HLAreporter: a tool for HLA typing from next generation sequencing data.

Pak Chung Sham,Jing Yang,Dingge Ying,Yan Zhang,Nattiya Hirankarn,Wanling Yang,Yu Lung Lau,Vorasuk Shotelersuk,Yazhi Huang

doi:10.1186/s13073-015-0145-3

Abstract

Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for widespread applications. Here we introduce a novel tool (HLAreporter) for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles, followed by de novo assembly of the gene-specific short reads. Accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly developed tools such as HLAminer and PHLAT. HLAreporter can be downloaded from http://paed.hku.hk/genome/.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-015-0145-3) contains supplementary material, which is available to authorized users.

Highlights

The human leukocyte antigens (HLAs) include a large number of genes crucial to immune system function
We introduce a novel approach for accurate HLA typing at high-digit resolution based on a strategy of comparing sequence reads with a comprehensive reference panel containing all the known HLA alleles for high efficiency mapping, followed by assembly of the mapped reads to contigs, stepwise matching and designation of the contigs to HLA alleles and decision on HLA allele calling
To study the mapping efficiency for this group of genes, we compared the number of reads captured for the HLA-DRB1 gene using a traditional single reference-based mapping method and the comprehensive reference panel (CRP)-based mapping developed in this study, using Burrows-Wheeler Aligner (BWA) as the mapping tool in both cases

Summary

Introduction

The human leukocyte antigens (HLAs) include a large number of genes crucial to immune system function. They play important roles in immune responses to infection, transplant rejection, pathogenesis of autoimmune diseases, adverse drug reaction, and cancer development. Typing HLA from NGS data can at least serve as a preliminary population screening tool to identify individuals who might have potential adverse drug responses or are potential organ donors, exact clinical use would require more stringent standards and procedures. Since having NGS data for large numbers of healthy individuals is rapidly becoming a reality, the potential benefits of HLA screening using this type of data is multi-fold

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