An efficient and robust method for analyzing population pharmacokinetic data in genome-wide pharmacogenomic studies: A generalized estimating equation approach

Kengo Nagashima, Yasunori Sato, Hisashi Noma, Chikuma Hamada

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Powerful array-based single-nucleotide polymorphism-typing platforms have recently heralded a new era in which genome-wide studies are conducted with increasing frequency. A genetic polymorphism associated with population pharmacokinetics (PK) is typically analyzed using nonlinear mixed-effect models (NLMM). Applying NLMM to large-scale data, such as those generated by genome-wide studies, raises several issues related to the assumption of random effects as follows: (i) computation time: it takes a long time to compute the marginal likelihood; (ii) convergence of iterative calculation: an adaptive Gauss-Hermite quadrature is generally used to estimate NLMM; however, iterative calculations may not converge in complex models; and (iii) random-effects misspecification leads to slightly inflated type-I error rates. As an alternative effective approach to resolving these issues, in this article, we propose a generalized estimating equation (GEE) approach for analyzing population PK data. In general, GEE analysis does not account for interindividual variability in PK parameters; therefore, the usual GEE estimators cannot be interpreted straightforwardly, and their validities have not been justified. Here, we propose valid inference methods for using GEE even under conditions of interindividual variability and provide theoretical justifications of the proposed GEE estimators for population PK data. In numerical evaluations by simulations, the proposed GEE approach exhibited high computational speed and stability relative to the NLMM approach. Furthermore, the NLMM analysis was sensitive to the misspecification of the random-effects distribution, and the proposed GEE inference is valid for any distributional form. We provided an illustration by using data from a genome-wide pharmacogenomic study of an anticancer drug.

Original languageEnglish
Pages (from-to)4838-4858
Number of pages21
JournalStatistics in Medicine
Volume32
Issue number27
DOIs
Publication statusPublished - 2013 Jan 1
Externally publishedYes

Fingerprint

Generalized Estimating Equations
Pharmacokinetics
Robust Methods
Nonlinear Mixed Effects Model
Genome
Population
Random Effects
Misspecification
Genetic Polymorphisms
Single Nucleotide Polymorphism
Valid
Estimator
Relative Stability
Marginal Likelihood
Type I Error Rate
Single nucleotide Polymorphism
Model Analysis
Polymorphism
Pharmacogenomic Testing
Hermite

Keywords

  • Gene screening
  • Generalized estimating equations
  • Genome-wide study
  • Misspecified models
  • Population pharmacokinetic data

ASJC Scopus subject areas

  • Epidemiology
  • Statistics and Probability

Cite this

An efficient and robust method for analyzing population pharmacokinetic data in genome-wide pharmacogenomic studies : A generalized estimating equation approach. / Nagashima, Kengo; Sato, Yasunori; Noma, Hisashi; Hamada, Chikuma.

In: Statistics in Medicine, Vol. 32, No. 27, 01.01.2013, p. 4838-4858.

Research output: Contribution to journalArticle

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