Bayesian group Lasso for nonparametric varying-coefficient models with application to functional genome-wide association studies
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Publication:746650
DOI10.1214/15-AOAS808zbMATH Open1397.62260arXiv1509.04017WikidataQ36161135 ScholiaQ36161135MaRDI QIDQ746650FDOQ746650
Authors: Jiahan Li, Zhong Wang, Rongling Wu, Runze Li 
Publication date: 28 October 2015
Published in: The Annals of Applied Statistics (Search for Journal in Brave)
Abstract: Although genome-wide association studies (GWAS) have proven powerful for comprehending the genetic architecture of complex traits, they are challenged by a high dimension of single-nucleotide polymorphisms (SNPs) as predictors, the presence of complex environmental factors, and longitudinal or functional natures of many complex traits or diseases. To address these challenges, we propose a high-dimensional varying-coefficient model for incorporating functional aspects of phenotypic traits into GWAS to formulate a so-called functional GWAS or fGWAS. The Bayesian group lasso and the associated MCMC algorithms are developed to identify significant SNPs and estimate how they affect longitudinal traits through time-varying genetic actions. The model is generalized to analyze the genetic control of complex traits using subject-specific sparse longitudinal data. The statistical properties of the new model are investigated through simulation studies. We use the new model to analyze a real GWAS data set from the Framingham Heart Study, leading to the identification of several significant SNPs associated with age-specific changes of body mass index. The fGWAS model, equipped with the Bayesian group lasso, will provide a useful tool for genetic and developmental analysis of complex traits or diseases.
Full work available at URL: https://arxiv.org/abs/1509.04017
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Nonparametric regression and quantile regression (62G08) Applications of statistics to biology and medical sciences; meta analysis (62P10) Ridge regression; shrinkage estimators (Lasso) (62J07)
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