[HTML][HTML] Multifactorial methods integrating haplotype and epistasis effects for genomic estimation and prediction of quantitative traits

Y Da, Z Liang, D Prakapenka - Frontiers in Genetics, 2022 - frontiersin.org
The rapid growth in genomic selection data provides unprecedented opportunities to
discover and utilize complex genetic effects for improving phenotypes, but the methodology …

Accounting for epistasis improves genomic prediction of phenotypes with univariate and bivariate models across environments

E Vojgani, T Pook, JWR Martini, AC Hölker… - Theoretical and Applied …, 2021 - Springer
Abstract Key Message The accuracy of genomic prediction of phenotypes can be increased
by including the top-ranked pairwise SNP interactions into the prediction model. Abstract We …

Orthogonal estimates of variances for additive, dominance, and epistatic effects in populations

ZG Vitezica, A Legarra, MA Toro, L Varona - Genetics, 2017 - academic.oup.com
Genomic prediction methods based on multiple markers have potential to include
nonadditive effects in prediction and analysis of complex traits. However, most …

Mixed model methods for genomic prediction and variance component estimation of additive and dominance effects using SNP markers

Y Da, C Wang, S Wang, G Hu - PloS one, 2014 - journals.plos.org
We established a genomic model of quantitative trait with genomic additive and dominance
relationships that parallels the traditional quantitative genetics model, which partitions a …

Detection of SNP epistasis effects of quantitative traits using an extended Kempthorne model

Y Mao, NR London, L Ma, D Dvorkin… - Physiological …, 2006 - journals.physiology.org
Epistasis effects (gene interactions) have been increasingly recognized as important genetic
factors underlying complex traits. The existence of a large number of single nucleotide …

Comparison of the Accuracy of Epistasis and Haplotype Models for Genomic Prediction of Seven Human Phenotypes

Z Liang, D Prakapenka, Y Da - Biomolecules, 2023 - mdpi.com
The accuracy of predicting seven human phenotypes of 3657–7564 individuals using global
epistasis effects was evaluated and compared to the accuracy of haplotype genomic …

Assumptions and properties of limiting pathway models for analysis of epistasis in complex traits

S Stringer, EM Derks, RS Kahn, WG Hill, NR Wray - PLoS One, 2013 - journals.plos.org
For most complex traits, results from genome-wide association studies show that the
proportion of the phenotypic variance attributable to the additive effects of individual SNPs …

[PDF][PDF] A unified approach to utilize phenotypic, full pedigree, andgenomic information for genetic evaluation

I Misztal, I Aguilar, A Legarra, S Tsuruta, D Johnson… - 2010 - ainfo.inia.uy
The concept of genomic selection (Meuwissen et al., 2001) generated great excitement in
the animal breeding community. With genomic information from SNP panels, one can …

Accurate prediction of genetic values for complex traits by whole-genome resequencing

T Meuwissen, M Goddard - Genetics, 2010 - academic.oup.com
Whole-genome resequencing technology has improved rapidly during recent years and is
expected to improve further such that the sequencing of an entire human genome sequence …

Haplotype-based genome-wide prediction models exploit local epistatic interactions among markers

Y Jiang, RH Schmidt, JC Reif - G3: Genes, Genomes, Genetics, 2018 - academic.oup.com
Genome-wide prediction approaches represent versatile tools for the analysis and
prediction of complex traits. Mostly they rely on marker-based information, but scenarios …