Bayesian model comparison in genetic association analysis: linear mixed modeling and SNP set testing

Biostatistics
Xiaoquan Wen

Abstract

We consider the problems of hypothesis testing and model comparison under a flexible Bayesian linear regression model whose formulation is closely connected with the linear mixed effect model and the parametric models for Single Nucleotide Polymorphism (SNP) set analysis in genetic association studies. We derive a class of analytic approximate Bayes factors and illustrate their connections with a variety of frequentist test statistics, including the Wald statistic and the variance component score statistic. Taking advantage of Bayesian model averaging and hierarchical modeling, we demonstrate some distinct advantages and flexibilities in the approaches utilizing the derived Bayes factors in the context of genetic association studies. We demonstrate our proposed methods using real or simulated numerical examples in applications of single SNP association testing, multi-locus fine-mapping and SNP set association testing.

References

Aug 7, 2007·PLoS Genetics·Bertrand Servin, Matthew Stephens
Feb 14, 2009·PLoS Genetics·Bo Eskerod Madsen, Sharon R Browning
Sep 19, 2009·Nature Reviews. Genetics·Matthew Stephens, David J Balding
Mar 17, 2011·PLoS Genetics·Benjamin M NealeMark J Daly
Jul 9, 2011·American Journal of Human Genetics·Michael C WuXihong Lin
Jun 16, 2012·Biostatistics·Seunggeun LeeXihong Lin
Jun 19, 2012·Nature Genetics·Xiang Zhou, Matthew Stephens
Sep 13, 2012·Genetic Epidemiology·Elizabeth D SchifanoXihong Lin
Feb 15, 2013·PLoS Genetics·Xiang ZhouMatthew Stephens
May 15, 2013·PLoS Genetics·Timothée FlutreMatthew Stephens

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Citations

Jan 4, 2019·Genetic Epidemiology·Nicholas B LarsonDaniel J Schaid

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