Bayesian, GLMM, Jeffreys’ prior, PQL, Reference prior, Uniform shrinkage prior, Variance component,

This paper was motivated by a double-blind randomized clinical trial of myopia intervention. In addition to the primary goal of comparing treatment effects, we are concerned with the modelling of correlation that may come from two possible sources, one among the longitudinal observations and the other between measurements taken from both eyes per subject. The data are nested repeated measurements. We suggest three models for analysis. Each one expresses the correlation differently in various covariance structures. We articulate their differences and describe the implementations in estimation using commercial statistical software. The computer output can be further utilized to perform model selection with Schwarz criterion. Simulation studies are conducted to evaluate the performance under each model. Data of the myopia intervention trial are reanalysed with these models for illustration. The results indicate that atropine is more effective in reducing the progression rate, the rates are homogeneous across subjects, and, among the suggested models, the one with independent random effects of two eyes fits best. We conclude that model selection is a crucial step before making inference with estimates; otherwise the correlation may be attributed incorrectly to a different mechanism. The same conclusion applies to other variance components as well.

The problem of variable selection in the generalized linear-mixed models (GLMMs) is pervasive in statistical practice. For the purpose of variable selection, many methodologies for determining the best subset of explanatory variables currently exist according to the model complexity and differences between applications. In this paper, we develop a "higher posterior probability model with bootstrap" (HPMB) approach to select explanatory variables without fitting all possible GLMMs involving a small or moderate number of explanatory variables. Furthermore, to save computational load, we propose an efficient approximation approach with Laplace's method and Taylor's expansion to approximate intractable integrals in GLMMs. Simulation studies and an application of HapMap data provide evidence that this selection approach is computationally feasible and reliable for exploring true candidate genes and gene-gene associations, after adjusting for complex structures among clusters.

No abstract

Multiple markers in linkage disequilibrium (LD) are usually used to localize the disease gene location. These markers may contribute to the disease etiology simultaneously. In contrast to the single-locus tests, we propose a genetic random effects model that accounts for the dependence between loci via their spatial structures. In this model, the locus-specific random effects measure not only the genetic disease risk, but also the correlations between markers. In other words, the model incorporates this relation in both mean and covariance structures, and the variance components play important roles. We consider two different settings for the spatial relations. The first is our proposal, relative distance function (RDF), which is intuitive in the sense that markers nearby are likely to correlate with each other. The second setting is a common exponential decay function (EDF). Under each setting, the inference of the genetic parameters is fully Bayesian with Markov chain Monte Carlo (MCMC) sampling. We demonstrate the validity and the utility of the proposed approach with two real datasets and simulation studies. The analyses show that the proposed model with either one of two spatial correlations performs better as compared with the single locus analysis. In addition, under the RDF model, a more precise estimate for the disease locus can be obtained even when the candidate markers are fairly dense. In all simulations, the inference under the true model provides unbiased estimates of the genetic parameters, and the model with the spatial correlation structure does lead to greater confidence interval coverage probabilities.