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HLA Typing pp 225-233 | Cite as

Comprehensive HLA Typing from a Current Allele Database Using Next-Generation Sequencing Data

  • Shuji Kawaguchi
  • Koichiro Higasa
  • Ryo Yamada
  • Fumihiko MatsudaEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1802)

Abstract

HLA allele information is essential for a variety of medical applications, such as genomic studies of multifactorial diseases, including immune system and inflammation-related disorders, and donor selection in organ transplantation and regenerative medicine. To obtain this information, an accurate HLA typing method that is applicable for any allele registered in HLA allele databases is needed. Here, we describe a method for determining alleles from a current HLA database using next-generation sequencing (NGS) results.

Keywords

HLA typing NGS Software Database Bioinformatics 

References

  1. 1.
    Gabriel C, Danzer M, Hackl C et al (2009) Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification. Hum Immunol 70:960–964.  https://doi.org/10.1016/j.humimm.2009.08.009CrossRefPubMedGoogle Scholar
  2. 2.
    Gabriel C, Fürst D, Faé I et al (2014) HLA typing by next-generation sequencing - getting closer to reality. Tissue Antigens 83:65–75.  https://doi.org/10.1111/tan.12298CrossRefPubMedGoogle Scholar
  3. 3.
    Lind C, Ferriola D, Mackiewicz K et al (2010) Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing. Hum Immunol 71:1033–1042.  https://doi.org/10.1016/j.humimm.2010.06.016CrossRefPubMedGoogle Scholar
  4. 4.
    Saiki RK, Walsh PS, Levenson CH, Erlich HA (1989) Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. Proc Natl Acad Sci U S A 86:6230–6234CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Santamaria P, Lindstrom AL, Boyce-Jacino MT et al (1993) HLA class I sequence-based typing. Hum Immunol 37:39–50CrossRefPubMedGoogle Scholar
  6. 6.
    Robinson J, Halliwell JA, Hayhurst JD et al (2015) The IPD and IMGT/HLA database: allele variant databases. Nucleic Acids Res 43:D423–D431.  https://doi.org/10.1093/nar/gku1161CrossRefPubMedGoogle Scholar
  7. 7.
    Kim HJ, Pourmand N (2013) HLA typing from RNA-seq data using hierarchical read weighting [corrected]. PLoS One 8:e67885.  https://doi.org/10.1371/journal.pone.0067885CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Bai Y, Ni M, Cooper B et al (2014) Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads. BMC Genomics 15:325.  https://doi.org/10.1186/1471-2164-15-325CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Huang Y, Yang J, Ying D et al (2015) HLAreporter: a tool for HLA typing from next generation sequencing data. Genome Med 7:25.  https://doi.org/10.1186/s13073-015-0145-3CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Szolek A, Schubert B, Mohr C et al (2014) OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics (Oxford) 30:3310–3316.  https://doi.org/10.1093/bioinformatics/btu548CrossRefGoogle Scholar
  11. 11.
    Kawaguchi S, Higasa K, Shimizu M et al (2017) HLA-HD: an accurate HLA typing algorithm for next-generation sequencing data. Hum Mutat 38:788–797.  https://doi.org/10.1002/humu.23230CrossRefPubMedGoogle Scholar
  12. 12.
    Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359.  https://doi.org/10.1038/nmeth.1923CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    1000 Genomes Project Consortium, Abecasis GR, Auton A et al (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491:56–65.  https://doi.org/10.1038/nature11632CrossRefPubMedGoogle Scholar
  14. 14.
    Adams SD, Barracchini KC, Chen D et al (2004) Ambiguous allele combinations in HLA class I and class II sequence-based typing: when precise nucleotide sequencing leads to imprecise allele identification. J Transl Med 2:30.  https://doi.org/10.1186/1479-5876-2-30CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    González-Galarza FF, Takeshita LYC, Santos EJM et al (2015) Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations. Nucleic Acids Res 43:D784–D788.  https://doi.org/10.1093/nar/gku1166CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Shuji Kawaguchi
    • 1
  • Koichiro Higasa
    • 1
  • Ryo Yamada
    • 1
  • Fumihiko Matsuda
    • 1
    Email author
  1. 1.Center for Genomic MedicineKyoto University Graduate School of MedicineKyotoJapan

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