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HLA Typing

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Cover of 'HLA Typing'

Table of Contents

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    Book Overview
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    Chapter 1 The Past, Present, and Future of HLA Typing in Transplantation
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    Chapter 2 Role of Human Leukocyte Antigens (HLA) in Autoimmune Diseases
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    Chapter 3 The IPD Databases: Cataloguing and Understanding Allele Variants
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    Chapter 4 Allele Frequency Net Database
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    Chapter 5 High-Resolution HLA-Typing by Next-Generation Sequencing of Randomly Fragmented Target DNA
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    Chapter 6 High-Throughput Contiguous Full-Length Next-Generation Sequencing of HLA Class I and II Genes from 96 Donors in a Single MiSeq Run
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    Chapter 7 Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA
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    Chapter 8 Super High Resolution for Single Molecule-Sequence-Based Typing of Classical HLA Loci Using Ion Torrent PGM
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    Chapter 9 High-Resolution Full-Length HLA Typing Method Using Third Generation (Pac-Bio SMRT) Sequencing Technology
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    Chapter 10 Full-Length HLA Class I Genotyping with the MinION Nanopore Sequencer
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    Chapter 11 Imputation-Based HLA Typing with SNPs in GWAS Studies
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    Chapter 12 In Silico Typing of Classical and Non-classical HLA Alleles from Standard RNA-Seq Reads
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    Chapter 13 PHLAT: Inference of High-Resolution HLA Types from RNA and Whole Exome Sequencing
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    Chapter 14 Using Exome and Amplicon-Based Sequencing Data for High-Resolution HLA Typing with ATHLATES
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    Chapter 15 HLA Typing from Short-Read Sequencing Data with OptiType
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    Chapter 16 Comprehensive HLA Typing from a Current Allele Database Using Next-Generation Sequencing Data
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    Chapter 17 Accurate Assembly and Typing of HLA using a Graph-Guided Assembler Kourami
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    Chapter 18 AmpliSAS and AmpliHLA: Web Server Tools for MHC Typing of Non-Model Species and Human Using NGS Data
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    Chapter 19 HLA Haplotype Frequency Estimation from Real-Life Data with the Hapl-o-Mat Software
Attention for Chapter 17: Accurate Assembly and Typing of HLA using a Graph-Guided Assembler Kourami
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Chapter title
Accurate Assembly and Typing of HLA using a Graph-Guided Assembler Kourami
Chapter number 17
Book title
HLA Typing
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-8546-3_17
Pubmed ID
Book ISBNs
978-1-4939-8545-6, 978-1-4939-8546-3
Authors

Heewook Lee, Carl Kingsford, Lee, Heewook, Kingsford, Carl

Abstract

Accurate typing of human leukocyte antigen (HLA) is essential for successful organ transplantation and HLA genes are heavily associated with various diseases. Widely used typing assays often involve a set of specially designed primers or probes requiring additional experiments. With the maturing of high-throughput sequencing (HTS) technologies, whole genome sequencing (WGS) as well as other HTS assays are becoming more accessible even in the clinical settings. We describe various computational methods capable of directly typing HLA genes using HTS data including Kourami, our HLA assembler. Kourami is the first HLA assembler capable of discovering novel alleles. Kourami assembles full-length sequences across the peptide-binding regions of HLA genes. Here, we focus on how a user would use Kourami on a new sample. We demonstrate the application by typing HLA alleles from a recently published WGS data with validated HLA types using Kourami.

Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 14 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 14 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 3 21%
Student > Bachelor 2 14%
Researcher 2 14%
Student > Master 2 14%
Unknown 5 36%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 4 29%
Agricultural and Biological Sciences 2 14%
Computer Science 1 7%
Immunology and Microbiology 1 7%
Unknown 6 43%