韩国人群的 HLA-A、-B、-C、-DRB1 等位基因和单倍型频率，以及下一代测序 HLA 分型的性能特征。

HLA-A, -B, -C, -DRB1 allele and haplotype frequencies of the Korean population and performance characteristics of HLA typing by next-generation sequencing.

机构信息

Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.

Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea.

出版信息

HLA. 2021 Mar;97(3):188-197. doi: 10.1111/tan.14167. Epub 2021 Feb 2.

DOI:10.1111/tan.14167

PMID:33314756

Abstract

INTRODUCTION

Human leukocyte antigen (HLA) identification at the allelic level is important for haematopoietic stem cell transplantation (HSCT). Next-generation sequencing (NGS) resolves ambiguous alleles by determining the phase of the polymorphisms. The aim of this study was to validate the software for HLA-SBT (sequence-based typing), assess Korean allele frequency, and characterise the performance of NGS-HLA typing.

METHODS

From the 2009 to 2016 registry, 1293 unrelated healthy donors with a complete dataset of previously characterised HLA-A, -B, -C, and -DRB1 loci were selected and assessed for frequency, haplotype inference, and relative linkage disequilibrium. For performance characteristics of NGS-HLA, alleles included in 1293 cases and ambiguous or alleles assigned as new by SBT-HLA software, or unassigned alleles were included. A total of 91 and 41 quality control samples resulted in 1056 alleles (132 samples × 4 loci × 2 diploid) for analysis. The GenDx NGSgo kit was used for NGS-HLA typing using the Illumina MiSeq platform.

RESULTS

A panel of 132 samples covered 231 alleles, including 53 HLA-A, 80 HLA-B, 43 HLA-C, and 55 HLA-DRB1 by HLA-SBT typing. Comparison of SBT-HLA and NGS-HLA typing showed 99.7% (1053/1056) concordance and discrepant cases were resolved by manual evaluation. Typing by NGS resulted in 67 HLA-A, 112 HLA-B, 71 HLA-C, and 72 HLA-DRB1 alleles. A total of 132 ambiguous, 4 new, and 1 unassigned alleles by HLA-SBT were resolved by NGS-HLA typing.

CONCLUSIONS

NGS-HLA typing provided robust and conclusive results without ambiguities, and its implementation could support HSCT in clinical settings.

摘要

简介

人类白细胞抗原（HLA）等位基因水平的鉴定对于造血干细胞移植（HSCT）非常重要。下一代测序（NGS）通过确定多态性的阶段来解决模棱两可的等位基因。本研究的目的是验证 HLA-SBT（基于序列的分型）软件，评估韩国等位基因频率，并描述 NGS-HLA 分型的性能。

方法

从 2009 年至 2016 年的登记处中，选择了 1293 名具有先前特征化的 HLA-A、-B、-C 和-DRB1 基因座完整数据集的无关健康供体，并对其频率、单倍型推断和相对连锁不平衡进行评估。对于 NGS-HLA 的性能特征，包括 1293 例中的等位基因、SBT-HLA 软件分配的新等位基因或未分配的等位基因、以及不确定的等位基因。总共 91 个和 41 个质量控制样本产生了 1056 个等位基因（132 个样本×4 个基因座×2 个二倍体）用于分析。使用 Illumina MiSeq 平台的 GenDx NGSgo 试剂盒进行 NGS-HLA 分型。

结果

132 个样本面板涵盖了 231 个等位基因，包括 HLA-SBT 分型的 53 个 HLA-A、80 个 HLA-B、43 个 HLA-C 和 55 个 HLA-DRB1。SBT-HLA 和 NGS-HLA 分型的比较显示 99.7%（1053/1056）一致，通过手动评估解决了不一致的情况。NGS 分型导致 67 个 HLA-A、112 个 HLA-B、71 个 HLA-C 和 72 个 HLA-DRB1 等位基因。通过 HLA-SBT 确定的 132 个不确定、4 个新的和 1 个未分配的等位基因通过 NGS-HLA 分型得到解决。