Modeling and testing for joint association using a genetic random field model
From MaRDI portal
Abstract: Substantial progress has been made in identifying single genetic variants predisposing to common complex diseases. Nonetheless, the genetic etiology of human diseases remains largely unknown. Human complex diseases are likely influenced by the joint effect of a large number of genetic variants instead of a single variant. The joint analysis of multiple genetic variants considering linkage disequilibrium (LD) and potential interactions can further enhance the discovery process, leading to the identification of new disease-susceptibility genetic variants. Motivated by the recent development in spatial statistics, we propose a new statistical model based on the random field theory, referred to as a genetic random field model (GenRF), for joint association analysis with the consideration of possible gene-gene interactions and LD. Using a pseudo-likelihood approach, a GenRF test for the joint association of multiple genetic variants is developed, which has the following advantages: 1. considering complex interactions for improved performance; 2. natural dimension reduction; 3. boosting power in the presence of LD; 4. computationally efficient. Simulation studies are conducted under various scenarios. Compared with a commonly adopted kernel machine approach, SKAT, GenRF shows overall comparable performance and better performance in the presence of complex interactions. The method is further illustrated by an application to the Dallas Heart Study.
Recommendations
- A hidden Markov random field model for genome-wide association studies
- Composite kernel machine regression based on likelihood ratio test for joint testing of genetic and gene–environment interaction effect
- A joint regression analysis for genetic association studies with outcome stratified samples
- Joint analysis of SNP and gene expression data in genetic association studies of complex diseases
- Set-based tests for genetic association in longitudinal studies
Cites work
- Algorithm AS 155: The Distribution of a Linear Combination of χ 2 Random Variables
- Asymptotic distribution of quadratic forms
- Gene-Trait Similarity Regression for Multimarker-Based Association Analysis
- scientific article; zbMATH DE number 3666013 (Why is no real title available?)
- scientific article; zbMATH DE number 3513115 (Why is no real title available?)
- Some Limit Theorems for Polynomials of Second Degree
- The fundamentals of modern statistical genetics
Cited in
(8)- Set-based tests for genetic association in longitudinal studies
- Joint analysis of SNP and gene expression data in genetic association studies of complex diseases
- A hidden Markov random field model for genome-wide association studies
- Two-way mixed-effects methods for joint association analysis using both host and pathogen genomes
- Composite kernel machine regression based on likelihood ratio test for joint testing of genetic and gene–environment interaction effect
- A conditional autoregressive model for genetic association analysis accounting for genetic heterogeneity
- Genetic risk prediction using a spatial autoregressive model with adaptive Lasso
- Competing risk modeling and testing for X-chromosome genetic association
This page was built for publication: Modeling and testing for joint association using a genetic random field model
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2927588)
