A Bayesian Hierarchical Model for Relating Multiple SNPs within Multiple Genes to Disease Risk
A variety of methods have been proposed for studying the association of multiple genes thought to be involved in a common pathway for a particular disease. Here, we present an extension of a Bayesian hierarchical modeling strategy that allows for multiple SNPs within each gene, with external prior i...
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| Format: | Article |
| Language: | English |
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Wiley
2013-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2013/406217 |
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| _version_ | 1832548607989907456 |
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| author | Lewei Duan Duncan C. Thomas |
| author_facet | Lewei Duan Duncan C. Thomas |
| author_sort | Lewei Duan |
| collection | DOAJ |
| description | A variety of methods have been proposed for studying the association of multiple genes thought to be involved in a common pathway for a particular disease. Here, we present an extension of a Bayesian hierarchical modeling strategy that allows for multiple SNPs within each gene, with external prior information at either the SNP or gene level. The model involves variable selection at the SNP level through latent indicator variables and Bayesian shrinkage at the gene level towards a prior mean vector and covariance matrix that depend on external information. The entire model is fitted using Markov chain Monte Carlo methods. Simulation studies show that the approach is capable of recovering many of the truly causal SNPs and genes, depending upon their frequency and size of their effects. The method is applied to data on 504 SNPs in 38 candidate genes involved in DNA damage response in the WECARE study of second breast cancers in relation to radiotherapy exposure. |
| format | Article |
| id | doaj-art-6ccfdb760725431bb923b37971dc4d1b |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2013-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-6ccfdb760725431bb923b37971dc4d1b2025-02-03T06:13:38ZengWileyInternational Journal of Genomics2314-436X2314-43782013-01-01201310.1155/2013/406217406217A Bayesian Hierarchical Model for Relating Multiple SNPs within Multiple Genes to Disease RiskLewei Duan0Duncan C. Thomas1Division of Biostatistics, Department of Preventive Medicine, University of Southern California (USC), 2001 N. Soto Street, Los Angeles, CA, USADivision of Biostatistics, Department of Preventive Medicine, University of Southern California (USC), 2001 N. Soto Street, Los Angeles, CA, USAA variety of methods have been proposed for studying the association of multiple genes thought to be involved in a common pathway for a particular disease. Here, we present an extension of a Bayesian hierarchical modeling strategy that allows for multiple SNPs within each gene, with external prior information at either the SNP or gene level. The model involves variable selection at the SNP level through latent indicator variables and Bayesian shrinkage at the gene level towards a prior mean vector and covariance matrix that depend on external information. The entire model is fitted using Markov chain Monte Carlo methods. Simulation studies show that the approach is capable of recovering many of the truly causal SNPs and genes, depending upon their frequency and size of their effects. The method is applied to data on 504 SNPs in 38 candidate genes involved in DNA damage response in the WECARE study of second breast cancers in relation to radiotherapy exposure.http://dx.doi.org/10.1155/2013/406217 |
| spellingShingle | Lewei Duan Duncan C. Thomas A Bayesian Hierarchical Model for Relating Multiple SNPs within Multiple Genes to Disease Risk International Journal of Genomics |
| title | A Bayesian Hierarchical Model for Relating Multiple SNPs within Multiple Genes to Disease Risk |
| title_full | A Bayesian Hierarchical Model for Relating Multiple SNPs within Multiple Genes to Disease Risk |
| title_fullStr | A Bayesian Hierarchical Model for Relating Multiple SNPs within Multiple Genes to Disease Risk |
| title_full_unstemmed | A Bayesian Hierarchical Model for Relating Multiple SNPs within Multiple Genes to Disease Risk |
| title_short | A Bayesian Hierarchical Model for Relating Multiple SNPs within Multiple Genes to Disease Risk |
| title_sort | bayesian hierarchical model for relating multiple snps within multiple genes to disease risk |
| url | http://dx.doi.org/10.1155/2013/406217 |
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