A Bayesian genome screening of maximum number of drinks as an alcoholism phenotype with the new Haseman-Elston method

Common human disorders, such as alcoholism, may be the result of interactions of many genes as well as environmental risk factors. Therefore, it is important to incorporate gene × gene and gene × environment interactions in complex disease gene mapping. In this study, we applied a robust Bayesian ge...

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Bibliographic Details
Main Authors:	Oh, Cheongeun, Wang, Shuang, Liu, Nianjun, Chen, Liang, Zhao, Hongyu
Format:	Online
Language:	English
Published:	BioMed Central 2005
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866822/

id	pubmed-1866822
recordtype	oai_dc
spelling	pubmed-18668222007-05-11 A Bayesian genome screening of maximum number of drinks as an alcoholism phenotype with the new Haseman-Elston method Oh, Cheongeun Wang, Shuang Liu, Nianjun Chen, Liang Zhao, Hongyu Proceedings Common human disorders, such as alcoholism, may be the result of interactions of many genes as well as environmental risk factors. Therefore, it is important to incorporate gene × gene and gene × environment interactions in complex disease gene mapping. In this study, we applied a robust Bayesian genome screening method that can incorporate interaction effects to map genes underlying alcoholism through its application to the data of the Collaborative Studies on Genetics of Alcoholism provided by Genetic Analysis Workshop 14. Our Bayesian genome screening method uses the regression-based stochastic variable selection, coupled with the new Haseman-Elston method to identify markers linked to phenotypes of interest. Compared to traditional linkage methods based on single-gene disease models, our method allows for multilocus disease models for simultaneous screening including both main and interaction (epistatic) effects. It is conceptually simple and computationally efficient through the use of Gibbs sampler. We conducted genome-wide analysis and comparison between scans based on microsatellites and single-nucleotide polymorphisms. A total of 328 microsatellites and 11,560 single-nucleotide polymorphisms (by Affymetrix) on 22 autosomal chromosomes and sex chromosome were used. BioMed Central 2005-12-30 /pmc/articles/PMC1866822/ /pubmed/16451573 http://dx.doi.org/10.1186/1471-2156-6-S1-S116 Text en Copyright © 2005 Oh et al; licensee BioMed Central Ltd http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Oh, Cheongeun Wang, Shuang Liu, Nianjun Chen, Liang Zhao, Hongyu
spellingShingle	Oh, Cheongeun Wang, Shuang Liu, Nianjun Chen, Liang Zhao, Hongyu A Bayesian genome screening of maximum number of drinks as an alcoholism phenotype with the new Haseman-Elston method
author_facet	Oh, Cheongeun Wang, Shuang Liu, Nianjun Chen, Liang Zhao, Hongyu
author_sort	Oh, Cheongeun
title	A Bayesian genome screening of maximum number of drinks as an alcoholism phenotype with the new Haseman-Elston method
title_short	A Bayesian genome screening of maximum number of drinks as an alcoholism phenotype with the new Haseman-Elston method
title_full	A Bayesian genome screening of maximum number of drinks as an alcoholism phenotype with the new Haseman-Elston method
title_fullStr	A Bayesian genome screening of maximum number of drinks as an alcoholism phenotype with the new Haseman-Elston method
title_full_unstemmed	A Bayesian genome screening of maximum number of drinks as an alcoholism phenotype with the new Haseman-Elston method
title_sort	bayesian genome screening of maximum number of drinks as an alcoholism phenotype with the new haseman-elston method
description	Common human disorders, such as alcoholism, may be the result of interactions of many genes as well as environmental risk factors. Therefore, it is important to incorporate gene × gene and gene × environment interactions in complex disease gene mapping. In this study, we applied a robust Bayesian genome screening method that can incorporate interaction effects to map genes underlying alcoholism through its application to the data of the Collaborative Studies on Genetics of Alcoholism provided by Genetic Analysis Workshop 14. Our Bayesian genome screening method uses the regression-based stochastic variable selection, coupled with the new Haseman-Elston method to identify markers linked to phenotypes of interest. Compared to traditional linkage methods based on single-gene disease models, our method allows for multilocus disease models for simultaneous screening including both main and interaction (epistatic) effects. It is conceptually simple and computationally efficient through the use of Gibbs sampler. We conducted genome-wide analysis and comparison between scans based on microsatellites and single-nucleotide polymorphisms. A total of 328 microsatellites and 11,560 single-nucleotide polymorphisms (by Affymetrix) on 22 autosomal chromosomes and sex chromosome were used.
publisher	BioMed Central
publishDate	2005
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866822/
_version_	1611396333238747136

A Bayesian genome screening of maximum number of drinks as an alcoholism phenotype with the new Haseman-Elston method

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