In Silico HLA Typing Using Standard RNA-Seq Sequence Reads

  • Sebastian BoegelEmail author
  • Jelle Scholtalbers
  • Martin Löwer
  • Ugur Sahin
  • John C. Castle
Part of the Methods in Molecular Biology book series (MIMB, volume 1310)


Next-generation sequencing (NGS) enables high-throughput transcriptome profiling using the RNA-Seq assay, resulting in billions of short sequence reads. Worldwide adoption has been rapid: many laboratories worldwide generate transcriptome sequence reads daily. Here, we describe methods for obtaining a sample’s human leukocyte antigen (HLA) class I and II types and HLA expression using standard NGS RNA-Seq sequence reads. We demonstrate the application using our algorithm, seq2HLA, and a publicly available RNA-Seq dataset from the Burkitt lymphoma cell line Raji.

Key words

HLA type HLA expression NGS RNA-Seq Immunoinformatics In silico 


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Sebastian Boegel
    • 1
    • 2
    Email author
  • Jelle Scholtalbers
    • 1
    • 4
  • Martin Löwer
    • 1
  • Ugur Sahin
    • 1
    • 2
    • 3
  • John C. Castle
    • 1
    • 5
  1. 1.TRON gGmbH – Translational Oncology at Johannes Gutenberg-University Medical Center gGmbH MainzMainzGermany
  2. 2.University Medical Center of the Johannes Gutenberg-University MainzMainzGermany
  3. 3.BioNTech AGMainzGermany
  4. 4.European Molecular Biology LaboratoryHeidelbergGermany
  5. 5.4-Antibody AGBaselSwitzerland

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