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.

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Currently, there is a lack of information on polymorphism of human leucocyte antigen-F (HLA-F) gene in ethnically diverse human populations. In this study, HLA-F allelic typing was performed for 690 individuals representing 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) and PCR-sequencing methods. Our results showed that (i) HLA-F*01 : 01 predominated in each population with a frequency >0.94 and HLA-F*01 : 03 was relatively more common in the two northern Chinese populations with a frequency of approximately 0.05; (ii) both geographical and ethnical factors are related to HLA-F allelic distribution, as evidenced by the significant difference in HLA-F allelic distribution between the Hunan Han population and the two northern Chinese populations; (iii) significant linkage disequilibrium (LD) was observed for haplotype HLA-A*03-F*01 : 03 in three populations. In most cases, this haplotype extended to HLA-E*01 : 03; and (iv) Ewens-Watterson homozygosity statistic at the HLA-F locus did not depart significantly from expectation in each of the four populations. Our data revealed a low level of HLA-F allelic variation in Chinese populations, suggesting that HLA-F gene may have existed before some of the HLA-A polymorphism and have been evolving under neutrality.