Main 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.

Contents:

Preface...Table of Contents...Contributing Authors...
1. The Past, Present, and Future of HLA Typing in TransplantationClaire Edgerly and Eric T. Weimer
2. Role of Human Leukocyte Antigens (HLA) in Autoimmune DiseasesGergely 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 DatabaseFaviel 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 DNAMichael Wittig, Simonas Juzenas, 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 DNAYuxin Yin, James Lan, and Qiuheng Zhang
8. Super High Resolution for Single Molecule-Sequence-Based Typing of Classical HLA loci using Ion Torrent PGMTakashi Shiina, Shingo Suzuki, Jerzy K. Kulski, and Hidetoshi Inoko
9. High Resolution Full-Length HLA Typing Method using Third Generation (Pac-Bio SMRT) Sequencing TechnologySheetal Ambardar and Malali Gowda
10. Full-Length HLA Class I Genotyping with the MinION Nanopore SequencerKathrin Lang, Vineeth Surendranath, Philipp Quenzel, Gerhard Schoefl, Alexander H. Schmidt, and Vinzenz Lange
11. Imputation-Based HLA Typing with SNPs in GWAS StudiesXiuwen Zheng
12. In Silico Typing of Classical and Non-Classical HLA Alleles from Standard RNA-Seq ReadsSebastian Boegel, Thomas Bukur, John C. Castle, and Ugur Sahin
13. PHLAT: Inference of High Resolution HLA Types from RNA and Whole Exome SequencingYu Bai, David Wang, and Wen Fury
14. Using Exome and Amplicon-Based Sequencing Data for High-Resolution HLA Typing with ATHLATESChang Liu and Xiao Yang
15. HLA Typing from Short-Read Sequencing Data with OptiTypeAndras Szolek
16. Comprehensive HLA Typing from a Current Allele Database using Next Generation Sequencing DataShuji Kawaguchi, Koichiro Higasa, Ryo Yamada, and Fumihiko Matsuda
17. Accurate Assembly and Typing of HLA using a Graph-Guided Assembler KouramiHeewook 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 SoftwareJurgen Sauter, Christian Schafer, and Alexander H. Schmidt