Bayesian model search and multilevel inference for SNP association studies
From MaRDI portal
(Redirected from Publication:614148)
Abstract: Technological advances in genotyping have given rise to hypothesis-based association studies of increasing scope. As a result, the scientific hypotheses addressed by these studies have become more complex and more difficult to address using existing analytic methodologies. Obstacles to analysis include inference in the face of multiple comparisons, complications arising from correlations among the SNPs (single nucleotide polymorphisms), choice of their genetic parametrization and missing data. In this paper we present an efficient Bayesian model search strategy that searches over the space of genetic markers and their genetic parametrization. The resulting method for Multilevel Inference of SNP Associations, MISA, allows computation of multilevel posterior probabilities and Bayes factors at the global, gene and SNP level, with the prior distribution on SNP inclusion in the model providing an intrinsic multiplicity correction. We use simulated data sets to characterize MISA's statistical power, and show that MISA has higher power to detect association than standard procedures. Using data from the North Carolina Ovarian Cancer Study (NCOCS), MISA identifies variants that were not identified by standard methods and have been externally ``validated in independent studies. We examine sensitivity of the NCOCS results to prior choice and method for imputing missing data. MISA is available in an R package on CRAN.
Recommendations
- Simultaneous SNP identification in association studies with missing data
- A Bayesian graphical model for genome-wide association studies (GWAS)
- Modeling the Association Between Clusters of SNPs and Disease Responses
- Bayesian model selection in complex linear systems, as illustrated in genetic association studies
- Bayesian Gaussian Mixture Models for High-Density Genotyping Arrays
Cites work
- scientific article; zbMATH DE number 4074232 (Why is no real title available?)
- scientific article; zbMATH DE number 3497315 (Why is no real title available?)
- scientific article; zbMATH DE number 1471711 (Why is no real title available?)
- scientific article; zbMATH DE number 1522700 (Why is no real title available?)
- scientific article; zbMATH DE number 5274667 (Why is no real title available?)
- scientific article; zbMATH DE number 3189754 (Why is no real title available?)
- A Direct Approach to False Discovery Rates
- Algorithms in bioinformatics. Proceedings of the workshops, Seoul, Korea, July 2004, and London, UK, February 2005.
- Bayes Factors
- Bayes and empirical-Bayes multiplicity adjustment in the variable-selection problem
- Bayesian model averaging: A tutorial. (with comments and a rejoinder).
- Bayesian model search and multilevel inference for SNP association studies
- Correlation and Large-Scale Simultaneous Significance Testing
- Empirical Bayes vs. fully Bayes variable selection
- Identification of SNP interactions using logic regression
- Inference from iterative simulation using multiple sequences
- Model uncertainty
Cited in
(14)- Bayesian Gaussian Mixture Models for High-Density Genotyping Arrays
- A new flexible Bayesian hypothesis test for multivariate data
- A Bayesian nonparametric multiple testing procedure for comparing several treatments against a control
- A Bayesian graphical model for genome-wide association studies (GWAS)
- Bayesian model selection in complex linear systems, as illustrated in genetic association studies
- A Bayesian method for detecting and characterizing allelic heterogeneity and boosting signals in genome-wide association studies
- Joint specification of model space and parameter space prior distributions
- Subjective Bayesian testing using calibrated prior probabilities
- Bayesian model selection using the median probability model
- Prior distributions for objective Bayesian analysis
- Bayesian model search and multilevel inference for SNP association studies
- Bayesian Genome- and Epigenome-Wide Association Studies with Gene Level Dependence
- Simultaneous SNP identification in association studies with missing data
- An integrated hierarchical Bayesian model for multivariate eQTL mapping
This page was built for publication: Bayesian model search and multilevel inference for SNP association studies
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q614148)
