title: An efficient and robust method for analyzing population pharmacokinetic data in genome-wide pharmacogenomic studies: a generalized estimating equation approach.
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.
authors.affiliation: Clinical Research Center, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8677, Japan; Graduate School of Engineering, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan; Faculty of Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado-shi, Saitama 350-0295, Japan.
authors.forename: Kengo
authors.initials: K
authors.lastname: Nagashima
authors.forename: Yasunori
authors.initials: Y
authors.lastname: Sato
authors.forename: Hisashi
authors.initials: H
authors.lastname: Noma
authors.forename: Chikuma
authors.initials: C
authors.lastname: Hamada
mesh_terms: D000964:Antimetabolites, Antineoplastic / Q000493:pharmacokinetics; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D003841:Deoxycytidine / Q000031:analogs & derivatives / Q000493:pharmacokinetics; D055106:Genome-Wide Association Study / Q000379:methods*; D006801:Humans; D015233:Models, Statistical; D010190:Pancreatic Neoplasms / Q000188:drug therapy / Q000235:genetics; D010597:Pharmacogenetics / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D000093542:Gemcitabine
chemical_list: D000964:Antimetabolites, Antineoplastic; D003841:Deoxycytidine; D000093542:Gemcitabine
keywords: gene screening; generalized estimating equations; genome-wide study; misspecified models; population pharmacokinetic data