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

Author

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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)

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.

Suggested Citation

  • A. Gurgul & K. Sieńko & K. Żukowski & K. Pawlina & M. Bugno-Poniewierska, 2014. "Imputation accuracy of bovine spongiform encephalopathy-associated PRNP indel polymorphisms from middle-density SNPs arrays," Czech Journal of Animal Science, Czech Academy of Agricultural Sciences, vol. 59(5), pages 244-249.
    • Handle: RePEc:caa:jnlcjs:v:59:y:2014:i:5:id:7405-cjas
    DOI: 10.17221/7405-CJAS
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    References listed on IDEAS

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    1. J. Strychalski & U. Czarnik & M. Pierzchała & C.S. Pareek, 2011. "Relationship between the insertion/deletion polymorphism within the promoter and the intron 1 sequence of the PRNP gene and milk performance traits in cattle," Czech Journal of Animal Science, Czech Academy of Agricultural Sciences, vol. 56(4), pages 151-156.
    2. Andrew F. Hill & Melanie Desbruslais & Susan Joiner & Katie C. L. Sidle & Ian Gowland & John Collinge & Lawrence J. Doey & Peter Lantos, 1997. "The same prion strain causes vCJD and BSE," Nature, Nature, vol. 389(6650), pages 448-450, October.
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    Cited by:

    1. Anita Kranjčevičová & Eva Kašná & Michaela Brzáková & Josef Přibyl & Luboš Vostrý, 2019. "Impact of reference population and marker density on accuracy of population imputation," Czech Journal of Animal Science, Czech Academy of Agricultural Sciences, vol. 64(10), pages 405-410.

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    More about this item

    Keywords

    BSE; cattle; indel; prion gene;
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