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 …

The effects of demography and long-term selection on the accuracy of genomic prediction with sequence data

IM MacLeod, BJ Hayes, ME Goddard - Genetics, 2014 - academic.oup.com
The use of dense SNPs to predict the genetic value of an individual for a complex trait is
often referred to as “genomic selection” in livestock and crops, but is also relevant to human …

A fast algorithm for BayesB type of prediction of genome-wide estimates of genetic value

THE Meuwissen, TR Solberg, R Shepherd… - Genetics Selection …, 2009 - Springer
Genomic selection uses genome-wide dense SNP marker genotyping for the prediction of
genetic values, and consists of two steps:(1) estimation of SNP effects, and (2) prediction of …

Toward genomic prediction from whole-genome sequence data: impact of sequencing design on genotype imputation and accuracy of predictions

T Druet, IM Macleod, BJ Hayes - Heredity, 2014 - nature.com
Genomic prediction from whole-genome sequence data is attractive, as the accuracy of
genomic prediction is no longer bounded by extent of linkage disequilibrium between DNA …

Genomic prediction of breeding values using a subset of SNPs identified by three machine learning methods

B Li, N Zhang, YG Wang, AW George, A Reverter… - Frontiers in …, 2018 - frontiersin.org
The analysis of large genomic data is hampered by issues such as a small number of
observations and a large number of predictive variables (commonly known as “large P small …

Characterizing bias in population genetic inferences from low-coverage sequencing data

E Han, JS Sinsheimer… - Molecular biology and …, 2014 - academic.oup.com
The site frequency spectrum (SFS) is of primary interest in population genetic studies,
because the SFS compresses variation data into a simple summary from which many …

Sequence-vs. chip-assisted genomic selection: accurate biological information is advised

M Pérez-Enciso, JC Rincón, A Legarra - Genetics Selection Evolution, 2015 - Springer
Background The development of next-generation sequencing technologies (NGS) has made
the use of whole-genome sequence data for routine genetic evaluations possible, which has …

Reliability of genomic predictions across multiple populations

APW De Roos, BJ Hayes, ME Goddard - Genetics, 2009 - academic.oup.com
Genomic prediction of future phenotypes or genetic merit using dense SNP genotypes can
be used for prediction of disease risk, forensics, and genomic selection of livestock and …

Assessing the effect of sequencing depth and sample size in population genetics inferences

M Fumagalli - PloS one, 2013 - journals.plos.org
Next-Generation Sequencing (NGS) technologies have dramatically revolutionised research
in many fields of genetics. The ability to sequence many individuals from one or multiple …

Different models of genetic variation and their effect on genomic evaluation

SA Clark, JM Hickey, JHJ Van der Werf - Genetics Selection Evolution, 2011 - Springer
Background The theory of genomic selection is based on the prediction of the effects of
quantitative trait loci (QTL) in linkage disequilibrium (LD) with markers. However, there is …