Bayesian variable selection regression for genome-wide association studies and other large-scale problems
From MaRDI portal
Abstract: We consider applying Bayesian Variable Selection Regression, or BVSR, to genome-wide association studies and similar large-scale regression problems. Currently, typical genome-wide association studies measure hundreds of thousands, or millions, of genetic variants (SNPs), in thousands or tens of thousands of individuals, and attempt to identify regions harboring SNPs that affect some phenotype or outcome of interest. This goal can naturally be cast as a variable selection regression problem, with the SNPs as the covariates in the regression. Characteristic features of genome-wide association studies include the following: (i) a focus primarily on identifying relevant variables, rather than on prediction; and (ii) many relevant covariates may have tiny effects, making it effectively impossible to confidently identify the complete "correct" subset of variables. Taken together, these factors put a premium on having interpretable measures of confidence for individual covariates being included in the model, which we argue is a strength of BVSR compared with alternatives such as penalized regression methods. Here we focus primarily on analysis of quantitative phenotypes, and on appropriate prior specification for BVSR in this setting, emphasizing the idea of considering what the priors imply about the total proportion of variance in outcome explained by relevant covariates. We also emphasize the potential for BVSR to estimate this proportion of variance explained, and hence shed light on the issue of "missing heritability" in genome-wide association studies.
Recommendations
- Scalable variational inference for Bayesian variable selection in regression, and its accuracy in genetic association studies
- Bayesian large-scale multiple regression with summary statistics from genome-wide association studies
- Fast model-fitting of Bayesian variable selection regression using the iterative complex factorization algorithm
- Assessing a spatial boost model for quantitative trait GWAS
- Multiple loci mapping via model-free variable selection
Cites work
- A review of Bayesian variable selection methods: what, how and which
- Bayes Model Averaging with Selection of Regressors
- Bayesian Analysis of Binary and Polychotomous Response Data
- Bayesian Model Averaging for Linear Regression Models
- Bayesian Variable Selection in Linear Regression
- scientific article; zbMATH DE number 4070082 (Why is no real title available?)
- scientific article; zbMATH DE number 1906319 (Why is no real title available?)
- scientific article; zbMATH DE number 845714 (Why is no real title available?)
- Least angle regression. (With discussion)
- Mixtures of g Priors for Bayesian Variable Selection
- Monte Carlo sampling methods using Markov chains and their applications
- Nonparametric regression using Bayesian variable selection
- Optimal predictive model selection.
- Rao-Blackwellisation of sampling schemes
- Regularization and Variable Selection Via the Elastic Net
- Small-world MCMC and convergence to multi-modal distributions: from slow mixing to fast mixing
- Variable Selection via Nonconcave Penalized Likelihood and its Oracle Properties
Cited in
(49)- Bayesian beta regression for bounded responses with unknown supports
- MMVBVS
- Bayesian large-scale multiple regression with summary statistics from genome-wide association studies
- Fast model-fitting of Bayesian variable selection regression using the iterative complex factorization algorithm
- Sticky PDMP samplers for sparse and local inference problems
- A global-local approach for detecting hotspots in multiple-response regression
- A novel Bayesian approach for variable selection in linear regression models
- Variable prioritization in nonlinear black box methods: a genetic association case study
- Approximate large-scale Bayesian spatial modeling with application to quantitative magnetic resonance imaging
- Improving the efficiency of genomic selection
- Application of whole-genome prediction methods for genome-wide association studies: a Bayesian approach
- Scalable variational inference for Bayesian variable selection in regression, and its accuracy in genetic association studies
- Bayesian clustering of spatial functional data with application to a human mobility study during COVID-19
- An Integrative Bayesian Modeling Approach to Imaging Genetics
- pi-MASS
- A Bayesian graphical model for genome-wide association studies (GWAS)
- Detection boundary and higher criticism approach for rare and weak genetic effects
- On the null distribution of Bayes factors in linear regression
- Bayesian model selection in complex linear systems, as illustrated in genetic association studies
- scientific article; zbMATH DE number 7370554 (Why is no real title available?)
- HDBRR: a statistical package for high-dimensional Bayesian ridge regression without MCMC
- Accelerating a Gibbs sampler for variable selection on genomics data with summarization and variable pre-selection combining an array DBMS and R
- A Scalable Empirical Bayes Approach to Variable Selection in Generalized Linear Models
- Bayesian Variable Selection for Gaussian Copula Regression Models
- Tree-based quantitative trait mapping in the presence of external covariates
- Skinny Gibbs: a consistent and scalable Gibbs sampler for model selection
- Variable selection in Bayesian generalized linear‐mixed models: An illustration using candidate gene case‐control association studies
- Assessing a spatial boost model for quantitative trait GWAS
- Bayesian variable selection for post-analytic interrogation of susceptibility loci
- Debiased lasso for generalized linear models with a diverging number of covariates
- Bayesian Model Averaging: A Systematic Review and Conceptual Classification
- Filtering the Rejection Set While Preserving False Discovery Rate Control
- Neuronized Priors for Bayesian Sparse Linear Regression
- Bayesian variable selection using Knockoffs with applications to genomics
- A Bayesian method for estimating gene‐level polygenicity under the framework of transcriptome‐wide association study
- Variable selection for nonparametric Gaussian process priors: Models and computational strategies
- Incorporating biological information into linear models: a Bayesian approach to the selection of pathways and genes
- Consistent skinny Gibbs in probit regression
- A Bayesian Partially Observable Online Change Detection Approach with Thompson Sampling
- Dimension-free relaxation times of informed MCMC samplers on discrete spaces
- Controlled Discovery and Localization of Signals via Bayesian Linear Programming
- Prior knowledge elicitation: the past, present, and future
- Provably Efficient Posterior Sampling for Sparse Linear Regression via Measure Decomposition
- Bayesian Multilevel Network Recovery Selection
- Scalable network-driven variable selection in Bayesian linear regression
- Correlation between relatives given complete genotypes: from identity by descent to identity by function
- Heritability estimation in high dimensional sparse linear mixed models
- Simultaneous Bayesian analysis of contingency tables in genetic association studies
- Comparison between the SSVS and the LASSO for genome wide association studies
This page was built for publication: Bayesian variable selection regression for genome-wide association studies and other large-scale problems
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q141819)
