Incorporating gene annotation into genomic prediction of complex phenotypes

N Gao, JWR Martini, Z Zhang, X Yuan, H Zhang… - Genetics, 2017 - academic.oup.com
Gao et al. propose several approaches to incorporate gene annotation into genomic
prediction and evaluate these new methods on populations..... Today, genomic prediction …

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 …

GVCHAP: a computing pipeline for genomic prediction and variance component estimation using haplotypes and SNP markers

D Prakapenka, C Wang, Z Liang, C Bian, C Tan… - Frontiers in …, 2020 - frontiersin.org
Haplotype prediction models open many possibilities to improve the accuracy of genomic
selection but require more data processing and computing time than single-SNP prediction …

[HTML][HTML] Haplotype analysis of genomic prediction using structural and functional genomic information for seven human phenotypes

Z Liang, C Tan, D Prakapenka, L Ma, Y Da - Frontiers in genetics, 2020 - frontiersin.org
Genomic prediction using multi-allelic haplotype models improved the prediction accuracy
for all seven human phenotypes, the normality transformed high density lipoproteins, low …

LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants

MJ Machiela, SJ Chanock - Bioinformatics, 2015 - academic.oup.com
Assessing linkage disequilibrium (LD) across ancestral populations is a powerful approach
for investigating population-specific genetic structure as well as functionally mapping …

[HTML][HTML] Haplotype blocks for genomic prediction: a comparative evaluation in multiple crop datasets

SE Weber, M Frisch, RJ Snowdon… - Frontiers in Plant …, 2023 - frontiersin.org
In modern plant breeding, genomic selection is becoming the gold standard for selection of
superior genotypes. The basis for genomic prediction models is a set of phenotyped lines …

Using genetic distance to infer the accuracy of genomic prediction

M Scutari, I Mackay, D Balding - PLoS genetics, 2016 - journals.plos.org
The prediction of phenotypic traits using high-density genomic data has many applications
such as the selection of plants and animals of commercial interest; and it is expected to play …

Genomic prediction in animals and plants: simulation of data, validation, reporting, and benchmarking

HD Daetwyler, MPL Calus, R Pong-Wong… - Genetics, 2013 - academic.oup.com
The genomic prediction of phenotypes and breeding values in animals and plants has
developed rapidly into its own research field. Results of genomic prediction studies are often …

The effect of using genealogy-based haplotypes for genomic prediction

V Edriss, RL Fernando, G Su, MS Lund… - Genetics Selection …, 2013 - Springer
Background Genomic prediction uses two sources of information: linkage disequilibrium
between markers and quantitative trait loci, and additive genetic relationships between …

Influence of genetic interactions on polygenic prediction

Z Dai, N Long, W Huang - G3: Genes, Genomes, Genetics, 2020 - academic.oup.com
Prediction of phenotypes from genotypes is an important objective to fulfill the promises of
genomics, precision medicine and agriculture. Although it's now possible to account for the …