Rafter, Pierce and Gormley, Isobel Claire and Parnell, Andrew and Kearney, John Francis and Berry, Donagh P. (2020) Concordance rate between copy number variants detected using either high- or medium-density single nucleotide polymorphism genotype panels and the potential of imputing copy number variants from flanking high density single nucleotide polymorphism haplotypes in cattle. BMC Genomics, 21 (1). ISSN 1471-2164

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Abstract

The trading of individual animal genotype information often involves only the exchange of the called genotypes and not necessarily the additional information required to effectively call structural variants. The main aim here was to determine if it is possible to impute copy number variants (CNVs) using the flanking single nucleotide polymorphism (SNP) haplotype structure in cattle. While this objective was achieved using high-density genotype panels (i.e., 713,162 SNPs), a secondary objective investigated the concordance of CNVs called with this high-density genotype panel compared to CNVs called from a medium-density panel (i.e., 45,677 SNPs in the present study). This is the first study to compare CNVs called from high-density and medium-density SNP genotypes from the same animals. High (and medium-density) genotypes were available on 991 Holstein-Friesian, 1015 Charolais, and 1394 Limousin bulls. The concordance between CNVs called from the medium-density and high-density genotypes were calculated separately for each animal. A subset of CNVs which were called from the high-density genotypes was selected for imputation. Imputation was carried out separately for each breed using a set of high-density SNPs flanking the midpoint of each CNV. A CNV was deemed to be imputed correctly when the called copy number matched the imputed copy number.

Item Type:	Article
Additional Information:	Cite as: Rafter, P., Gormley, I.C., Parnell, A.C. et al. Concordance rate between copy number variants detected using either high- or medium-density single nucleotide polymorphism genotype panels and the potential of imputing copy number variants from flanking high density single nucleotide polymorphism haplotypes in cattle. BMC Genomics 21, 205 (2020). https://doi.org/10.1186/s12864-020-6627-8 Copyright: Any Website Author's Homepage Institutional Repository Named Repository (PubMed Central) Journal Website
Keywords:	CNV; Bovine; PennCNV; QuantiSNP; Beagle; FImpute; SNP; Imputation;
Academic Unit:	Faculty of Science and Engineering > Mathematics and Statistics Faculty of Science and Engineering > Research Institutes > Hamilton Institute Faculty of Social Sciences > Research Institutes > Irish Climate Analysis and Research Units, ICARUS
Item ID:	16260
Identification Number:	https://doi.org/10.1186/s12864-020-6627-8
Depositing User:	Andrew Parnell
Date Deposited:	06 Jul 2022 09:48
Journal or Publication Title:	BMC Genomics
Publisher:	BMC Genomics
Refereed:	Yes
URI:	Publisher
Use Licence:	This item is available under a Creative Commons Attribution Non Commercial Share Alike Licence (CC BY-NC-SA). Details of this licence are available here

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