Advertisement

HLA Typing pp 63-88 | Cite as

High-Resolution HLA-Typing by Next-Generation Sequencing of Randomly Fragmented Target DNA

  • Michael WittigEmail author
  • Simonas Juzenas
  • Melanie Vollstedt
  • Andre Franke
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1802)

Abstract

PCR- or probe-based targeted capturing enables the enrichment of specific genomic loci prior to Next-Generation Sequencing (NGS). Here, we describe a probe-based protocol, which allows for high-resolution HLA typing of DNA samples by NGS. We also describe existing software tools that can be used for the subsequent HLA data analysis. Key prerequisites that warrant an accurate HLA calling are specific mappings of the sequencing reads, phasing of the mapped reads, and the possibility to perform a manual inspection/curation of the read mapping.

Keywords

Next-Generation Sequencing NGS Targeted enrichment In-solution capture Sequencing HLA typing HLA analysis RNA baits 

References

  1. 1.
    Hosomichi K, Shiina T, Tajima A, Inoue I (2015) The impact of next-generation sequencing technologies on HLA research. J Hum Genet 60(11):665–673.  https://doi.org/10.1038/jhg.2015.102CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Wetmur JG, Fresco J (1991) DNA probes: applications of the principles of nucleic acid hybridization. Crit Rev Biochem Mol Biol 26:227–259CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Adey A, Morrison HG, Asan, Xun X, Kitzman JO, Turner EH, Stackhouse B, MacKenzie AP, Caruccio NC, Zhang X et al (2010) Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol 11:R119CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Walsh PS, Erlich HA, Higuchi R (1992) Preferential PCR amplification of alleles: mechanisms and solutions. Genome Res 1:241–250CrossRefGoogle Scholar
  5. 5.
    Voorter CE, Kik MC, van den Berg-Loonen EM (1998) High-resolution HLA typing for the DQB1 gene by sequence-based typing. Tissue Antigens 51:80–87CrossRefPubMedGoogle Scholar
  6. 6.
    Lefranc MP, Giudicelli V, Kaas Q, Duprat E, Jabado-Michaloud J, Scaviner D, Ginestoux C, Clément O, Chaume D, Lefranc G (2005) IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res 33:D593–D597CrossRefPubMedGoogle Scholar
  7. 7.
    Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C et al (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27:182–189CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Wittig M, Anmarkrud JA, Kässens JC, Koch S, Forster M, Ellinghaus E, Hov JR, Sauer S, Schimmler M, Ziemann M, Görg S, Jacob F, Karlsen TH, Franke A (2015) Development of a high-resolution NGS-based HLA-typing and analysis pipeline. Nucleic Acids Res 43(11):e70.  https://doi.org/10.1093/nar/gkv184CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Szolek A, Schubert B, Mohr C, Sturm M, Feldhahn M, Kohlbacher O (2014) OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics 30(23):3310–3316.  https://doi.org/10.1093/bioinformatics/btu54CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Xie C, Yeo ZX, Wong M, Piper J, Long T, Kirkness EF, Biggs WH, Bloom K, Spellman S, Vierra-Green C, Brady C, Scheuermann RH, Telenti A, Howard S, Brewerton S, Turpaz Y, Venter JC (2017) Fast and accurate HLA typing from short-read next-generation sequence data with xHLA. Proc Natl Acad Sci U S A 114(30):8059–8064.  https://doi.org/10.1073/pnas.1707945114CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

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

Authors and Affiliations

  • Michael Wittig
    • 1
    Email author
  • Simonas Juzenas
    • 1
    • 2
  • Melanie Vollstedt
    • 1
  • Andre Franke
    • 1
  1. 1.Institute of Clinical Molecular BiologyKiel UniversityKielGermany
  2. 2.Laboratory of Clinical and Molecular Gastroenterology, Institute for Digestive ResearchLithuanian University of Health SciencesKaunasLithuania

Personalised recommendations