Modeling correlated marker effects in genome-wide prediction via Gaussian concentration graph models
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Abstract: In genome-wide prediction, independence of marker allele substitution effects is typically assumed; however, since early stages of this technology it has been known that nature points to correlated effects. In statistics, graphical models have been identified as a useful and powerful tool for covariance estimation in high dimensional problems and it is an area that has recently experienced a great expansion. In particular, Gaussian concentration graph models (GCGM) have been widely studied. These are models in which the distribution of a set of random variables, the marker effects in this case, is assumed to be Markov with respect to an undirected graph G. In this paper, Bayesian (Bayes G and Bayes G-D) and frequentist (GML-BLUP) methods adapting the theory of GCGM to genome-wide prediction were developed. Different approaches to define the graph G based on domain-specific knowledge were proposed, and two propositions and a corollary establishing conditions to find decomposable graphs were proven. These methods were implemented in small simulated and real datasets. In our simulations, scenarios where correlations among allelic substitution effects were expected to arise due to various causes were considered, and graphs were defined on the basis of physical marker positions. Results showed improvements in correlation between phenotypes and predicted breeding values and accuracies of predicted breeding values when accounting for partially correlated allele substitution effects. Extensions to the multiallelic loci case were described and some possible refinements incorporating more flexible priors in the Bayesian setting were discussed. Our models are promising because they allow incorporation of biological information in the prediction process, and because they are more flexible and general than other models accounting for correlated marker effects that have been proposed previously.
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Cites work
- scientific article; zbMATH DE number 3567782 (Why is no real title available?)
- scientific article; zbMATH DE number 1220667 (Why is no real title available?)
- scientific article; zbMATH DE number 837912 (Why is no real title available?)
- A Metropolis-Hastings based method for sampling from the \(G\)-Wishart distribution in Gaussian graphical models
- A Simple Method for Computing the Inverse of a Numerator Relationship Matrix Used in Prediction of Breeding Values
- A convex pseudolikelihood framework for high dimensional partial correlation estimation with convergence guarantees
- Cholesky decomposition of a hyper inverse Wishart matrix
- Conjugate priors for exponential families
- Covariance regularization by thresholding
- Flexible covariance estimation in graphical Gaussian models
- Gaussian Markov distributions over finite graphs
- Hyper Inverse Wishart Distribution for Non-decomposable Graphs and its Application to Bayesian Inference for Gaussian Graphical Models
- Hyper Markov laws in the statistical analysis of decomposable graphical models
- Improving the efficiency of genomic selection
- Independence Structure of Natural Conjugate Densities to Exponential Families and the Gibbs' Sampler
- Schur products and matrix completions
- Simulation of hyper-inverse Wishart distributions in graphical models
- Sparse matrix decompositions and graph characterizations
- The hidden life of latent variables: Bayesian learning with mixed graph models
- Wishart distributions for decomposable covariance graph models
- Wishart distributions for decomposable graphs
Cited in
(2)- Joint genome-wide prediction in several populations accounting for randomness of genotypes: a hierarchical Bayes approach. II: Multivariate spike and slab priors for marker effects and derivation of approximate Bayes and fractional Bayes factors for the complete family of models
- Joint genome-wide prediction in several populations accounting for randomness of genotypes: a hierarchical Bayes approach. I: Multivariate Gaussian priors for marker effects and derivation of the joint probability mass function of genotypes
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