HLA Typing

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.

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

Inhalt
The Past, Present, and Future of HLA Typing in Transplantation.- Role of Human Leukocyte Antigens (HLA) in Autoimmune Diseases.- The IPD Databases: Cataloguing and Understanding Allele Variants.- Allele Frequency Net Database.- High Resolution HLA-Typing by Next Generation Sequencing of Randomly Fragmented Target DNA.- High-Throughput Contiguous Full-Length Next Generation Sequencing of HLA Class I and II Genes from 96 Donors in a Single MiSeq Run.- Application of High-Throughput Next Generation Sequencing for HLA Typing on Buccal Extracted DNA.- Super High Resolution for Single Molecule-Sequence-Based Typing of Classical HLA loci using Ion Torrent PGM.- High Resolution Full-Length HLA Typing Method using Third Generation (Pac-Bio SMRT) Sequencing Technology.- Full-Length HLA Class I Genotyping with the MinION Nanopore Sequencer.- Imputation-Based HLA Typing with SNPs in GWAS Studies.- In Silico Typing of Classical and Non-Classical HLA Alleles from Standard RNA-Seq Reads.- PHLAT: Inference of High Resolution HLA Types from RNA and Whole Exome Sequencing.- Using Exome and Amplicon-Based Sequencing Data for High-Resolution HLA Typing with ATHLATES.- HLA Typing from Short-Read Sequencing Data with OptiType.- Comprehensive HLA Typing from a Current Allele Database using Next Generation Sequencing Data.- Accurate Assembly and Typing of HLA using a Graph-Guided Assembler Kourami.- AmpliSAS and AmpliHLA: Web Server Tools for MHC Typing of Non-Model Species and Human using NGS Data.- HLA Haplotype Frequency Estimation from Real-Life Data with the Hapl-o-Mat Software.