-
Article
Open AccessCorrection: Sequence-based GWAS meta-analyses for beef production traits
-
Article
Open AccessSequence-based GWAS meta-analyses for beef production traits
Combining the results of within-population genome-wide association studies (GWAS) based on whole-genome sequences into a single meta-analysis (MA) is an accurate and powerful method for identifying variants as...
-
Article
Open AccessAccounting for overlap** annotations in genomic prediction models of complex traits
It is now widespread in livestock and plant breeding to use genoty** data to predict phenotypes with genomic prediction models. In parallel, genomic annotations related to a variety of traits are increasing ...
-
Article
Open AccessConfirmed effects of candidate variants for milk production, udder health, and udder morphology in dairy cattle
Over the last years, genome-wide association studies (GWAS) based on imputed whole-genome sequences (WGS) have been used to detect quantitative trait loci (QTL) and highlight candidate genes for important trai...
-
Article
Open AccessThe impact of genomic selection on genetic diversity and genetic gain in three French dairy cattle breeds
In France, implementation of genomic evaluations in dairy cattle breeds started in 2009 and this has modified the breeding schemes drastically. In this context, the goal of our study was to understand the impa...
-
Article
Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
Stature is affected by many polymorphisms of small effect in humans 1 . In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a ...
-
Article
Open AccessWithin-breed and multi-breed GWAS on imputed whole-genome sequence variants reveal candidate mutations affecting milk protein composition in dairy cattle
Genome-wide association studies (GWAS) were performed at the sequence level to identify candidate mutations that affect the expression of six major milk proteins in Montbéliarde (MON), Normande (NOR), and Hols...
-
Article
Open AccessA comparison of methods for whole-genome QTL map** using dense markers in four livestock species
With dense genoty**, many choices exist for methods to detect quantitative trait loci (QTL) in livestock populations. However, no across-species study has been conducted on the performance of different metho...
-
Article
Open AccessHigh-density marker imputation accuracy in sixteen French cattle breeds
Genoty** with the medium-density Bovine SNP50 BeadChip® (50K) is now standard in cattle. The high-density BovineHD BeadChip®, which contains 777 609 single nucleotide polymorphisms (SNPs), was developed in 2010...
-
Article
Open AccessAnalysis of North American Rheumatoid Arthritis Consortium data using a penalized logistic regression approach
We applied a penalized regression approach to single-nucleotide polymorphisms in regions on chromosomes 1, 6, and 9 of the North American Rheumatoid Arthritis Consortium data. Results were compared with a stan...
-
Article
Open AccessDealing with missing phase and missing data in phylogeny-based analysis
We recently described a new method to identify disease susceptibility loci, based on the analysis of the evolutionary relationships between haplotypes of cases and controls. However, haplotypes are often unkno...
-
Article
Open AccessEfficiency of multiple imputation to test for association in the presence of missing data
The presence of missing data in association studies is an important problem, particularly with high-density single-nucleotide polymorphism (SNP) maps, because the probability that at least one genotype is miss...
-
Article
Open AccessValidation of the reshaped shared epitope HLA-DRB1 classification in rheumatoid arthritis
Recently, we proposed a classification of HLA-DRB1 alleles that reshapes the shared epitope hypothesis in rheumatoid arthritis (RA); according to this model, RA is associated with the RAA shared epitope sequen...
