Impact of reference population size and marker density on accuracy of population imputation

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60460709%3A41210%2F19%3A79606" target="_blank" >RIV/60460709:41210/19:79606 - isvavai.cz</a>
Result on the web
<a href="https://www.agriculturejournals.cz/web/cjas.htm?type=article&id=148_2019-CJAS" target="_blank" >https://www.agriculturejournals.cz/web/cjas.htm?type=article&id=148_2019-CJAS</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.17221/148/2019-CJAS" target="_blank" >10.17221/148/2019-CJAS</a>

Result language
angličtina
Original language name
Impact of reference population size and marker density on accuracy of population imputation
Original language description
The effect of the reference population size and the number of missing single nucleotide polymorphisms (SNPs) on imputation accuracy was determined. The population imputation method using the FImpute software was applied. The dataset used for the purpose of this study was taken from the database of the Holstein Cattle Breeders Association of the Czech Republic. It contains 1000 animals genotyped with the Illumina BovineSNP50 v.2 BeadChip. Two datasets were created, the first containing the original genotypes, including the missing SNPs, the second containing the same genotypes modified to avoid missing data. In these datasets, animals were randomly selected for a reference population (10, 25, 50 and 75%) and there were randomly selected SNPs for deletion (15, 30, 55, 70, and 95%) in animals that were not used as the reference population. Subsequently, the data accuracy was determined by two parameters: correlation between original and imputed SNPs and percentage of correctly imputed SNPs. Since animal
Czech name
—
Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
40201 - Animal and dairy science; (Animal biotechnology to be 4.4)

Project
<a href="/en/project/QK1810253" target="_blank" >QK1810253: Improvement of national-wide genomic evaluation of dairy cattle by including cows with domestic production records into genotyped reference population</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach

Publication year
2019
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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