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

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HLA Typing

Part of the book series: Methods in Molecular Biology ((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.

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Author information

Authors and Affiliations

  1. TRON gGmbH – Translational Oncology at Johannes Gutenberg-University Medical Center gGmbH, Mainz, Germany

    Sebastian Boegel, Thomas Bukur, John C. Castle & Ugur Sahin

  2. Agenus Inc, Lexington MA, USA

    John C. Castle

Authors
  1. Sebastian Boegel
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  2. Thomas Bukur
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  3. John C. Castle
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  4. Ugur Sahin
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Editors and Affiliations

  1. Johannes Gutenberg University of Mainz, Mainz, Germany

    Sebastian Boegel

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Boegel, S., Bukur, T., Castle, J.C., Sahin, U. (2018). In Silico Typing of Classical and Non-classical HLA Alleles from Standard RNA-Seq Reads. In: Boegel, S. (eds) HLA Typing. Methods in Molecular Biology, vol 1802. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8546-3_12

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  • DOI: https://doi.org/10.1007/978-1-4939-8546-3_12

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8545-6

  • Online ISBN: 978-1-4939-8546-3

  • eBook Packages: Springer Protocols

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