Distributions of HLA‐A, ‐B, and ‐DRB1 alleles typed by amplicon‐based next generation sequencing in Korean volunteer donors for unrelated hematopoietic stem cell transplantation

Abstract

HLA genes play a pivotal role for successful hematopoietic stem cell transplantation (HSCT). There is an increasing need for sophisticated screening of donor HLA genotypes for unrelated HSCT. Next generation sequencing (NGS) has emerged as an alternative for classical Sanger sequence for HLA typing. In this study, HLA‐A, ‐B, and ‐DRB1 alleles were genotyped at the allelic (6‐digit) level using MiSeqDx in 26,202 volunteers from the Korean Network for Organ Sharing. Exon 2 and 3 of HLA‐A and ‐B and exon 2 of HLA‐DRB1 were amplified by polymerase chain reaction (PCR) and each allele was determined by matching the targeted exons and the reference sequence consisting of the IPD‐IMGT/HLA Database. Seventy alleles of HLA‐A, 102 alleles of HLA‐B, and 69 alleles of HLA‐DRB1 were identified. According to common and well‐documented catalogs, 34 alleles in HLA‐A, 61 in HLA‐B, and 45 in HLA‐DRB1 locus were common alleles, and 12, 14, and 11 kinds, were well‐documented alleles, respectively. Thirteen novel alleles including 3 alleles in HLA‐A, 8 alleles in HLA‐B, and 2 alleles in HLA‐DRB1 loci were found. Ten haplotypes with a frequency of more than 1.0% accounted for 22.4% of the total haplotype frequencies. Cis/trans ambiguities of HLA‐A and ‐B loci by combination of exons 2 and 3 were analyzed to be 0.17% of 3 and 3.95% of 22 genotypes, respectively. This information on rare and novel alleles found by accurate HLA typing with NGS may be helpful for unrelated HSCT among Koreans.

Allele and haplotype frequencies of human leukocyte antigen-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 by next generation sequencing-based typing in Koreans in South Korea

“…Compared with previous studies [9,23,24,27,30], the HLA-C, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 alleles that were determined at high resolution in this study could be helpful for a clinical decision. The tolerance of a mismatch will depend on the patient's clinic and the discrepancy between unmatched alleles.…”

“…We first reported all the 11 loci HLA typing in South Koreans. In order to obtain high-resolution HLA types (3rd field allele types), 173 healthy Koreans were the HLA typed for all 11 HLA loci using next generation DNA sequencing (HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1 and -DPB1), of which were 100% concordant across HLA-A, -B, and -DRB1 (to 3rd field) [9]. No historical data was present for 3rd field of HLA-C, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 (Table 1).…”

“…High-resolution and highthroughput HLA typing methods have been validated using amplicon-based next generation DNA sequencing [6,7], greatly simplifying the workflow [8]. We reported on the distributions of HLA-A, -B (exon 2 and 3) and -DRB1 (exon 2) using amplicon-based NGS in a previous study [9]. Furthermore, HLA typing using NGS has subsequently been performed by longrange amplification, sequencing platforms, and analysis algorithms [10][11][12].…”

“…The distribution of HLA alleles differed significantly between ethnic groups, and specific alleles and haplotypes are characteristic of each ethnic group [9,14,16,17,[20][21][22][23][24][25][26][27][28][29][30][31][32]. Transplant and disease-related studies, such as organ or hematopoietic stem cell transplantation, require data on the distribution of HLA alleles and haplotypes in each ethnic group [3,[33][34][35].…”

Comprehensive Analysis of CD4+ T Cell Response Cross-Reactive to SARS-CoV-2 Antigens at the Single Allele Level of HLA Class II

“…The genomic DNA was isolated from the red blood cells and granulocytes (Tiangen Biotech Corporation). The HLA was then genotyped using polymerase chain reaction sequencing-based typing and next-generation sequencing ( Table 1 ) (NCBI BioProject Accession: PRJNA721949) (MiSeqDx, Illumina), as previously described ( 24 , 25 ). The resolution of the HLA types was converted to 4-digits from 6-digits to analyze the HLA molecules at the protein level.…”