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Single-Trait and Multiple-Trait Genomic Prediction From Multi-Class Bayesian Alphabet Models Using Biological Information

Genomic prediction has been widely used in multiple areas and various genomic prediction methods have been developed. The majority of these methods, however, focus on statistical properties and ignore the abundant useful biological information like genome annotation or previously discovered causal v...

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Autores principales: Wang, Zigui, Cheng, Hao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8542848/
https://www.ncbi.nlm.nih.gov/pubmed/34707638
http://dx.doi.org/10.3389/fgene.2021.717457
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author Wang, Zigui
Cheng, Hao
author_facet Wang, Zigui
Cheng, Hao
author_sort Wang, Zigui
collection PubMed
description Genomic prediction has been widely used in multiple areas and various genomic prediction methods have been developed. The majority of these methods, however, focus on statistical properties and ignore the abundant useful biological information like genome annotation or previously discovered causal variants. Therefore, to improve prediction performance, several methods have been developed to incorporate biological information into genomic prediction, mostly in single-trait analysis. A commonly used method to incorporate biological information is allocating molecular markers into different classes based on the biological information and assigning separate priors to molecular markers in different classes. It has been shown that such methods can achieve higher prediction accuracy than conventional methods in some circumstances. However, these methods mainly focus on single-trait analysis, and available priors of these methods are limited. Thus, in both single-trait and multiple-trait analysis, we propose the multi-class Bayesian Alphabet methods, in which multiple Bayesian Alphabet priors, including RR-BLUP, BayesA, BayesB, BayesCΠ, and Bayesian LASSO, can be used for markers allocated to different classes. The superior performance of the multi-class Bayesian Alphabet in genomic prediction is demonstrated using both real and simulated data. The software tool JWAS offers open-source routines to perform these analyses.
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spelling pubmed-85428482021-10-26 Single-Trait and Multiple-Trait Genomic Prediction From Multi-Class Bayesian Alphabet Models Using Biological Information Wang, Zigui Cheng, Hao Front Genet Genetics Genomic prediction has been widely used in multiple areas and various genomic prediction methods have been developed. The majority of these methods, however, focus on statistical properties and ignore the abundant useful biological information like genome annotation or previously discovered causal variants. Therefore, to improve prediction performance, several methods have been developed to incorporate biological information into genomic prediction, mostly in single-trait analysis. A commonly used method to incorporate biological information is allocating molecular markers into different classes based on the biological information and assigning separate priors to molecular markers in different classes. It has been shown that such methods can achieve higher prediction accuracy than conventional methods in some circumstances. However, these methods mainly focus on single-trait analysis, and available priors of these methods are limited. Thus, in both single-trait and multiple-trait analysis, we propose the multi-class Bayesian Alphabet methods, in which multiple Bayesian Alphabet priors, including RR-BLUP, BayesA, BayesB, BayesCΠ, and Bayesian LASSO, can be used for markers allocated to different classes. The superior performance of the multi-class Bayesian Alphabet in genomic prediction is demonstrated using both real and simulated data. The software tool JWAS offers open-source routines to perform these analyses. Frontiers Media S.A. 2021-10-11 /pmc/articles/PMC8542848/ /pubmed/34707638 http://dx.doi.org/10.3389/fgene.2021.717457 Text en Copyright © 2021 Wang and Cheng. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Wang, Zigui
Cheng, Hao
Single-Trait and Multiple-Trait Genomic Prediction From Multi-Class Bayesian Alphabet Models Using Biological Information
title Single-Trait and Multiple-Trait Genomic Prediction From Multi-Class Bayesian Alphabet Models Using Biological Information
title_full Single-Trait and Multiple-Trait Genomic Prediction From Multi-Class Bayesian Alphabet Models Using Biological Information
title_fullStr Single-Trait and Multiple-Trait Genomic Prediction From Multi-Class Bayesian Alphabet Models Using Biological Information
title_full_unstemmed Single-Trait and Multiple-Trait Genomic Prediction From Multi-Class Bayesian Alphabet Models Using Biological Information
title_short Single-Trait and Multiple-Trait Genomic Prediction From Multi-Class Bayesian Alphabet Models Using Biological Information
title_sort single-trait and multiple-trait genomic prediction from multi-class bayesian alphabet models using biological information
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8542848/
https://www.ncbi.nlm.nih.gov/pubmed/34707638
http://dx.doi.org/10.3389/fgene.2021.717457
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