IDEAS home Printed from https://ideas.repec.org/a/caa/jnlcjs/v59y2014i5id7405-cjas.html
   My bibliography  Save this article

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

Author

Listed:
  • 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
    as

    Download full text from publisher

    File URL: http://cjas.agriculturejournals.cz/doi/10.17221/7405-CJAS.html
    Download Restriction: free of charge

    File URL: http://cjas.agriculturejournals.cz/doi/10.17221/7405-CJAS.pdf
    Download Restriction: free of charge

    File URL: https://libkey.io/10.17221/7405-CJAS?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    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.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    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.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Eric P. M. Grist, 2005. "Transmissible Spongiform Encephalopathy Risk Assessment: The UK experience," Risk Analysis, John Wiley & Sons, vol. 25(3), pages 519-532, June.
    2. Gerald C. Shurson, 2020. "“What a Waste”—Can We Improve Sustainability of Food Animal Production Systems by Recycling Food Waste Streams into Animal Feed in an Era of Health, Climate, and Economic Crises?," Sustainability, MDPI, vol. 12(17), pages 1-34, August.
    3. Didier Calavas & V. Supervie & E. Morignat & D. Costagliola & C. Ducrot, 2007. "Complementary Approach of Data Analysis and Modeling to Estimate the Pattern of the BSE Epidemic: The Example of France," Risk Analysis, John Wiley & Sons, vol. 27(5), pages 1141-1150, October.

    More about this item

    Keywords

    BSE; cattle; indel; prion gene;
    All these keywords.

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:caa:jnlcjs:v:59:y:2014:i:5:id:7405-cjas. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Ivo Andrle (email available below). General contact details of provider: https://www.cazv.cz/en/home/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.