Imputation accuracy of bovine spongiform encephalopathy-associated PRNP indel polymorphisms from middle-density SNPs arrays

A. Gurgul, K. Sieńko, K. Żukowski, K. Pawlina and M. Bugno-Poniewierska
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A. Gurgul: Laboratory of Genomics, National Research Institute of Animal Production, Balice, Poland
K. Sieńko: Department of Genetics, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
K. Żukowski: Department of Animal Breeding and Genetics, National Research Institute of Animal Production, Balice, Poland
K. Pawlina: Laboratory of Genomics, National Research Institute of Animal Production, Balice, Poland
M. Bugno-Poniewierska: Laboratory of Genomics, National Research Institute of Animal Production, Balice, Poland

Czech Journal of Animal Science, 2014, vol. 59, issue 5, 244-249

Abstract: Statistical methods of imputation allow predicting genotypes of markers (which were not genotyped in the whole population) based on known linkage disequilibrium relationships between the flanking polymorphisms and the information obtained from reference datasets used as a pattern. In this study we attempted to predict genotypes of two bovine spongiform encephalopathy (BSE) susceptibility associated indel polymorphisms located in the promoter region of PRNP gene relying on the data obtained from middle density SNPs arrays in a sample of the population of Holstein cattle. The two SNPs panels spanning PRNP locus were tested in terms of imputation efficiency. Both panels gave satisfactory imputation results showing high accuracy and high probabilities of imputed genotypes. Our results suggest that the approach applied can be used to evaluate the frequency of the disease associated polymorphisms in large populations of animals genotyped with whole-genome SNPs panels based on a limited-size reference population and small financial outlays.

Keywords: BSE; cattle; indel; prion gene (search for similar items in EconPapers)
Date: 2014
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DOI: 10.17221/7405-CJAS

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