Next-Generation Sequencing Data-Based Association Testing of a Group of Genetic Markers for Complex Responses Using a Generalized Linear Model Framework.

Association testing has been widely used to study the relationship between genetic variants and phenotypes. Most association testing methods are genotype-based, i.e. first estimate genotype and then regress phenotype on estimated genotype and other variables. Directly testing methods based on next generation sequencing (NGS) data without genotype calling have been proposed and shown advantage over genotype-based methods in the scenarios when genotype calling is not accurate. NGS data-based single-variant testing have been proposed including our previously proposed single-variant testing method, i.e. UNC combo method [1]. NGS data-based group testing methods for continuous phenotype have also been proposed by us using a linear model framework which can handle continuous responses [2]. In this paper, we extend our linear model-based framework to a generalized linear model-based framework so that the methods can handle other types of responses especially binary responses which is commonly-faced in association studies. We have conducted extensive simulation studies to evaluate the performance of different estimators and compare our estimators with their corresponding genotype-based methods. We found that all methods have Type I errors controlled, and our NGS data-based testing methods have better performance than their corresponding genotype-based methods in the literature for other types of responses including binary responses (logistic regression) and count responses (Poisson regression especially when sequencing depth is low. In conclusion, we have extended our previous linear model (LM) framework to a generalized linear model (GLM) framework and derived NGS data-based testing methods for a group of genetic variants. Compared with our previously proposed LM-based methods [2], the new GLM-based methods can handle more complex responses (for example, binary responses and count responses) in addition to continuous responses. Our methods have filled the literature gap and shown advantage over their corresponding genotype-based methods in the literature.

Linear high-dimensional mediation models adjusting for confounders using propensity score method.

High-dimensional mediation analysis has been developed to study whether epigenetic phenotype in a high-dimensional data form would mediate the causal pathway of exposure to disease. However, most existing models are designed based on the assumption that there are no confounders between the exposure, the mediators, and the outcome. In practice, this assumption may not be feasible since high-dimensional mediation analysis (HIMA) tends to be observational where a randomized controlled trial (RCT) cannot be conducted for some economic or ethical reasons. Thus, to deal with the confounders in HIMA cases, we proposed three propensity score-related approaches named PSR (propensity score regression), PSW (propensity score weighting), and PSU (propensity score union) to adjust for the confounder bias in HIMA, and compared them with the traditional covariate regression method. The procedures mainly include four parts: calculating the propensity score, sure independence screening, MCP (minimax concave penalty) variable selection, and joint-significance testing. Simulation results show that the PSU model is the most recommended. Applying our models to the TCGA lung cancer dataset, we find that smoking may lead to lung disease through the mediation effect of some specific DNA-methylation sites, including site Cg24480765 in gene RP11-347H15.2 and site Cg22051776 in gene KLF3.

Detecting associated genes for complex traits shared across East Asian and European populations under the framework of composite null hypothesis testing.

BACKGROUND: Detecting trans-ethnic common associated genetic loci can offer important insights into shared genetic components underlying complex diseases/traits across diverse continental populations. However, effective statistical methods for such a goal are currently lacking. METHODS: By leveraging summary statistics available from global-scale genome-wide association studies, we herein proposed a novel genetic overlap detection method called CONTO (COmposite Null hypothesis test for Trans-ethnic genetic Overlap) from the perspective of high-dimensional composite null hypothesis testing. Unlike previous studies which generally analyzed individual genetic variants, CONTO is a gene-centric method which focuses on a set of genetic variants located within a gene simultaneously and assesses their joint significance with the trait of interest. By borrowing the similar principle of joint significance test (JST), CONTO takes the maximum P value of multiple associations as the significance measurement. RESULTS: Compared to JST which is often overly conservative, CONTO is improved in two aspects, including the construction of three-component mixture null distribution and the adjustment of trans-ethnic genetic correlation. Consequently, CONTO corrects the conservativeness of JST with well-calibrated P values and is much more powerful validated by extensive simulation studies. We applied CONTO to discover common associated genes for 31 complex diseases/traits between the East Asian and European populations, and identified many shared trait-associated genes that had otherwise been missed by JST. We further revealed that population-common genes were generally more evolutionarily conserved than population-specific or null ones. CONCLUSION: Overall, CONTO represents a powerful method for detecting common associated genes across diverse ancestral groups; our results provide important implications on the transferability of GWAS discoveries in one population to others.

A Review of High-Dimensional Mediation Analyses in DNA Methylation Studies.

DNA methylation alterations have been widely studied as mediators of environmentally induced disease risks. With new advances in technique, epigenome-wide DNA methylation data (EWAS) have become the new standard for epigenetic studies in human populations. However, to date most epigenetic studies of mediation effects only involve selected (gene-specific) candidate methylation markers. There is an urgent need for appropriate analytical methods for EWAS mediation analysis. In this chapter, we provide an overview of recent advances on high-dimensional mediation analysis, with application to two DNA methylation data.

Testing for mediation effect with application to human microbiome data.

Mediation analysis has been commonly used to study the effect of an exposure on an outcome through a mediator. In this paper, we are interested in exploring the mediation mechanism of microbiome, whose special features make the analysis challenging. We consider the isometric logratio transformation of the relative abundance as the mediator variable. Then, we present a de-biased Lasso estimate for the mediator of interest and derive its standard error estimator, which can be used to develop a test procedure for the interested mediation effect. Extensive simulation studies are conducted to assess the performance of our method. We apply the proposed approach to test the mediation effect of human gut microbiome between the dietary fiber intake and body mass index.

Variance component tests of multivariate mediation effects under composite null hypotheses.

Mediation effects of multiple mediators are determined by two associations: one between an exposure and mediators ( S - M ) and the other between the mediators and an outcome conditional on the exposure ( M - Y ). The test for mediation effects is conducted under a composite null hypothesis, that is, either one of the S - M and M - Y associations is zero or both are zeros. Without accounting for the composite null, the type 1 error rate within a study containing a large number of multimediator tests may be much less than the expected. We propose a novel test to address the issue. For each mediation test j , j=1,…,J , we examine the S - M and M - Y associations using two separate variance component tests. Assuming a zero-mean working distribution with a common variance for the element-wise S - M (and M - Y ) associations, score tests for the variance components are constructed. We transform the test statistics into two normally distributed statistics under the null. Using a recently developed result, we conduct J hypothesis tests accounting for the composite null hypothesis by adjusting for the variances of the normally distributed statistics for the S - M and M - Y associations. Advantages of the proposed test over other methods are illustrated in simulation studies and a data application where we analyze lung cancer data from The Cancer Genome Atlas to investigate the smoking effect on gene expression through DNA methylation in 15 114 genes.

Power and sample size calculations for evaluating mediation effects in longitudinal studies.

Current methods of power and sample size calculations for the design of longitudinal studies to evaluate mediation effects are mostly based on simulation studies and do not provide closed-form formulae. A further challenge due to the longitudinal study design is the consideration of missing data, which almost always occur in longitudinal studies due to staggered entry or drop out. In this article, we consider the product of coefficients as a measure for the longitudinal mediation effect and evaluate three methods for testing the hypothesis on the longitudinal mediation effect: the joint significant test, the normal approximation and the test of b methods. Formulae for power and sample size calculations are provided under each method while taking into account missing data. Performance of the three methods under limited sample size are examined using simulation studies. An example from the Einstein aging study is provided to illustrate the methods.