Simultaneous SNP identification in association studies with missing data

DOI10.1214/11-AOAS516zbMATH Open1243.62134arXiv1207.0280MaRDI QIDQ439128FDOQ439128

Authors: Vikneswaran Gopal, John M. Davis, George Casella, Xiaobo Li, Zhen Li 

Publication date: 1 August 2012

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: Association testing aims to discover the underlying relationship between genotypes (usually Single Nucleotide Polymorphisms, or SNPs) and phenotypes (attributes, or traits). The typically large data sets used in association testing often contain missing values. Standard statistical methods either impute the missing values using relatively simple assumptions, or delete them, or both, which can generate biased results. Here we describe the Bayesian hierarchical model BAMD (Bayesian Association with Missing Data). BAMD is a Gibbs sampler, in which missing values are multiply imputed based upon all of the available information in the data set. We estimate the parameters and prove that updating one SNP at each iteration preserves the ergodic property of the Markov chain, and at the same time improves computational speed. We also implement a model selection option in BAMD, which enables potential detection of SNP interactions. Simulations show that unbiased estimates of SNP effects are recovered with missing genotype data. Also, we validate associations between SNPs and a carbon isotope discrimination phenotype that were previously reported using a family based method, and discover an additional SNP associated with the trait. BAMD is available as an R-package from http://cran.r-project.org/package=BAMD

Full work available at URL: https://arxiv.org/abs/1207.0280

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zbMATH Keywords

hierarchical modelsGibbs samplinggenome-wide associationBayes models

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Numerical analysis or methods applied to Markov chains (65C40) Genetics and epigenetics (92D10)

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Cited In (10)

• Robust score tests with missing data in genomics studies
• Bayesian epistasis association mapping via SNP imputation
• Simultaneous SNP identification in association studies with missing data
• Model, properties and imputation method of missing SNP genotype data utilizing mutual information
• Bayesian model search and multilevel inference for SNP association studies
• Title not available (Why is that?)
• Analysis of case-control association studies: SNPs, imputation and haplotypes
• Modeling informatively missing genotypes in haplotype analysis
• Bayesian analysis of case control polygenic etiology studies with missing data
• Sure independence screening in the presence of missing data

Uses Software

• R
• tsbridge
• MISA
• STRUCTURE
• BAMD

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