Schütz, Ekkehard

[["dc.bibliographiccitation.artnumber","3"],["dc.bibliographiccitation.journal","Genetics, selection, evolution : GSE"],["dc.bibliographiccitation.volume","47"],["dc.contributor.author","Schütz, Ekkehard"],["dc.contributor.author","Brenig, Bertram"],["dc.date.accessioned","2019-07-09T11:42:26Z"],["dc.date.available","2019-07-09T11:42:26Z"],["dc.date.issued","2015"],["dc.description.abstract","BACKGROUND: Parentage control is moving from short tandem repeats- to single nucleotide polymorphism (SNP) systems. For SNP-based parentage control in cattle, the ISAG-ICAR Committee proposes a set of 100/200 SNPs but quality criteria are lacking. Regarding German Holstein-Friesian cattle with only a limited number of evaluated individuals, the exclusion probability is not well-defined. We propose a statistical procedure for excluding single SNPs from parentage control, based on case-by-case evaluation of the GenCall score, to minimize parentage exclusion, based on miscalled genotypes. Exclusion power of the ISAG-ICAR SNPs used for the German Holstein-Friesian population was adjusted based on the results of more than 25,000 individuals. RESULTS: Experimental data were derived from routine genomic selection analyses of the German Holstein-Friesian population using the Illumina BovineSNP50 v2 BeadChip (20,000 individuals) or the EuroG10K variant (7000 individuals). Averages and standard deviations of GenCall scores for the 200 SNPs of the ISAG-ICAR recommended panel were calculated and used to calculate the downward Z-value. Based on minor allelic frequencies in the Holstein-Friesian population, one minus exclusion probability was equal to 1.4×10⁻¹⁰ and 7.2×10⁻²⁶, with one and two parents, respectively. Two monomorphic SNPs from the 100-SNP ISAG-ICAR core-panel did not contribute. Simulation of 10,000 parentage control combinations, using the GenCall score data from both BeadChips, showed that with a Z-value greater than 3.66 only about 2.5% parentages were excluded, based on the ISAG-ICAR recommendations (core-panel: ≥ 90 SNPs for one, ≥ 85 SNPs for two parents). When applied to real data from 1750 single parentage assessments, the optimal threshold was determined to be Z = 5.0, with only 34 censored cases and reduction to four (0.2%) doubtful parentages. About 70 parentage exclusions due to weak genotype calls were avoided, whereas true exclusions (n = 34) were unaffected. CONCLUSIONS: Using SNPs for parentage evaluation provides a high exclusion power also for parent identification. SNPs with a low GenCall score show a high tendency towards intra-molecular secondary structures and substantially contribute to false exclusion of parentages. We propose a method that controls this error without excluding too many parent combinations from the evaluation."],["dc.format.extent","7"],["dc.identifier.doi","10.1186/s12711-014-0085-1"],["dc.identifier.pmid","25651826"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/13450"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/58668"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","1297-9686"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.subject.mesh","Animals"],["dc.subject.mesh","Biometry"],["dc.subject.mesh","Breeding"],["dc.subject.mesh","Cattle"],["dc.subject.mesh","Fathers"],["dc.subject.mesh","Gene Frequency"],["dc.subject.mesh","Genetic Markers"],["dc.subject.mesh","Genomics"],["dc.subject.mesh","Genotype"],["dc.subject.mesh","Polymorphism, Single Nucleotide"],["dc.subject.mesh","Probability"],["dc.title","Analytical and statistical consideration on the use of the ISAG-ICAR-SNP bovine panel for parentage control, using the Illumina BeadChip technology: example on the German Holstein population."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]