HLA Typing

Description

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. Front Matter ....Pages i-xi The Past, Present, and Future of HLA Typing in Transplantation (Claire H. Edgerly, Eric T. Weimer)....Pages 1-10 Role of Human Leukocyte Antigens (HLA) in Autoimmune Diseases (Gergely Bodis, Victoria Toth, Andreas Schwarting)....Pages 11-29 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 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 High-Resolution HLA-Typing by Next-Generation Sequencing of Randomly Fragmented Target DNA (Michael Wittig, Simonas Juzenas, Melanie Vollstedt, Andre Franke)....Pages 63-88 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 Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA (Yuxin Yin, James Lan, Qiuheng Zhang)....Pages 101-113 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 High-Resolution Full-Length HLA Typing Method Using Third Generation (Pac-Bio SMRT) Sequencing Technology (Sheetal Ambardar, Malali Gowda)....Pages 135-153 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 Imputation-Based HLA Typing with SNPs in GWAS Studies (Xiuwen Zheng)....Pages 163-176 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 PHLAT: Inference of High-Resolution HLA Types from RNA and Whole Exome Sequencing (Yu Bai, David Wang, Wen Fury)....Pages 193-201 Using Exome and Amplicon-Based Sequencing Data for High-Resolution HLA Typing with ATHLATES (Chang Liu, Xiao Yang)....Pages 203-213 HLA Typing from Short-Read Sequencing Data with OptiType (András Szolek)....Pages 215-223 Comprehensive HLA Typing from a Current Allele Database Using Next-Generation Sequencing Data (Shuji Kawaguchi, Koichiro Higasa, Ryo Yamada, Fumihiko Matsuda)....Pages 225-233 Accurate Assembly and Typing of HLA using a Graph-Guided Assembler Kourami (Heewook Lee, Carl Kingsford)....Pages 235-247 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 HLA Haplotype Frequency Estimation from Real-Life Data with the Hapl-o-Mat Software (Jürgen Sauter, Christian Schäfer, Alexander H. Schmidt)....Pages 275-284 Back Matter ....Pages 285-287