Statistical model and inference for pharmacokinetic data

In this paper, we consider a statistical model for the drug concentration–time profiles that are obtained in a pharmacokinetic (PK) study when the drug is orally administered. In the proposed statistical PK model, the subject-specific concentration–time curve is described by the one-compartment PK model with first-order absorption and elimination. Moreover, a multivariate generalized gamma distribution is developed for the joint distribution of the drug concentrations that are repeatedly measured from the same subject. We then construct confidence intervals for the subject–exposure parameters which provide a further insight into the individual exposure of the drug under study. The proposed statistical PK model and the associated inference are then applied to illustrate a real data set. A simulation study is also implemented to investigate the performances of the coverage probability and expected length of the proposed confidence intervals. Finally, we give conclusions and discussions on the application of the proposed procedures.     

Incomplete block designs for complete diallel crosses and their analysis

A large number of incomplete block designs for Griffing's complete diallel cross-systems I, II and III, involving from five to 12 lines, are suggested, using two-associate triangular partially balanced incomplete block designs. Analysis of incomplete block designs for complete diallel cross-systems has been carried out assuming the most appropriate model for genetic yield, as advocated by Hinklemnann. This includes estimation of the general combining ability, specific combining ability and reciprocal cross- effects. An illustration of the design for each system is presented.     

Optimal parametric design with applications to pharmacokinetic and pharmacodynamic trials

This paper considers optimal parametric designs, i.e. designs represented by probability measures determined by a set of parameters, for nonlinear models and illustrates their use in designs for pharmacokinetic (PK) and pharmacokinetic/pharmacodynamic (PK/PD) trials. For some practical problems, such as designs for modelling PK/PD relationship, this is often the only feasible type of design, as the design points follow a PK model and cannot be directly controlled. Even for ordinary design problems the parametric designs have some advantages over the traditional designs, which often have too few design points for model checking and may not be robust to model and parameter misspecifications. We first describe methods and algorithms to construct the parametric design for ordinary nonlinear design problems and show that the parametric designs are robust to parameter misspecification and have good power for model discrimination. Then we extend this design method to construct optimal repeated measurement designs for nonlinear mixed models. We also use this parametric design for modelling a PK/PD relationship and propose a simulation based algorithm. The application of parametric designs is illustrated with a three-parameter open one-compartment PK model for the ordinary design and repeated measurement design, and an Emax model for the phamacokinetic/pharmacodynamic trial design.     

Optimal multi-criteria designs for Fourier regression models

Riccomagno, Schwabe and Wynn (RSW) (1997) have given a necessary and sufficient condition for obtaining a complete Fourier regression model with a design based on lattice points that is D-optimal. However, in practice, the number of factors to be considered may be large, or the experimental data may be restricted or not homogeneous. To address these difficulties we extend the results of RSW to obtain a sufficient condition for an incomplete interaction Fourier model design based on lattice points that is D-, A-, E- and G-optimal. We also propose an algorithm for finding such optimal designs that requires fewer design points than those obtained using RSW's generators when the underlying model is a complete interaction model.     

Balanced incomplete Latin square designs

Latin squares have been widely used to design an experiment where the blocking factors and treatment factors have the same number of levels. For some experiments, the size of blocks may be less than the number of treatments. Since not all the treatments can be compared within each block, a new class of designs called balanced incomplete Latin squares (BILS) is proposed. A general method for constructing BILS is proposed by an intelligent selection of certain cells from a complete Latin square via orthogonal Latin squares. The optimality of the proposed BILS designs is investigated. It is shown that the proposed transversal BILS designs are asymptotically optimal for all the row, column and treatment effects. The relative efficiencies of a delete-one-transversal BILS design with respect to the optimal designs for both cases are also derived; it is shown to be close to 100%, as the order becomes large.     

Design and inference for 3‐stage bioequivalence testing with serial sampling data

A bioequivalence test is to compare bioavailability parameters, such as the maximum observed concentration (C_max) or the area under the concentration‐time curve, for a test drug and a reference drug. During the planning of a bioequivalence test, it requires an assumption about the variance of C_max or area under the concentration‐time curve for the estimation of sample size. Since the variance is unknown, current 2‐stage designs use variance estimated from stage 1 data to determine the sample size for stage 2. However, the estimation of variance with the stage 1 data is unstable and may result in too large or too small sample size for stage 2. This problem is magnified in bioequivalence tests with a serial sampling schedule, by which only one sample is collected from each individual and thus the correct assumption of variance becomes even more difficult. To solve this problem, we propose 3‐stage designs. Our designs increase sample sizes over stages gradually, so that extremely large sample sizes will not happen. With one more stage of data, the power is increased. Moreover, the variance estimated using data from both stages 1 and 2 is more stable than that using data from stage 1 only in a 2‐stage design. These features of the proposed designs are demonstrated by simulations. Testing significance levels are adjusted to control the overall type I errors at the same level for all the multistage designs.     

Pharmacokinetic parameters estimation using adaptive Bayesian P-splines models

In preclinical and clinical experiments, pharmacokinetic (PK) studies are designed to analyse the evolution of drug concentration in plasma over time i.e. the PK profile. Some PK parameters are estimated in order to summarize the complete drug's kinetic profile: area under the curve (AUC), maximal concentration (C(max)), time at which the maximal concentration occurs (t(max)) and half-life time (t(1/2)).Several methods have been proposed to estimate these PK parameters. A first method relies on interpolating between observed concentrations. The interpolation method is often chosen linear. This method is simple and fast. Another method relies on compartmental modelling. In this case, nonlinear methods are used to estimate parameters of a chosen compartmental model. This method provides generally good results. However, if the data are sparse and noisy, two difficulties can arise with this method. The first one is related to the choice of the suitable compartmental model given the small number of data available in preclinical experiment for instance. Second, nonlinear methods can fail to converge. Much work has been done recently to circumvent these problems (J. Pharmacokinet. Pharmacodyn. 2007; 34:229-249, Stat. Comput., to appear, Biometrical J., to appear, ESAIM P&S 2004; 8:115-131).In this paper, we propose a Bayesian nonparametric model based on P-splines. This method provides good PK parameters estimation, whatever be the number of available observations and the level of noise in the data. Simulations show that the proposed method provides better PK parameters estimations than the interpolation method, both in terms of bias and precision. The Bayesian nonparametric method provides also better AUC and t(1/2) estimations than a correctly specified compartmental model, whereas this last method performs better in t(max) and C(max) estimations.We extend the basic model to a hierarchical one that treats the case where we have concentrations from different subjects. We are then able to get individual PK parameter estimations. Finally, with Bayesian methods, we can get easily some uncertainty measures by obtaining credibility sets for each PK parameter.     

Search for suitable incomplete block designs for complete diallel cross systems

The suitability of incomplete block designs for each complete diallel cross system I, II, III and IV, under the general genetic model is examined, and a set of necessary conditions obtained. In this connection, modifications in available designs are suggested and illustrated. A table of suitable designs with higher efficiency for complete diallel cross systems is presented.     

Statistical methodology for binary data from a set of partially structured two-way random cross-classifications

A complete two-way cross-classification design is not practical in many settings. For example, in a toxicological study where 30 male rats are mated with 30 female rats and each mating outcome (successful or unsuccessful)is observed, time and resource considerations can make the use of the complete design prohibitively costly. Partially structured variations of this design are, therefore, of interest (e.g., the balanced disjoint rectangle design, the fully diagonal design, and the "S"-design). Methodology for analyzing binary data from such incomplete designs is illustrated with an example. This methodology, which is based on infinite population sampling arguments, allows the estimation of the mean response, among-row correlation coefficient, among-column correlation coefficient, and the within-cell correlation coefficient as well as their standard errors.     

A robust pairwise likelihood method for incomplete longitudinal binary data arising in clusters

Clustered longitudinal data feature cross‐sectional associations within clusters, serial dependence within subjects, and associations between responses at different time points from different subjects within the same cluster. Generalized estimating equations are often used for inference with data of this sort since they do not require full specification of the response model. When data are incomplete, however, they require data to be missing completely at random unless inverse probability weights are introduced based on a model for the missing data process. The authors propose a robust approach for incomplete clustered longitudinal data using composite likelihood. Specifically, pairwise likelihood methods are described for conducting robust estimation with minimal model assumptions made. The authors also show that the resulting estimates remain valid for a wide variety of missing data problems including missing at random mechanisms and so in such cases there is no need to model the missing data process. In addition to describing the asymptotic properties of the resulting estimators, it is shown that the method performs well empirically through simulation studies for complete and incomplete data. Pairwise likelihood estimators are also compared with estimators obtained from inverse probability weighted alternating logistic regression. An application to data from the Waterloo Smoking Prevention Project is provided for illustration. The Canadian Journal of Statistics 39: 34–51; 2011 © 2010 Statistical Society of Canada     

Constructing optimal designs for fitting pharmacokinetic models

We consider some computational issues that arise when searching for optimal designs for pharmacokinetic (PK) studies. Special factors that distinguish these are (i) repeated observations are taken from each subject and the observations are usually described by a nonlinear mixed model (NLMM), (ii) design criteria depend on the model fitting procedure, (iii) in addition to providing efficient parameter estimates, the design must also permit model checking, (iv) in practice there are several design constraints, (v) the design criteria are computationally expensive to evaluate and often numerical integration is needed and finally (vi) local optimisation procedures may fail to converge or get trapped at local optima.We review current optimal design algorithms and explore the possibility of using global optimisation procedures. We use these latter procedures to find some optimal designs.For multi-purpose designs we suggest two surrogate design criteria for model checking and illustrate their use.     

Regression analysis of panel count data with covariate-dependent observation and censoring times

Panel count data often occur in a long-term study where the primary end point is the time to a specific event and each subject may experience multiple recurrences of this event. Furthermore, suppose that it is not feasible to keep subjects under observation continuously and the numbers of recurrences for each subject are only recorded at several distinct time points over the study period. Moreover, the set of observation times may vary from subject to subject. In this paper, regression methods, which are derived under simple semiparametric models, are proposed for the analysis of such longitudinal count data. Especially, we consider the situation when both observation and censoring times may depend on covariates. The new procedures are illustrated with data from a well-known cancer study.     

IDENTIFYING TREATMENT EFFECTS IN MULTI-CHANNEL MEASUREMENTS IN ELECTROENCEPHALOGRAPHIC STUDIES: MULTIVARIATE PERMUTATION TESTS AND MULTIPLE COMPARISONS

A versatile procedure is described comprising an application of statistical techniques to the analysis of the large, multi‐dimensional data arrays produced by electroencephalographic (EEG) measurements of human brain function. Previous analytical methods have been unable to identify objectively the precise times at which statistically significant experimental effects occur, owing to the large number of variables (electrodes) and small number of subjects, or have been restricted to two‐treatment experimental designs. Many time‐points are sampled in each experimental trial, making adjustment for multiple comparisons mandatory. Given the typically large number of comparisons and the clear dependence structure among time‐points, simple Bonferroni‐type adjustments are far too conservative. A three‐step approach is proposed: (i) summing univariate statistics across variables; (ii) using permutation tests for treatment effects at each time‐point; and (iii) adjusting for multiple comparisons using permutation distributions to control family‐wise error across the whole set of time‐points. Our approach provides an exact test of the individual hypotheses while asymptotically controlling family‐wise error in the strong sense, and can provide tests of interaction and main effects in factorial designs. An application to two experimental data sets from EEG studies is described, but the approach has application to the analysis of spatio‐temporal multivariate data gathered in many other contexts.     

Computation aspects of the parameter estimates of linear mixed effects model in multivariate repeated measures set-up

The number of parameters mushrooms in a linear mixed effects (LME) model in the case of multivariate repeated measures data. Computation of these parameters is a real problem with the increase in the number of response variables or with the increase in the number of time points. The problem becomes more intricate and involved with the addition of additional random effects. A multivariate analysis is not possible in a small sample setting. We propose a method to estimate these many parameters in bits and pieces from baby models, by taking a subset of response variables at a time, and finally using these bits and pieces at the end to get the parameter estimates for the mother model, with all variables taken together. Applying this method one can calculate the fixed effects, the best linear unbiased predictions (BLUPs) for the random effects in the model, and also the BLUPs at each time of observation for each response variable, to monitor the effectiveness of the treatment for each subject. The proposed method is illustrated with an example of multiple response variables measured over multiple time points arising from a clinical trial in osteoporosis.     

A semi‐parametric approach to fitting a nonlinear mixed PK/PD model with an effect compartment using SAS

Modelling of the relationship between concentration (PK) and response (PD) plays an important role in drug development. The modelling becomes complicated when the drug concentration and response measurements are not taken simultaneously and/or hysteresis occurs between the response and the concentration. A model‐based approach fits a joint pharmacokinetic (PK) and concentration–response (PK/PD) model, including an effect compartment if necessary, to concentration and response data. However, this approach relies on the PK data being well described by a common PK model. We propose an algorithm for a semi‐parametric approach to fitting nonlinear mixed PK/PD models including an effect compartment using linear interpolation and extrapolation for concentration data. This approach is independent of the PK model, and the algorithm can easily be implemented using SAS PROC NLMIXED. Practical issues in programming and computing are also discussed. The properties of this approach are examined using simulations. This approach is used to analyse data from a study of the PK/PD relationship between insulin and glucose levels. Copyright © 2005 John Wiley & Sons, Ltd.     

Use of n-ary block designs in diallel crosses evaluation

To fill the gap between theory and practice of modern statistical designs, this paper presents the use of n-ary block designs in the evaluation of balanced incomplete block (BIB) designs for all the four Griffing's (1956) complete dialled crosses (CDC) systems, the construction of which is proposed here by adopting a suitable BIB design and associating its treatments with the crosses under a CDC system.     

Generalizing the information content for stepped wedge designs: A marginal modeling approach

Stepped wedge trials are increasingly adopted because practical constraints necessitate staggered roll-out. While a complete design requires clusters to collect data in all periods, resource and patient-centered considerations may call for an incomplete stepped wedge design to minimize data collection burden. To study incomplete designs, we expand the metric of information content to discrete outcomes. We operate under a marginal model with general link and variance functions, and derive information content expressions when data elements (cells, sequences, periods) are omitted. We show that the centrosymmetric patterns of information content can hold for discrete outcomes with the variance-stabilizing link function. We perform numerical studies under the canonical link function, and find that while the patterns of information content for cells are approximately centrosymmetric for all examined underlying secular trends, the patterns of information content for sequences or periods are more sensitive to the secular trend, and may be far from centrosymmetric.     

Optimal 3×3 factorial and 3-ray designs for drug interaction experiments with dichotomous responses

The only information available to an investigator designing an initial combination drug study is for each drug used singly. The designs that we investigated are constructed using this information. Within the major body of the paper we consider experiments using nine points arrived at from 3x3 factorial and 3-ray design plans for which D-optimal solutions are obtained under the hypothesis of no interaction.