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Bayesian inference for two-phase studies with categorical covariates.

ABSTRACT: In this article, we consider two-phase sampling in the situation in which all covariates are categorical. Two-phase designs are appealing from an efficiency perspective since they allow sampling to be concentrated in informative cells. A number of likelihood-based methods have been developed for the analysis of two-phase data, but we describe a Bayesian approach which has previously been unavailable. The methods are first compared with existing approaches via a simulation study, and are then applied to data collected on Wilms tumor. The benefits of a Bayesian approach include relaxation of the reliance on asymptotic inference, particularly in sparse data situations, and the potential to model data with complex dependencies, for example, via the introduction of random effects. The sparse data situation is illustrated via a simulated example.

SUBMITTER: Ross M

PROVIDER: S-EPMC3714402 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature

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Bayesian inference for two-phase studies with categorical covariates.

Ross Michelle M Wakefield Jon J

Biometrics 20130422 2

In this article, we consider two-phase sampling in the situation in which all covariates are categorical. Two-phase designs are appealing from an efficiency perspective since they allow sampling to be concentrated in informative cells. A number of likelihood-based methods have been developed for the analysis of two-phase data, but we describe a Bayesian approach which has previously been unavailable. The methods are first compared with existing approaches via a simulation study, and are then app ...[more]

PMID: 23607570

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Project description:The two-phase sampling design is a cost-efficient way of collecting expensive covariate information on a judiciously selected sub-sample. It is natural to apply such a strategy for collecting genetic data in a sub-sample enriched for exposure to environmental factors for gene-environment interaction (G × E) analysis. In this paper, we consider two-phase studies of G × E interaction where phase I data are available on exposure, covariates and disease status. Stratified sampling is done to prioritize individuals for genotyping at phase II conditional on disease and exposure. We consider a Bayesian analysis based on the joint retrospective likelihood of phase I and phase II data. We address several important statistical issues: (i) we consider a model with multiple genes, environmental factors and their pairwise interactions. We employ a Bayesian variable selection algorithm to reduce the dimensionality of this potentially high-dimensional model; (ii) we use the assumption of gene-gene and gene-environment independence to trade-off between bias and efficiency for estimating the interaction parameters through use of hierarchical priors reflecting this assumption; (iii) we posit a flexible model for the joint distribution of the phase I categorical variables using the non-parametric Bayes construction of Dunson and Xing (2009). We carry out a small-scale simulation study to compare the proposed Bayesian method with weighted likelihood and pseudo likelihood methods that are standard choices for analyzing two-phase data. The motivating example originates from an ongoing case-control study of colorectal cancer, where the goal is to explore the interaction between the use of statins (a drug used for lowering lipid levels) and 294 genetic markers in the lipid metabolism/cholesterol synthesis pathway. The sub-sample of cases and controls on which these genetic markers were measured is enriched in terms of statin users. The example and simulation results illustrate that the proposed Bayesian approach has a number of advantages for characterizing joint effects of genotype and exposure over existing alternatives and makes efficient use of all available data in both phases.

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Bayesian inference for two-phase studies with categorical covariates.

Publications

Bayesian inference for two-phase studies with categorical covariates.

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