HLA Typing: Methods and Protocols

ISBN-13: 9781493993215 / Angielski / Miękka / 2019 / 287 str.

Sebastian Boegel

Spis treści

Preface...

Table of Contents...

Contributing Authors...

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

Claire Edgerly and Eric T. Weimer

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

Gergely Bodis, Victoria Toth, and Andreas Schwarting

3. The IPD Databases: Cataloguing and Understanding Allele Variants 

Jashan P. Abraham, Dominic J. Barker, James Robinson, Giuseppe Maccari, and Steven G.E. Marsh

4. Allele Frequency Net Database

Faviel F. Gonzalez-Galarza, Antony McCabe, Eduardo J. Melo dos Santos, Louise Takeshita, Gurpreet Ghattaoraya, Andrew R. Jones, and Derek Middleton

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

Michael Wittig, Simonas Juzėnas, Melanie Vollstedt, and Andre Franke

6. 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, and Rasmi Thomas

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

Yuxin Yin, James Lan, and Qiuheng Zhang

8. Super High Resolution for Single Molecule-Sequence-Based Typing of Classical HLA loci using Ion Torrent PGM

Takashi Shiina, Shingo Suzuki, Jerzy K. Kulski, and Hidetoshi Inoko

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

Sheetal Ambardar and Malali Gowda

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

Kathrin Lang, Vineeth Surendranath, Philipp Quenzel, Gerhard Schöfl, Alexander H. Schmidt, and Vinzenz Lange

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

Xiuwen Zheng

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

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

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

Yu Bai, David Wang, and Wen Fury

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

Chang Liu and Xiao Yang

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

András Szolek

16. Comprehensive HLA Typing from a Current Allele Database using Next Generation Sequencing Data

Shuji Kawaguchi, Koichiro Higasa, Ryo Yamada, and Fumihiko Matsuda

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

Heewook Lee and Carl Kingsford

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

Alvaro Sebastian, Magdalena Migalska, and Aleksandra Biedrzycka

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

Jürgen Sauter, Christian Schäfer, and Alexander H. Schmidt

Blurb

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.