Back to basics for Bayesian model building in genomic selection.

Genetics
Hanni P Kärkkäinen, Mikko J Sillanpää

Abstract

Numerous Bayesian methods of phenotype prediction and genomic breeding value estimation based on multilocus association models have been proposed. Computationally the methods have been based either on Markov chain Monte Carlo or on faster maximum a posteriori estimation. The demand for more accurate and more efficient estimation has led to the rapid emergence of workable methods, unfortunately at the expense of well-defined principles for Bayesian model building. In this article we go back to the basics and build a Bayesian multilocus association model for quantitative and binary traits with carefully defined hierarchical parameterization of Student's t and Laplace priors. In this treatment we consider alternative model structures, using indicator variables and polygenic terms. We make the most of the conjugate analysis, enabled by the hierarchical formulation of the prior densities, by deriving the fully conditional posterior densities of the parameters and using the acquired known distributions in building fast generalized expectation-maximization estimation algorithms.

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Citations

Jul 25, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Crispin M Mutshinda, Mikko J Sillanpää
Feb 7, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Frank Technow, Albrecht E Melchinger
Jun 6, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Haixiao HuShaojiang Chen
Jul 16, 2013·Theoretical Population Biology·Serge Sverdlov, Elizabeth A Thompson
Sep 14, 2012·Annals of Human Genetics·Hanni P Kärkkāinen, Mikko J Sillanpää
Jul 10, 2013·Genetics, Selection, Evolution : GSE·Timo KnürrMikko J Sillanpää
Jan 24, 2014·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Zhigang GuoGilles Gay
Aug 26, 2015·BMC Genetics·Camila Ferreira AzevedoPatricio Muñoz
Apr 10, 2015·PloS One·Leena PasanenMikko J Sillanpää
Jun 21, 2016·PloS One·Charles-Elie RabierBrigitte Mangin
Jul 4, 2013·G3 : Genes - Genomes - Genetics·Hanni P Kärkkäinen, Mikko J Sillanpää
Jun 19, 2016·G3 : Genes - Genomes - Genetics·Alencar XavierKaty Martin Rainey
Nov 7, 2019·G3 : Genes - Genomes - Genetics·Alencar Xavier
Feb 20, 2019·PloS One·Brigitte ManginEllen Goudemand-Dugue
Aug 11, 2020·Statistical Applications in Genetics and Molecular Biology·Saheb Foroutaifar
Sep 26, 2015·Genetics·Hanni P KärkkäinenMikko J Sillanpää
Aug 23, 2017·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Jianbo HeJunyi Gai
Oct 7, 2017·Frontiers in Plant Science·Brigitte ManginNicolas B Langlade
Jun 27, 2018·Heredity·Luís Felipe Ventorim FerrãoAntonio Augusto Franco Garcia
Dec 13, 2019·Theoretical Population Biology·Daniel GianolaChris-Carolin Schön
May 29, 2021·BMC Genomic Data·Matthew T McGowanStephen P Ficklin
Jul 27, 2021·The Plant Genome·Osval Antonio Montesinos-LópezJosé Crossa

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