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HLA Typing

Methods and Protocols

  • Book
  • © 2024
  • Latest edition

Overview

Editors:
  1. Sebastian Boegel

    1. Medizinische Klinik - Rheumatologie, Johannes Gutenberg University of Mainz, Mainz, Germany

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 2809)

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About this book

This edition provides a collection of state-of-art methods and tools for human leukocyte antigen (HLA) and major histocompatibility complex (MHC) research. The book explores updated as well as novel in silico tools, resources, and wet lab protocols for HLA typing, including determination of the HLA class I and class II type of an individual in clinical work and research, such as in transplantation medicine and vaccine development in the context of infectious diseases or cancer immunotherapies. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed information and implementation advice that leads to best results. 

Up-to-date and practical, HLA Typing: Methods and Protocols, Second Edition serves as a valuable resource for any researcher interested in learning more about this vital field.

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. HLA Genes: A Hallmark of Functional Genetic Variation and Complex Evolution

    • Tobias L. Lenz
    Pages 1-18

  3. Allele Frequency Net Database

    • Faviel F. Gonzalez-Galarza, Antony McCabe, Eduardo J. Melo dos Santos, Gurpreet Ghattaoraya, Andrew R. Jones, Derek Middleton
    Pages 19-36

  4. AmpliSAS and AmpliHLA: Web Server and Local Tools for MHC Typing of Non-model Species and Human Using NGS Data

    • Alvaro Sebastian, Magdalena Migalska, Tomasz Gaczorek
    Pages 37-66

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

    • Shuji Kawaguchi, Koichiro Higasa, Ryo Yamada, Fumihiko Matsuda
    Pages 67-75

  6. Deep Learning-Based HLA Allele Imputation Applicable to GWAS

    • Tatsuhiko Naito
    Pages 77-85

  7. Benchmarking NGS-Based HLA Typing Algorithms

    • Nikolas Hallberg Thuesen, Michael Schantz Klausen
    Pages 87-99

  8. HLA Typing and Mutation Calling from Normal and Tumor Whole Genome Sequencing Data with ALPHLARD-NT

    • Shuto Hayashi, Seiya Imoto
    Pages 101-113

  9. NanoHLA: A Method for Human Leukocyte Antigen Class I Genes Typing Without Error Correction Based on Nanopore Sequencing Data

    • Jidong Lang, Liu Qin
    Pages 115-126

  10. Imputation-Based HLA Typing with GWAS SNPs

    • Xiuwen Zheng, John Lee
    Pages 127-143

  11. Full-Length Characterization of Novel HLA-DRB1 Alleles for Reference Database Submission

    • Kathrin Putke, Viviane Albrecht, Christin Paech, Madlen Pahlke, Bianca Schöne, Steffen Klasberg et al.
    Pages 145-156

  12. Submitting Novel Full-Length HLA, MIC, and KIR Alleles with TypeLoader2

    • Bianca Schöne, Markus Fuhrmann, Vineeth Surendranath, Alexander H. Schmidt, Vinzenz Lange, Gerhard Schöfl
    Pages 157-169

  13. PIRCHE-II Risk and Acceptable Mismatch Profile Analysis in Solid Organ Transplantation

    • Matthias Niemann, Benedict M. Matern, Eric Spierings
    Pages 171-192

  14. Graph-Based Imputation Methods and Their Applications to Single Donors and Families

    • Sapir Israeli, Martin Maiers, Yoram Louzoun
    Pages 193-214

  15. How to Predict Binding Specificity and Ligands for New MHC-II Alleles with MixMHC2pred

    • Julien Racle, David Gfeller
    Pages 215-235

  16. DeepHLApan: A Deep Learning Approach for the Prediction of Peptide-HLA Binding and Immunogenicity

    • Jingcheng Wu, Jiaoyang Li, Shuqing Chen, Zhan Zhou
    Pages 237-244

  17. In Silico: Predicting Intrinsic Features of HLA Class-I Restricted Neoantigens

    • Ting Sun, Beibei Xin, Yubo Fan, Jing Zhang
    Pages 245-261

  18. Designing High Binding Affinity Peptides for MHC Class I Using MAM: An In Silico Approach

    • Yu Wei Zhang
    Pages 263-274

  19. MHCtools 1.5: Analysis of MHC Sequencing Data in R

    • Jacob Roved
    Pages 275-295

  20. Back Matter

    Pages 297-298
    Download chapter PDF
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Editors and Affiliations

  • Medizinische Klinik - Rheumatologie, Johannes Gutenberg University of Mainz, Mainz, Germany

    Sebastian Boegel

Accessibility Information

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This ebook is designed with accessibility in mind, aiming to meet the ePub Accessibility 1.0 AA and WCAG 2.0 Level AA standards. Its features include described images and other non-text content, screenreader-friendly navigation and accessible math. Math is represented either as MathML, LaTeX or in images. If math is represented as image, Alt Text might not be present. We recognize the importance of accessibility, and we welcome queries about accessibility for any of our products. If you have a question or an access need, please get in touch with us at [email protected].

Bibliographic Information

  • Book Title: HLA Typing

  • Book Subtitle: Methods and Protocols

  • Editors: Sebastian Boegel

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-3874-3

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2024

  • Hardcover ISBN: 978-1-0716-3873-6Published: 23 June 2024

  • Softcover ISBN: 978-1-0716-3876-7Published: 24 June 2025

  • eBook ISBN: 978-1-0716-3874-3Published: 22 June 2024

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XI, 298

  • Number of Illustrations: 18 b/w illustrations, 57 illustrations in colour

  • Topics: Immunology, Biomedicine, general

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