to influence to some extent the final covariate selection process and resulted in a strategy not previously described as the best under several conditions This approach is an interesting tool against data-driven misspecification when strong prior knowledge is available. A new methodology revolving around "digital twins" in pharmacometrics was presented as another alternative to making analysis results robust with respect to model approximations. The method filtered the simulations based on observed data. The selected avatars are both insurance that some of the simulated data are mimicking reasonably well the observations at clinical endpoints of interest, and a diagnostic tool for model misspecification when the avatar subset is too different from the raw model simulations. In conclusion, the new pharmacometric approaches provide robust methods towards model misspecification, which opens up new possibilities for the use of pharmacometrics models in drug development.
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| 18. |
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| 19. |
- Dodds, Michael G, et al.
(författare)
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Robust population pharmacokinetic experiment design.
- 2005
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Ingår i: Journal of Pharmacokinetics and Pharmacodynamics. - : Springer Science and Business Media LLC. - 1567-567X .- 1573-8744. ; 32:1, s. 33-64
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Tidskriftsartikel (refereegranskat)abstract
- The population approach to estimating mixed effects model parameters of interest in pharmacokinetic (PK) studies has been demonstrated to be an effective method in quantifying relevant population drug properties. The information available for each individual is usually sparse. As such, care should be taken to ensure that the information gained from each population experiment is as efficient as possible by designing the experiment optimally, according to some criterion. The classic approach to this problem is to design "good" sampling schedules, usually addressed by the D-optimality criterion. This method has the drawback of requiring exact advanced knowledge (expected values) of the parameters of interest. Often, this information is not available. Additionally, if such prior knowledge about the parameters is misspecified, this approach yields designs that may not be robust for parameter estimation. In order to incorporate uncertainty in the prior parameter specification, a number of criteria have been suggested. We focus on ED-optimality. This criterion leads to a difficult numerical problem, which is made tractable here by a novel approximation of the expectation integral usually solved by stochastic integration techniques. We present two case studies as evidence of the robustness of ED-optimal designs in the face of misspecified prior information. Estimates from replicate simulated population data show that such misspecified ED-optimal designs recover parameter estimates that are better than similarly misspecified D-optimal designs, and approach estimates gained from D-optimal designs where the parameters are correctly specified.
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| 20. |
- Duffull, Stephen B., et al.
(författare)
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Assessing robustness of designs for random effects parameters for nonlinear mixed-effects models
- 2017
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Ingår i: Journal of Pharmacokinetics and Pharmacodynamics. - : Springer Science and Business Media LLC. - 1567-567X .- 1573-8744. ; 44:6, s. 611-616
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Tidskriftsartikel (refereegranskat)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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| 21. |
- Ernest, C. Steven, II, et al.
(författare)
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Methodological Comparison of In Vitro Binding Parameter Estimation : Sequential vs. Simultaneous Non-linear Regression
- 2010
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Ingår i: Pharmaceutical research. - : Springer Science and Business Media LLC. - 0724-8741 .- 1573-904X. ; 27:5, s. 866-877
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Tidskriftsartikel (refereegranskat)abstract
- Analysis of simulated data was compared using sequential (NLR) and simultaneous non-linear regression (SNLR) to evaluate precision and accuracy of ligand binding parameter estimation. Commonly encountered experimental error, specifically residual error of binding measurements (RE), experiment-to-experiment variability (BEV) and non-specific binding (B-NS), were examined for impact of parameter estimation using both methods. Data from equilibrium, dissociation, association and non-specific binding experiments were fit simultaneously (SNLR) using NONMEM VI compared to the common practice of analyzing data from each experiment separately and assigning these as exact values (NLR) for estimation of the subsequent parameters. The greatest contributing factor to bias and variability in parameter estimation was RE of the measured concentrations of ligand bound; however, SNLR provided more accurate and less bias estimates. Subtraction of B-NS from total ligand binding data provided poor estimation of specific ligand binding parameters using both NLR and SNLR. Additional methods examined demonstrated that the use of SNLR provided better estimation of specific binding parameters, whereas there was considerable bias using NLR. NLR cannot account for BEV, whereas SNLR can provide approximate estimates of BEV. SNLR provided superior resolution of parameter estimation in both precision and accuracy compared to NLR.
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| 22. |
- Ernest II, Charles
(författare)
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Benefits of Non-Linear Mixed Effect Modeling and Optimal Design : Pre-Clinical and Clinical Study Applications
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Despite the growing promise of pharmaceutical research, inferior experimentation or interpretation of data can inhibit breakthrough molecules from finding their way out of research institutions and reaching patients. This thesis provides evidence that better characterization of pre-clinical and clinical data can be accomplished using non-linear mixed effect modeling (NLMEM) and more effective experiments can be conducted using optimal design (OD). To demonstrate applicability of NLMEM and OD in pre-clinical applications, in vitro ligand binding studies were examined. NLMEMs were used to evaluate precision and accuracy of ligand binding parameter estimation from different ligand binding experiments using sequential (NLR) and simultaneous non-linear regression (SNLR). SNLR provided superior resolution of parameter estimation in both precision and accuracy compared to NLR. OD of these ligand binding experiments for one and two binding site systems including commonly encountered experimental errors was performed. OD was employed using D- and ED-optimality. OD demonstrated that reducing the number of samples, measurement times, and separate ligand concentrations provides robust parameter estimation and more efficient and cost effective experimentation.To demonstrate applicability of NLMEM and OD in clinical applications, a phase advanced sleep study formed the basis of this investigation. A mixed-effect Markov-chain model based on transition probabilities as multinomial logistic functions using polysomnography data in phase advanced subjects was developed and compared the sleep architecture between this population and insomniac patients. The NLMEM was sufficiently robust for describing the data characteristics in phase advanced subjects, and in contrast to aggregated clinical endpoints, which provide an overall assessment of sleep behavior over the night, described the dynamic behavior of the sleep process. OD of a dichotomous, non-homogeneous, Markov-chain phase advanced sleep NLMEM was performed using D-optimality by computing the Fisher Information Matrix for each Markov component. The D-optimal designs improved the precision of parameter estimates leading to more efficient designs by optimizing the doses and the number of subjects in each dose group. This thesis provides examples how studies in drug development can be optimized using NLMEM and OD. This provides a tool than can lower the cost and increase the overall efficiency of drug development.
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| 23. |
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| 24. |
- Ernest II, Charles, et al.
(författare)
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Optimal clinical trial design based on a dichotomous Markov-chain mixed-effect sleep model
- 2014
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Ingår i: Journal of Pharmacokinetics and Pharmacodynamics. - : Springer Science and Business Media LLC. - 1567-567X .- 1573-8744. ; 41:6, s. 639-654
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Tidskriftsartikel (refereegranskat)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 (FIMtotal). 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 FIMtotal 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 FIMtotal. Through the use of an approximate analytic solution and weighting schemes, the FIMtotal 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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| 25. |
- Ernest II, Charles Steven, et al.
(författare)
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Simultaneous optimal experimental design for in vitro binding parameter estimation
- 2013
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Ingår i: Journal of Pharmacokinetics and Pharmacodynamics. - : Springer Science+Business Media B.V.. - 1567-567X .- 1573-8744. ; 40:5, s. 573-585
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Tidskriftsartikel (refereegranskat)abstract
- Simultaneous optimization of in vitro ligand binding studies using an optimal design software package that can incorporate multiple design variables through non-linear mixed effect models and provide a general optimized design regardless of the binding site capacity and relative binding rates for a two binding system. Experimental design optimization was employed with D- and ED-optimality using PopED 2.8 including commonly encountered factors during experimentation (residual error, between experiment variability and non-specific binding) for in vitro ligand binding experiments: association, dissociation, equilibrium and non-specific binding experiments. Moreover, a method for optimizing several design parameters (ligand concentrations, measurement times and total number of samples) was examined. With changes in relative binding site density and relative binding rates, different measurement times and ligand concentrations were needed to provide precise estimation of binding parameters. However, using optimized design variables, significant reductions in number of samples provided as good or better precision of the parameter estimates compared to the original extensive sampling design. Employing ED-optimality led to a general experimental design regardless of the relative binding site density and relative binding rates. Precision of the parameter estimates were as good as the extensive sampling design for most parameters and better for the poorly estimated parameters. Optimized designs for in vitro ligand binding studies provided robust parameter estimation while allowing more efficient and cost effective experimentation by reducing the measurement times and separate ligand concentrations required and in some cases, the total number of samples.
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