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HLA Typing

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Sebastian Boegel

    1. Johannes Gutenberg University of Mainz, Mainz, Germany

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

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

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. The Past, Present, and Future of HLA Typing in Transplantation

    • Claire H. Edgerly, Eric T. Weimer
    Pages 1-10

  3. Role of Human Leukocyte Antigens (HLA) in Autoimmune Diseases

    • Gergely Bodis, Victoria Toth, Andreas Schwarting
    Pages 11-29

  4. The IPD Databases: Cataloguing and Understanding Allele Variants

    • Jashan P. Abraham, Dominic J. Barker, James Robinson, Giuseppe Maccari, Steven G. E. Marsh
    Pages 31-48

  5. Allele Frequency Net Database

    • Faviel F. Gonzalez-Galarza, Antony McCabe, Eduardo J. Melo dos Santos, Louise Takeshita, Gurpreet Ghattaoraya, Andrew R. Jones et al.
    Pages 49-62

  6. High-Resolution HLA-Typing by Next-Generation Sequencing of Randomly Fragmented Target DNA

    • Michael Wittig, Simonas Juzenas, Melanie Vollstedt, Andre Franke
    Pages 63-88

  7. High-Throughput Contiguous Full-Length Next-Generation Sequencing of HLA Class I and II Genes from 96 Donors in a Single MiSeq Run

    • Philip K. Ehrenberg, Aviva Geretz, Rasmi Thomas
    Pages 89-100

  8. Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA

    • Yuxin Yin, James Lan, Qiuheng Zhang
    Pages 101-113

  9. Super High Resolution for Single Molecule-Sequence-Based Typing of Classical HLA Loci Using Ion Torrent PGM

    • Takashi Shiina, Shingo Suzuki, Jerzy K. Kulski, Hidetoshi Inoko
    Pages 115-133

  10. High-Resolution Full-Length HLA Typing Method Using Third Generation (Pac-Bio SMRT) Sequencing Technology

    • Sheetal Ambardar, Malali Gowda
    Pages 135-153

  11. Full-Length HLA Class I Genotyping with the MinION Nanopore Sequencer

    • Kathrin Lang, Vineeth Surendranath, Philipp Quenzel, Gerhard Schöfl, Alexander H. Schmidt, Vinzenz Lange
    Pages 155-162

  12. Imputation-Based HLA Typing with SNPs in GWAS Studies

    • Xiuwen Zheng
    Pages 163-176

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

    • Sebastian Boegel, Thomas Bukur, John C. Castle, Ugur Sahin
    Pages 177-191

  14. PHLAT: Inference of High-Resolution HLA Types from RNA and Whole Exome Sequencing

    • Yu Bai, David Wang, Wen Fury
    Pages 193-201

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

    • Chang Liu, Xiao Yang
    Pages 203-213

  16. HLA Typing from Short-Read Sequencing Data with OptiType

    • András Szolek
    Pages 215-223

  17. Comprehensive HLA Typing from a Current Allele Database Using Next-Generation Sequencing Data

    • Shuji Kawaguchi, Koichiro Higasa, Ryo Yamada, Fumihiko Matsuda
    Pages 225-233

  18. Accurate Assembly and Typing of HLA using a Graph-Guided Assembler Kourami

    • Heewook Lee, Carl Kingsford
    Pages 235-247

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

    • Alvaro Sebastian, Magdalena Migalska, Aleksandra Biedrzycka
    Pages 249-273

  20. HLA Haplotype Frequency Estimation from Real-Life Data with the Hapl-o-Mat Software

    • Jürgen Sauter, Christian Schäfer, Alexander H. Schmidt
    Pages 275-284
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Keywords

About this book

This volume explores the rapidly evolving field of HLA typing and its use in both the laboratory setting and in silico methods. The chapters in this book discuss high-throughput methods for HLA typing; wet lab protocols; microarray data and its uses; in silico tools for the identification of HLA alleles from DNA and RNA next-generation-sequencing data, as well as HLA haplotype frequency estimation. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and practical, HLA Typing: Methods and Protocols is a valuable resource for any researcher interested in learning more about this developing field.



Editors and Affiliations

  • Johannes Gutenberg University of Mainz, Mainz, Germany

    Sebastian Boegel

Bibliographic Information

  • Book Title: HLA Typing

  • Book Subtitle: Methods and Protocols

  • Editors: Sebastian Boegel

  • Series Title: Methods in Molecular Biology

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

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2018

  • Hardcover ISBN: 978-1-4939-8545-6Published: 02 June 2018

  • Softcover ISBN: 978-1-4939-9321-5Published: 25 July 2019

  • eBook ISBN: 978-1-4939-8546-3Published: 01 June 2018

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 287

  • Number of Illustrations: 14 b/w illustrations, 38 illustrations in colour

  • Topics: Immunology

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