High Imputation Accuracy in Layer Chicken from Sequence Data on a Few Key Ancestors

M. Heidaritabar, M.P.L. Calus, A. Vereijken, M.A.M. Groenen, J.W.M. Bastiaansen

Research output: Chapter in Book/Report/Conference proceedingConference paperAcademicpeer-review

Abstract

We assessed a scenario designed to mimic the imputation of full genome sequence data in White layer chickens, genotyped at medium (60K) density. Factors affecting accuracy were the size of the reference population, the level of the relationship between the reference and test populations and minor allele frequency of the SNP being imputed. Genotype imputation based on 22 or 62 carefully selected reference animals resulted in accuracies between 0.78 and 0.87. So, a very small reference population already provided satisfactory results. These results suggest that full genome SNP imputation is possible in layer chicken when a suitable pool of key ancestors is sequenced. SNPs with low MAF were more difficult to impute. Accuracies did not reduce when test populations were 1, 2, or 3 generations away from the reference animals
Original languageEnglish
Title of host publicationProceedings, 10th World Congress of Genetics Applied to Livestock Production
Pages660
Publication statusPublished - 2014
Event10th WCGALP, Vancouver, Canada -
Duration: 17 Aug 201422 Aug 2014

Conference

Conference10th WCGALP, Vancouver, Canada
Period17/08/1422/08/14

Fingerprint

ancestry
chickens
genome
gene frequency
animals
testing
genotype

Cite this

Heidaritabar, M., Calus, M. P. L., Vereijken, A., Groenen, M. A. M., & Bastiaansen, J. W. M. (2014). High Imputation Accuracy in Layer Chicken from Sequence Data on a Few Key Ancestors. In Proceedings, 10th World Congress of Genetics Applied to Livestock Production (pp. 660)
Heidaritabar, M. ; Calus, M.P.L. ; Vereijken, A. ; Groenen, M.A.M. ; Bastiaansen, J.W.M. / High Imputation Accuracy in Layer Chicken from Sequence Data on a Few Key Ancestors. Proceedings, 10th World Congress of Genetics Applied to Livestock Production. 2014. pp. 660
@inproceedings{aaf37d83c225479abef7cc6496ca91a7,
title = "High Imputation Accuracy in Layer Chicken from Sequence Data on a Few Key Ancestors",
abstract = "We assessed a scenario designed to mimic the imputation of full genome sequence data in White layer chickens, genotyped at medium (60K) density. Factors affecting accuracy were the size of the reference population, the level of the relationship between the reference and test populations and minor allele frequency of the SNP being imputed. Genotype imputation based on 22 or 62 carefully selected reference animals resulted in accuracies between 0.78 and 0.87. So, a very small reference population already provided satisfactory results. These results suggest that full genome SNP imputation is possible in layer chicken when a suitable pool of key ancestors is sequenced. SNPs with low MAF were more difficult to impute. Accuracies did not reduce when test populations were 1, 2, or 3 generations away from the reference animals",
author = "M. Heidaritabar and M.P.L. Calus and A. Vereijken and M.A.M. Groenen and J.W.M. Bastiaansen",
note = "https://asas.org/docs/default-source/wcgalp-posters/660_paper_8829_manuscript_574_0.pdf?sfvrsn=2",
year = "2014",
language = "English",
pages = "660",
booktitle = "Proceedings, 10th World Congress of Genetics Applied to Livestock Production",

}

Heidaritabar, M, Calus, MPL, Vereijken, A, Groenen, MAM & Bastiaansen, JWM 2014, High Imputation Accuracy in Layer Chicken from Sequence Data on a Few Key Ancestors. in Proceedings, 10th World Congress of Genetics Applied to Livestock Production. pp. 660, 10th WCGALP, Vancouver, Canada, 17/08/14.

High Imputation Accuracy in Layer Chicken from Sequence Data on a Few Key Ancestors. / Heidaritabar, M.; Calus, M.P.L.; Vereijken, A.; Groenen, M.A.M.; Bastiaansen, J.W.M.

Proceedings, 10th World Congress of Genetics Applied to Livestock Production. 2014. p. 660.

Research output: Chapter in Book/Report/Conference proceedingConference paperAcademicpeer-review

TY - GEN

T1 - High Imputation Accuracy in Layer Chicken from Sequence Data on a Few Key Ancestors

AU - Heidaritabar, M.

AU - Calus, M.P.L.

AU - Vereijken, A.

AU - Groenen, M.A.M.

AU - Bastiaansen, J.W.M.

N1 - https://asas.org/docs/default-source/wcgalp-posters/660_paper_8829_manuscript_574_0.pdf?sfvrsn=2

PY - 2014

Y1 - 2014

N2 - We assessed a scenario designed to mimic the imputation of full genome sequence data in White layer chickens, genotyped at medium (60K) density. Factors affecting accuracy were the size of the reference population, the level of the relationship between the reference and test populations and minor allele frequency of the SNP being imputed. Genotype imputation based on 22 or 62 carefully selected reference animals resulted in accuracies between 0.78 and 0.87. So, a very small reference population already provided satisfactory results. These results suggest that full genome SNP imputation is possible in layer chicken when a suitable pool of key ancestors is sequenced. SNPs with low MAF were more difficult to impute. Accuracies did not reduce when test populations were 1, 2, or 3 generations away from the reference animals

AB - We assessed a scenario designed to mimic the imputation of full genome sequence data in White layer chickens, genotyped at medium (60K) density. Factors affecting accuracy were the size of the reference population, the level of the relationship between the reference and test populations and minor allele frequency of the SNP being imputed. Genotype imputation based on 22 or 62 carefully selected reference animals resulted in accuracies between 0.78 and 0.87. So, a very small reference population already provided satisfactory results. These results suggest that full genome SNP imputation is possible in layer chicken when a suitable pool of key ancestors is sequenced. SNPs with low MAF were more difficult to impute. Accuracies did not reduce when test populations were 1, 2, or 3 generations away from the reference animals

M3 - Conference paper

SP - 660

BT - Proceedings, 10th World Congress of Genetics Applied to Livestock Production

ER -

Heidaritabar M, Calus MPL, Vereijken A, Groenen MAM, Bastiaansen JWM. High Imputation Accuracy in Layer Chicken from Sequence Data on a Few Key Ancestors. In Proceedings, 10th World Congress of Genetics Applied to Livestock Production. 2014. p. 660