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Evaluation of genotyping concordance for commercial bovine SNP arrays using quality‐assurance samples
Author(s) -
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.
Publication year - 2019
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12800
Subject(s) - genotyping , snp , concordance , snp genotyping , biology , genetics , snp array , molecular inversion probe , autosome , single nucleotide polymorphism , allele , chromosome , genome wide association study , genotype , computational biology , gene
Summary 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 ( GDR s) 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 SNP s had considerably elevated GDR s and GER s compared to the SNP s 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 SNP s with a GER greater than 1% is provided. Interpretation of association effects of these SNP s, 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.