Evaluation of genotyping concordance for commercial bovine SNP arrays using quality-assurance samples

X. L. Wu, J. Xu, H. Li, R. Ferretti, J. He, J. Qiu, Q. Xiao, B. Simpson, T. Michell, S. D. Kachman, R. G. Tait, S. Bauck

Research output: Contribution to journalArticle

Abstract

SNP arrays are widely used in genetic research and agricultural genomics applications, and the quality of SNP genotyping data is of paramount importance. In the present study, SNP genotyping concordance and discordance were evaluated for commercial bovine SNP arrays based on two types of quality assurance (QA) samples provided by Neogen GeneSeek. The genotyping discordance rates (GDRs) between chips were on average between 0.06% and 0.37% based on the QA type I data and between 0.05% and 0.15% based on the QA type II data. The average genotyping error rate (GER) pertaining to single SNP chips, based on the QA type II data, varied between 0.02% and 0.08% per SNP and between 0.01% and 0.06% per sample. These results indicate that genotyping concordance rate was high (i.e. from 99.63% to 99.99%). Nevertheless, mitochondrial and Y chromosome SNPs had considerably elevated GDRs and GERs compared to the SNPs on the 29 autosomes and X chromosome. The majority of genotyping errors resulted from single allotyping errors, which also included the opposite instances for allele ‘dropout’ (i.e. from AB to AA or BB). Simultaneous allotyping errors on both alleles (e.g. mistaking AA for BB or vice versa) were relatively rare. Finally, a list of SNPs with a GER greater than 1% is provided. Interpretation of association effects of these SNPs, for example in genome-wide association studies, needs to be taken with caution. The genotyping concordance information needs to be considered in the optimal design of future bovine SNP arrays.

Original languageEnglish (US)
Pages (from-to)367-371
Number of pages5
JournalAnimal genetics
Volume50
Issue number4
DOIs
StatePublished - Aug 2019

Fingerprint

genotyping
Single Nucleotide Polymorphism
quality control
cattle
sampling
dropouts
alleles
autosomes
Y chromosome
X chromosome
Alleles
Genetic Research
genomics
Y Chromosome
Genome-Wide Association Study
X Chromosome
Genomics
genotyping errors

Keywords

  • bovine SNP chips
  • genotyping errors
  • mendelian errors
  • quality assurance

ASJC Scopus subject areas

  • Animal Science and Zoology
  • Genetics

Cite this

Wu, X. L., Xu, J., Li, H., Ferretti, R., He, J., Qiu, J., ... Bauck, S. (2019). Evaluation of genotyping concordance for commercial bovine SNP arrays using quality-assurance samples. Animal genetics, 50(4), 367-371. https://doi.org/10.1111/age.12800

Evaluation of genotyping concordance for commercial bovine SNP arrays using quality-assurance samples. / Wu, X. L.; Xu, J.; Li, H.; Ferretti, R.; He, J.; Qiu, J.; Xiao, Q.; Simpson, B.; Michell, T.; Kachman, S. D.; Tait, R. G.; Bauck, S.

In: Animal genetics, Vol. 50, No. 4, 08.2019, p. 367-371.

Research output: Contribution to journalArticle

Wu, XL, Xu, J, Li, H, Ferretti, R, He, J, Qiu, J, Xiao, Q, Simpson, B, Michell, T, Kachman, SD, Tait, RG & Bauck, S 2019, 'Evaluation of genotyping concordance for commercial bovine SNP arrays using quality-assurance samples', Animal genetics, vol. 50, no. 4, pp. 367-371. https://doi.org/10.1111/age.12800
Wu, X. L. ; Xu, J. ; Li, H. ; Ferretti, R. ; He, J. ; Qiu, J. ; Xiao, Q. ; Simpson, B. ; Michell, T. ; Kachman, S. D. ; Tait, R. G. ; Bauck, S. / Evaluation of genotyping concordance for commercial bovine SNP arrays using quality-assurance samples. In: Animal genetics. 2019 ; Vol. 50, No. 4. pp. 367-371.
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