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.
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.
authors: Ekkehard
authors: E
authors: Schütz
authors: Institute of Veterinary Medicine, Burckhardtweg 2, Göttingen, D-37077, Germany. bbrenig@gwdg.de.
authors: Bertram
authors: B
authors: Brenig
mesh_terms: D000818:Animals; D001699:Biometry; D001947:Breeding / Q000706:statistics & numerical data; D002417:Cattle / Q000145:classification / Q000235:genetics*; D005220:Fathers; D005787:Gene Frequency; D005819:Genetic Markers / Q000235:genetics; D023281:Genomics / Q000295:instrumentation / Q000379:methods / Q000706:statistics & numerical data*; D005838:Genotype; D020641:Polymorphism, Single Nucleotide; D011336:Probability
chemical_list: D005819:Genetic Markers
references: Anim Genet. 2004 Feb;35(1):44-9
references: 14731229
references: J Dairy Sci. 2013 May;96(5):3336-9
references: 23497995
references: Anim Genet. 2010 Oct;41(5):551-3
references: 20331599
references: J Dairy Sci. 2009 Jul;92(7):3431-6
references: 19528621
references: Bioinformatics. 2007 Oct 15;23(20):2741-6
references: 17846035
references: Genet Mol Biol. 2013 Jul;36(2):185-91
references: 23885200
references: Anim Genet. 2014 Aug;45(4):572-5
references: 24730981
references: Anim Genet. 1997 Dec;28(6):397-400
references: 9616104
references: Anal Chem. 2010 Jul 15;82(14):6303-7
references: 20565067
references: Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6229-34
references: 21444804
references: J Dairy Sci. 2011 Apr;94(4):2114-7
references: 21427003
references: J Dairy Sci. 2000 Jan;83(1):181-7
references: 10659978