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Using Exome and Amplicon-Based Sequencing Data for High-Resolution HLA Typing with ATHLATES

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HLA Typing

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

Abstract

ATHLATES (accurate typing of human leukocyte antigen through exome sequencing) was originally developed to analyze whole-exome sequencing (exome-seq) data from the Illumina platform and to predict the HLA genotype at 2-field or higher resolution. HLA locus-specific reads are first collected by stringent read mapping to the IMGT/HLA database. ATHLATES then performs read assembly, candidate allele identification, and genotype inference. Here, we describe the protocol of using ATHLATES for the above purpose and expand the application to analyze targeted sequencing data using amplicons of full HLA genes.

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Author information

Authors and Affiliations

  1. Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA

    Chang Liu

  2. Grail, Inc., Menlo Park, CA, USA

    Xiao Yang

Authors
  1. Chang Liu
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  2. Xiao Yang
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Corresponding author

Correspondence to Chang Liu .

Editor information

Editors and Affiliations

  1. Johannes Gutenberg University of Mainz, Mainz, Germany

    Sebastian Boegel

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Liu, C., Yang, X. (2018). Using Exome and Amplicon-Based Sequencing Data for High-Resolution HLA Typing with ATHLATES. 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_14

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  • DOI: https://doi.org/10.1007/978-1-4939-8546-3_14

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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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