IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0101025.html
   My bibliography  Save this article

A New Genotype Imputation Method with Tolerance to High Missing Rate and Rare Variants

Author

Listed:
  • Yumei Yang
  • Qishan Wang
  • Qiang Chen
  • Rongrong Liao
  • Xiangzhe Zhang
  • Hongjie Yang
  • Youmin Zheng
  • Zhiwu Zhang
  • Yuchun Pan

Abstract

We report a novel algorithm, iBLUP, to impute missing genotypes by simultaneously and comprehensively using identity by descent and linkage disequilibrium information. The simulation studies showed that the algorithm exhibited drastically tolerance to high missing rate, especially for rare variants than other common imputation methods, e.g. BEAGLE and fastPHASE. At a missing rate of 70%, the accuracy of BEAGLE and fastPHASE dropped to 0.82 and 0.74 respectively while iBLUP retained an accuracy of 0.95. For minor allele, the accuracy of BEAGLE and fastPHASE decreased to −0.1 and 0.03, while iBLUP still had an accuracy of 0.61.We implemented the algorithm in a publicly available software package also named iBLUP. The application of iBLUP for processing real sequencing data in an outbred pig population was demonstrated.

Suggested Citation

  • Yumei Yang & Qishan Wang & Qiang Chen & Rongrong Liao & Xiangzhe Zhang & Hongjie Yang & Youmin Zheng & Zhiwu Zhang & Yuchun Pan, 2014. "A New Genotype Imputation Method with Tolerance to High Missing Rate and Rare Variants," PLOS ONE, Public Library of Science, vol. 9(6), pages 1-7, June.
    • Handle: RePEc:plo:pone00:0101025
    DOI: 10.1371/journal.pone.0101025
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0101025
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0101025&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0101025?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
    ---><---

    References listed on IDEAS

    as
    1. Brendan Maher, 2008. "Personal genomes: The case of the missing heritability," Nature, Nature, vol. 456(7218), pages 18-21, November.
    Full references (including those not matched with items on IDEAS)

    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. Chuong B Do & David A Hinds & Uta Francke & Nicholas Eriksson, 2012. "Comparison of Family History and SNPs for Predicting Risk of Complex Disease," PLOS Genetics, Public Library of Science, vol. 8(10), pages 1-16, October.
    2. Iuliana Ionita-Laza & Joseph D Buxbaum & Nan M Laird & Christoph Lange, 2011. "A New Testing Strategy to Identify Rare Variants with Either Risk or Protective Effect on Disease," PLOS Genetics, Public Library of Science, vol. 7(2), pages 1-6, February.
    3. Aida Bianco & Eusebio Chiefari & Carmelo G A Nobile & Daniela Foti & Maria Pavia & Antonio Brunetti, 2015. "The Association between HMGA1 rs146052672 Variant and Type 2 Diabetes: A Transethnic Meta-Analysis," PLOS ONE, Public Library of Science, vol. 10(8), pages 1-15, August.
    4. Chung-Feng Kao & Jia-Rou Liu & Hung Hung & Po-Hsiu Kuo, 2015. "A Robust GWSS Method to Simultaneously Detect Rare and Common Variants for Complex Disease," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-14, April.
    5. Dominic Russ & John A Williams & Victor Roth Cardoso & Laura Bravo-Merodio & Samantha C Pendleton & Furqan Aziz & Animesh Acharjee & Georgios V Gkoutos, 2022. "Evaluating the detection ability of a range of epistasis detection methods on simulated data for pure and impure epistatic models," PLOS ONE, Public Library of Science, vol. 17(2), pages 1-19, February.
    6. von Stumm, Sophie & Kandaswamy, Radhika & Maxwell, Jessye, 2023. "Gene-environment interplay in early life cognitive development," Intelligence, Elsevier, vol. 98(C).
    7. Charles-Elie Rabier & Philippe Barre & Torben Asp & Gilles Charmet & Brigitte Mangin, 2016. "On the Accuracy of Genomic Selection," PLOS ONE, Public Library of Science, vol. 11(6), pages 1-23, June.
    8. Janet Currie, 2011. "Ungleichheiten bei der Geburt: Einige Ursachen und Folgen," Perspektiven der Wirtschaftspolitik, Verein für Socialpolitik, vol. 12(s1), pages 42-65, May.
    9. Karen Kapur & Toby Johnson & Noam D Beckmann & Joban Sehmi & Toshiko Tanaka & Zoltán Kutalik & Unnur Styrkarsdottir & Weihua Zhang & Diana Marek & Daniel F Gudbjartsson & Yuri Milaneschi & Hilma Holm , 2010. "Genome-Wide Meta-Analysis for Serum Calcium Identifies Significantly Associated SNPs near the Calcium-Sensing Receptor (CASR) Gene," PLOS Genetics, Public Library of Science, vol. 6(7), pages 1-12, July.
    10. Bingley, Paul & Cappellari, Lorenzo & Tatsiramos, Konstantinos, 2023. "On the Origins of Socio-Economic Inequalities: Evidence from Twin Families," IZA Discussion Papers 16520, Institute of Labor Economics (IZA).
    11. Kettlewell, Nathan & Tymula, Agnieszka & Yoo, Hong Il, 2023. "The Heritability of Economic Preferences," IZA Discussion Papers 16633, Institute of Labor Economics (IZA).
    12. Gang Fang & Majda Haznadar & Wen Wang & Haoyu Yu & Michael Steinbach & Timothy R Church & William S Oetting & Brian Van Ness & Vipin Kumar, 2012. "High-Order SNP Combinations Associated with Complex Diseases: Efficient Discovery, Statistical Power and Functional Interactions," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-15, April.
    13. Kozlitina Julia & Schucany William R., 2015. "A robust distribution-free test for genetic association studies of quantitative traits," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 14(5), pages 443-464, November.
    14. Le Rouzic, Arnaud & Skaug, Hans J. & Hansen, Thomas F., 2010. "Estimating genetic architectures from artificial-selection responses: A random-effect framework," Theoretical Population Biology, Elsevier, vol. 77(2), pages 119-130.
    15. Janet Currie, 2011. "Inequality at Birth: Some Causes and Consequences," American Economic Review, American Economic Association, vol. 101(3), pages 1-22, May.
    16. Shashaank Vattikuti & Juen Guo & Carson C Chow, 2012. "Heritability and Genetic Correlations Explained by Common SNPs for Metabolic Syndrome Traits," PLOS Genetics, Public Library of Science, vol. 8(3), pages 1-8, March.
    17. Xinge Jessie Jeng & Zhongyin John Daye & Wenbin Lu & Jung-Ying Tzeng, 2016. "Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level," PLOS Computational Biology, Public Library of Science, vol. 12(6), pages 1-23, June.
    18. Pan, Qing & Zhao, Yunpeng, 2016. "Integrative weighted group lasso and generalized local quadratic approximation," Computational Statistics & Data Analysis, Elsevier, vol. 104(C), pages 66-78.
    19. Qiuyi Zhang & Yang Zhao & Ruyang Zhang & Yongyue Wei & Honggang Yi & Fang Shao & Feng Chen, 2016. "A Comparative Study of Five Association Tests Based on CpG Set for Epigenome-Wide Association Studies," PLOS ONE, Public Library of Science, vol. 11(6), pages 1-13, June.
    20. Gabriel E Hoffman & Benjamin A Logsdon & Jason G Mezey, 2013. "PUMA: A Unified Framework for Penalized Multiple Regression Analysis of GWAS Data," PLOS Computational Biology, Public Library of Science, vol. 9(6), pages 1-19, June.

    More about this item

    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:plo:pone00:0101025. 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: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    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.