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AmpliSAS and AmpliHLA: Web Server Tools for MHC Typing of Non-Model Species and Human Using NGS Data

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HLA Typing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1802))

Abstract

AmpliSAS and AmpliHLA are web server tools for automatic genotyping of MHC genes from high-throughput sequencing data. AmpliSAS is designed specifically to analyze amplicon sequencing data from non-model species and it is able to perform de-novo genotyping without any previous knowledge of the reference alleles. AmpliHLA is a human-specific version, it performs HLA typing by comparing sequenced variants against human reference alleles from the IMGT/HLA database. Here we describe four genotyping protocols: the first two use amplicon sequencing data to genotype the MHC genes of a passerine bird and human respectively; the third and fourth present the HLA typing of a human cell line starting from RNA and exome sequencing data respectively.

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Author information

Authors and Affiliations

  1. Sixth Researcher, Poznan, Poland

    Alvaro Sebastian

  2. Instituto Aragonés de Empleo (INAEM), Zaragoza, Spain

    Alvaro Sebastian

  3. Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland

    Alvaro Sebastian & Magdalena Migalska

  4. Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland

    Aleksandra Biedrzycka

Authors
  1. Alvaro Sebastian
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  2. Magdalena Migalska
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  3. Aleksandra Biedrzycka
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Editors and Affiliations

  1. Johannes Gutenberg University of Mainz, Mainz, Germany

    Sebastian Boegel

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Sebastian, A., Migalska, M., Biedrzycka, A. (2018). AmpliSAS and AmpliHLA: Web Server Tools for MHC Typing of Non-Model Species and Human Using NGS Data. 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_18

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  • DOI: https://doi.org/10.1007/978-1-4939-8546-3_18

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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

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