HLA Typing pp 155-162 | Cite as

Full-Length HLA Class I Genotyping with the MinION Nanopore Sequencer

  • Kathrin Lang
  • Vineeth Surendranath
  • Philipp Quenzel
  • Gerhard Schöfl
  • Alexander H. Schmidt
  • Vinzenz LangeEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1802)


Nanopore sequencing, a paradigm change in sequencing technologies, offers a new cost-effective and scalable platform for HLA genotyping. Among the new generation of high-throughput sequencing technologies, the MinION nanopore sequencer is the first to offer a non-template-based direct DNA sensing sequencing technology. Oxford Nanopore Technologies (ONT) introduced the first version of the MinION in 2014; since then, the platform has gone through multiple iterations resulting in higher throughput and sequencing accuracy. The “what you put in is what you get” nature of the platform enables molecules to be sequenced without fragmentation. This results in ultra-long read lengths in the order of tens of kilobases enabling entire genes to be characterized with fully phased sequence information. With release R9.5, the MinION platform has reached a quality that enables HLA genotyping with minor shortcomings in long homopolymer regions. Within this chapter, we describe a protocol for sequencing and genotyping HLA Class I alleles using the MinION.


HLA Full-length Genotyping Nanopore sequencing MinION 

Supplementary material

439348_1_En_10_MOESM1_ESM.docx (18 kb)
Data 1 Supplementary Document 1 (DOCX 18 kb) (3 kb)
Data 2 Supplementary Document 2 (ZIP 4 kb)


  1. 1.
    Loman NJ, Quick J, Simpson JT (2015) A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods 12:733–735. Scholar
  2. 2.
    Ip CLC, Loose M, Tyson JR et al (2015) MinION analysis and reference consortium: phase 1 data release and analysis. F1000Research 4:1075. Scholar
  3. 3.
    Jain M, Tyson JR, Loose M et al (2017) MinION analysis and reference consortium: phase 2 data release and analysis of R9.0 chemistry. F1000Research 6:760. Scholar
  4. 4.
    Ton KNT, Cree SL, Gronert-Sum SJ, et al (2017) Multiplexed nanopore sequencing of HLA-B locus in Māori and Polynesian samples. bioRxiv. doi:
  5. 5.
    Liu C, Xiao F, Hoisington-Lopez J, et al (2017) Accurate typing of class I human leukocyte antigen by Oxford nanopore sequencing. bioRxiv. doi:
  6. 6.
    Jain M, Koren S, Quick J, et al (2017) Nanopore sequencing and assembly of a human genome with ultra-long reads. bioRxiv. doi:
  7. 7.
    Ehrenberg PK, Geretz A, Sindhu RK et al (2017) High-throughput next-generation sequencing to genotype six classical HLA loci from 96 donors in a single MiSeq run. HLA 90:284. Scholar
  8. 8.
    Jain M, Fiddes IT, Miga KH et al (2015) Improved data analysis for the MinION nanopore sequencer. Nat Methods 12:351–356. Scholar
  9. 9.
    Duke JL, Lind C, Mackiewicz K et al (2016) Determining performance characteristics of an NGS-based HLA typing method for clinical applications. HLA 87:141–152. Scholar

Copyright information

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

Authors and Affiliations

  • Kathrin Lang
    • 1
  • Vineeth Surendranath
    • 1
  • Philipp Quenzel
    • 1
  • Gerhard Schöfl
    • 1
  • Alexander H. Schmidt
    • 1
    • 2
  • Vinzenz Lange
    • 1
    Email author
  1. 1.DKMS Life Science LabDresdenGermany
  2. 2.DKMSTübingenGermany

Personalised recommendations