Accuracy of imputation to whole-genome sequence in sheep.

Animals Genome-Wide Association Study / standards Polymorphism, Single Nucleotide Sheep / genetics Software / standards Whole Genome Sequencing / standards

Journal

Genetics, selection, evolution : GSE
ISSN: 1297-9686
Titre abrégé: Genet Sel Evol
Pays: France
ID NLM: 9114088

Informations de publication

Date de publication:
17 Jan 2019
Historique:
received: 19 06 2018
accepted: 18 12 2018
entrez: 19 1 2019
pubmed: 19 1 2019
medline: 16 3 2019
Statut: epublish

Résumé

The use of whole-genome sequence (WGS) data for genomic prediction and association studies is highly desirable because the causal mutations should be present in the data. The sequencing of 935 sheep from a range of breeds provides the opportunity to impute sheep genotyped with single nucleotide polymorphism (SNP) arrays to WGS. This study evaluated the accuracy of imputation from SNP genotypes to WGS using this reference population of 935 sequenced sheep. The accuracy of imputation from the Ovine Infinium The mean imputation accuracy was high for all target breeds and was increased by combining smaller breed sets into a multi-breed reference. We found that the Minimac3 software imputation quality statistic (R

Sections du résumé

BACKGROUND BACKGROUND
The use of whole-genome sequence (WGS) data for genomic prediction and association studies is highly desirable because the causal mutations should be present in the data. The sequencing of 935 sheep from a range of breeds provides the opportunity to impute sheep genotyped with single nucleotide polymorphism (SNP) arrays to WGS. This study evaluated the accuracy of imputation from SNP genotypes to WGS using this reference population of 935 sequenced sheep.
RESULTS RESULTS
The accuracy of imputation from the Ovine Infinium
CONCLUSIONS CONCLUSIONS
The mean imputation accuracy was high for all target breeds and was increased by combining smaller breed sets into a multi-breed reference. We found that the Minimac3 software imputation quality statistic (R

Identifiants

DOI: 10.1186/s12711-018-0443-5 PMID: 30654735 PMC: PMC6337865
pubmed: 30654735
doi: 10.1186/s12711-018-0443-5
pii: 10.1186/s12711-018-0443-5
pmc: PMC6337865
doi:

Types de publication

Evaluation Study Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

1

Références

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Auteurs

Sunduimijid Bolormaa (S)

Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Rd, Bundoora, VIC, 3083, Australia. bolormaa.sunduimijid@ecodev.vic.gov.au.
Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia. bolormaa.sunduimijid@ecodev.vic.gov.au.

Amanda J Chamberlain (AJ)

Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Rd, Bundoora, VIC, 3083, Australia.

Majid Khansefid (M)

Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Rd, Bundoora, VIC, 3083, Australia.
Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.

Paul Stothard (P)

Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, T6G 2R3, Canada.

Andrew A Swan (AA)

Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.
Animal Genetics and Breeding Unit, University of New England, Armidale, NSW, 2351, Australia.

Brett Mason (B)

Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Rd, Bundoora, VIC, 3083, Australia.

Claire P Prowse-Wilkins (CP)

Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Rd, Bundoora, VIC, 3083, Australia.

Naomi Duijvesteijn (N)

Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.
School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.

Nasir Moghaddar (N)

Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.
School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.

Julius H van der Werf (JH)

Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.
School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.

Hans D Daetwyler (HD)

Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Rd, Bundoora, VIC, 3083, Australia.
Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.
School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.

Iona M MacLeod (IM)

Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Rd, Bundoora, VIC, 3083, Australia.
Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.

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Classifications MeSH

Recherchemedicale.com › Eucaryotes › Animaux › Accuracy of imputation to whole-genome...
Recherchemedicale.com › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Épidémiologie moléculaire › Étude d'association pangénomique › Accuracy of imputation to whole-genome...
Recherchemedicale.com › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › Polymorphisme de nucléotide simple › Accuracy of imputation to whole-genome...
Recherchemedicale.com › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Artiodactyla › Ruminants › Ovis › Accuracy of imputation to whole-genome...
Recherchemedicale.com › Sciences de l'information › Méthodologies informatiques › Logiciel › Accuracy of imputation to whole-genome...
Recherchemedicale.com › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Séquençage du génome entier › Accuracy of imputation to whole-genome...