A variational Bayes algorithm for fast and accurate multiple locus genome-wide association analysis.

BMC Bioinformatics
Benjamin A LogsdonJason G Mezey

Abstract

The success achieved by genome-wide association (GWA) studies in the identification of candidate loci for complex diseases has been accompanied by an inability to explain the bulk of heritability. Here, we describe the algorithm V-Bay, a variational Bayes algorithm for multiple locus GWA analysis, which is designed to identify weaker associations that may contribute to this missing heritability. V-Bay provides a novel solution to the computational scaling constraints of most multiple locus methods and can complete a simultaneous analysis of a million genetic markers in a few hours, when using a desktop. Using a range of simulated genetic and GWA experimental scenarios, we demonstrate that V-Bay is highly accurate, and reliably identifies associations that are too weak to be discovered by single-marker testing approaches. V-Bay can also outperform a multiple locus analysis method based on the lasso, which has similar scaling properties for large numbers of genetic markers. For demonstration purposes, we also use V-Bay to confirm associations with gene expression in cell lines derived from the Phase II individuals of HapMap. V-Bay is a versatile, fast, and accurate multiple locus GWA analysis tool for the practitioner interested ...Continue Reading

References

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Citations

Dec 16, 2010·Bioinformatics·Jiahan LiRongling Wu
Apr 2, 2011·BMC Bioinformatics·Xia JiangShyam Visweswaran
Jul 5, 2013·PLoS Computational Biology·Gabriel E HoffmanJason G Mezey
Feb 15, 2013·PLoS Genetics·Xiang ZhouMatthew Stephens
Dec 3, 2011·Genetics·Wenzhao Yang, Robert J Tempelman
Apr 17, 2014·Journal of the American Medical Informatics Association : JAMIA·Xia JiangRichard E Neapolitan
Feb 1, 2014·Genetic Epidemiology·Benjamin A LogsdonUNKNOWN NHLBI GO Exome Sequencing Project
Feb 14, 2015·Genetic Epidemiology·Xia Jiang, Richard E Neapolitan
Mar 20, 2015·Briefings in Bioinformatics·Xia Jiang, Richard E Neapolitan
Feb 5, 2015·BMC Genomics·Ling WangGuang Guo
Jan 15, 2015·Nucleic Acids Research·Benjamin A LogsdonSu-In Lee
Dec 8, 2015·IEEE Transactions on Cybernetics·Yaojie LuShima Khatibisepehr
Aug 14, 2018·Biometrical Journal. Biometrische Zeitschrift·Dörte Wittenburg, Volkmar Liebscher
Apr 10, 2017·G3 : Genes - Genomes - Genetics·Osval A Montesinos-LópezRaymundo Buenrostro-Mariscal
May 24, 2017·Molecular Genetics and Genomics : MGG·Weiwei DuanFeng Chen
Oct 28, 2016·Genetics·Damian BrzyskiChiara Sabatti
Jun 19, 2013·Genetics·Zitong Li, Mikko J Sillanpää
Jul 9, 2020·Computational and Structural Biotechnology Journal·Huanhuan Zhu, Xiang Zhou
Dec 29, 2020·Bioinformatics·Matthew Kerin, Jonathan Marchini
May 22, 2021·Nature Genetics·Joelle MbatchouJonathan Marchini

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Software Mentioned

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