Distributions of MICA and MICB Alleles Typed by Amplicon-Based Next-Generation Sequencing in South Koreans

IF 5.9 4区医学 Q2 CELL BIOLOGY

HLA Pub Date : 2024-10-29 DOI:10.1111/tan.15735

Eun-Jeong Choi, Hyoung-Jae Kim, Jin-Hyeok Kim, In-Cheol Baek

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引用次数: 0

Abstract

Major histocompatibility complex class I chain-related genes A and B (MICA and MICB) play a role as ligands in activating the NKG2D receptor expressed in natural killer cells, γδ T-cells and αβ CD8 T-cells and have been defined in human diseases and haematopoietic stem cell transplantation (HSCT). MICA and MICB alleles were genotyped at the three-field level by amplicon-based next-generation sequencing (NGS) using a MiSeqDx system and compared with the results from previous studies in healthy South Korean donors. Exons 2–5 of MICA and exons 2–4 of MICB were amplified using a multiplex polymerase chain reaction (PCR). Sequence reads of ≥ 51 depth counts were consistently obtained for each sample exon, and target exons were determined to match reference sequences contained in the IPD-IMGT/HLA database. MICA and MICB alleles were tested using exon combinations. The program was designed to recognise specific sequences and discriminate between the MICA*008:01:01/*027 alleles. A total of 22 alleles were found in MICA and MICB. We observed 1 HLA-C ~ HLA-B ~ MICA ~ MICB ~ HLA-DRB1 haplotype with significant linkage disequilibrium between alleles at all neighbouring HLA loci. These results are consistent with previous microarray results. Genotyping of MICA and MICB was possible using 11-loci HLA genes. We updated the distribution of MICA and MICB based on three-field allele and haplotype frequencies containing linkage disequilibrium in South Koreans using amplicon-based NGS. These data suggest that high-resolution MICA and MICB typing data obtained using NGS may aid in performing HSCT and disease association studies.

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通过基于扩增子的下一代测序技术分析韩国人的 MICA 和 MICB 等位基因分布情况。

主要组织相容性复合体 I 类链相关基因 A 和 B（MICA 和 MICB）作为配体在激活表达于自然杀伤细胞、γδ T 细胞和 αβ CD8 T 细胞的 NKG2D 受体方面发挥作用，并已在人类疾病和造血干细胞移植（HSCT）中得到确定。通过使用 MiSeqDx 系统进行基于扩增子的下一代测序（NGS），在三个字段水平上对 MICA 和 MICB 等位基因进行了基因分型，并与之前在韩国健康供体中的研究结果进行了比较。使用多重聚合酶链反应（PCR）扩增了 MICA 的 2-5 号外显子和 MICB 的 2-4 号外显子。每个样本外显子的序列读数深度均≥51，并确定目标外显子与 IPD-IMGT/HLA 数据库中的参考序列相匹配。使用外显子组合检测了 MICA 和 MICB 等位基因。该程序旨在识别特定序列并区分 MICA*008:01:01/*027 等位基因。在 MICA 和 MICB 中总共发现了 22 个等位基因。我们观察到 1 个 HLA-C ~ HLA-B ~ MICA ~ MICB ~ HLA-DRB1 单倍型，在所有相邻 HLA 位点的等位基因之间存在显著的连锁不平衡。这些结果与之前的微阵列结果一致。使用 11 个 HLA 基因位点可对 MICA 和 MICB 进行基因分型。我们利用基于扩增子的 NGS，根据南韩人中含有连锁不平衡的三区等位基因和单倍型频率，更新了 MICA 和 MICB 的分布。这些数据表明，利用 NGS 获得的高分辨率 MICA 和 MICB 分型数据有助于开展造血干细胞移植和疾病相关研究。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

HLA Immunology and Microbiology-Immunology

CiteScore

3.00

自引率

28.80%

发文量

368

期刊介绍： HLA, the journal, publishes articles on various aspects of immunogenetics. These include the immunogenetics of cell surface antigens, the ontogeny and phylogeny of the immune system, the immunogenetics of cell interactions, the functional aspects of cell surface molecules and their natural ligands, and the role of tissue antigens in immune reactions. Additionally, the journal covers experimental and clinical transplantation, the relationships between normal tissue antigens and tumor-associated antigens, the genetic control of immune response and disease susceptibility, and the biochemistry and molecular biology of alloantigens and leukocyte differentiation. Manuscripts on molecules expressed on lymphoid cells, myeloid cells, platelets, and non-lineage-restricted antigens are welcomed. Lastly, the journal focuses on the immunogenetics of histocompatibility antigens in both humans and experimental animals, including their tissue distribution, regulation, and expression in normal and malignant cells, as well as the use of antigens as markers for disease.