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HLA Typing pp 177-191 | Cite as

In Silico Typing of Classical and Non-classical HLA Alleles from Standard RNA-Seq Reads

  • Sebastian Boegel
  • Thomas Bukur
  • John C. Castle
  • Ugur Sahin
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1802)

Abstract

Next-Generation Sequencing (NGS) enables the rapid generation of billions of short nucleic acid sequence fragments (i.e., “sequencing reads”). Especially, the adoption of gene expression profiling using whole transcriptome sequencing (i.e., “RNA-Seq”) has been rapid. Here, we describe an in silico method, seq2HLA, that takes standard RNA-Seq reads as input and determines a sample’s (classical and non-classical) HLA class I and class II types as well as HLA expression. We demonstrate the application of seq2HLA using publicly available RNA-Seq data from the Burkitt’s lymphoma cell line DAUDI and the choriocarcinoma cell line JEG-3.

Keywords

HLA type HLA expression NGS RNA-Seq Immunoinformatics In silico Non-classical HLA class I 

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Copyright information

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

Authors and Affiliations

  • Sebastian Boegel
    • 1
  • Thomas Bukur
    • 1
  • John C. Castle
    • 1
    • 2
  • Ugur Sahin
    • 1
  1. 1.TRON gGmbH – Translational Oncology at Johannes Gutenberg-University Medical Center gGmbHMainzGermany
  2. 2.Agenus IncLexington MAUSA

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