Characterization of HLA‐E polymorphism in four distinct populations in Mainland China

Abstract

In this study, human leukocyte antigen (HLA)-E allelic typing was performed for 690 individuals from two southern Chinese Han populations (Hunan Han and Guangdong Han) and two northern Chinese populations (Inner Mongolia Han and Inner Mongolia Mongol) using polymerase chain reaction-sequence-specific priming (PCR-SSP) method. Our data showed that (1) HLA-E*01:01 and HLA-E*01:03, but not E*01:04 allele, were detected in the four populations, HLA-E distribution differed significantly between each of the two southern Chinese Han populations and the Inner Mongolia Mongol population, and between Hunan Han population and Inner Mongolia Han population; (2) HLA-G*01:05N-A*30-E*01:01-C*06-B*13:02-DRB1*07 was a conserved extended haplotype in the Chinese Han populations; (3) five HLA-A-E haplotypes showed significant linkage disequilibrium (LD) in at least one population, including HLA-A*02-E*01:03 in populations except for the Inner Mongolia Mongol group, HLA-A*01-E*01:01 and HLA-A*30-E*01:01 in the Hunan Han and the Inner Mongolia Han populations, HLA-A*33-E*01:01 in the two southern Chinese Han populations and HLA-A*03-E*01:03 in the Inner Mongolia Mongol group; and (4) Ewens-Watterson homozygosity test showed a trend for balancing selection at the HLA-E locus in each of the four populations. Our data unraveled the peculiarity in terms of HLA-E allelic and haplotypic repertoire in four main ethnic groups in Mainland China, findings shown here are valuable for future studies of the potential role of HLA-E in allogeneic organ transplantation and HLA-linked disease association in related ethnic groups.

Killer cell immunoglobulin-like receptor (KIR) genes in 4 distinct populations and 51 families in mainland China

“…In addition, a novel KIR gene profile was detected in the IMM group. This finding was consistent with our reports on HLA non-classical genes in these 4 populations [29,45], and further demonstrated the peculiarity in terms of allelic and haplotypic repertoire of immune response related genes in this ethnic group.…”

MICB polymorphism in a southern Chinese Han population: The identification of two new MICB alleles, MICB∗005:06 and MICB∗026

“…HLA-A ⁄ 30-C ⁄ 06-B ⁄ 13:02-MICA ⁄ 008:01-MICB ⁄ 005:02-DRB1 ⁄ 07 appeared to be a conserved extended haplotype in this population. HLA-A ⁄ 30-C ⁄ 06-B ⁄ 13:02-DRB1 ⁄ 07 has been reported in several Asian populations [20,[31][32][33], suggesting that this haplotype may have been maintained by selective force(s).…”

NKG2C copy number variations in five distinct populations in mainland China and susceptibility to nasopharyngeal carcinoma (NPC)

“…The following strategy was used to control data quality: (a) each gel was reviewed by two observers, any discrepant result was repeated in an independent PCR-SSP assay; (b) four homozygotes for NKG2C gene deletion and five homozygotes for wild type NKG2C gene, all of which were randomly selected, were further sequenced in both directions by Sanger sequencing [14], using PCR primers and the ABI PRISM BigDye Terminator v3.1 sequencing kit on an ABI PRISM 3730 DNA sequencer and (c) in HLA-E allelic typing, single blinded PCR-SSP was performed for 44 DNA samples, which were randomly selected from our sample inventory with known HLA-E genotypes [14].…”

“…The size of the amplicons was determined by comparison against the migration of a 100-bp DNA ladder (Solarbio, Beijing, China). HLA-E ⁄ 01:01 and HLA-E ⁄ 01:03 alleles were examined for all of the 653 NPC patients using PCR-SSP technology [14]. Appropriate control DNAs of HLA-E ⁄ 01:01 and HLA-E ⁄ 01:03, as well as a blank control for which double-distilled water was used as DNA template, were included in each batch of PCR reactions.…”

“…Several factors have been implicated in the etiology of NPC, including genetic determinants (most notably the HLA gene complex encoding the human leukocyte antigen), environmental exposures and Epstein-Barr virus (EBV) infection [12]. HLA-E, the only known ligand for NKG2A and NKG2C receptors, has HLA-E ⁄ 01:01 and HLA-E ⁄ 01:03 alleles in the general population [13,14]. An increase in HLA-E ⁄ 01:03 allele was observed in NPC patients of Thai origin, suggesting a possible role for HLA-E in NPC development, possibly via NK cell or cytotoxic lymphocyte function [15]; however, such an association was not established in a subsequent case-control study in Tunisians [16].…”