Sequence polymorphism and evolutionary analysis of HLA-A, -B, and -C loci in the northern Han Chinese population
10.13303/j.cjbt.issn.1004-549x.2026.06.006
- VernacularTitle:国内北方汉族人群HLA-A、-B、-C基因序列多态性与进化分析
- Author:
Wenqian SONG
1
;
Wanzhen YU
2
;
Suning BAI
2
;
Liying WANG
1
;
Linnan SHAO
1
;
Shihang ZHOU
1
;
Xiaohua LIANG
1
Author Information
1. Dalian Blood Center, Dalian 116001, China
2. College of Laboratory Medicine, Dalian Medical University, Dalian 116044, China
- Publication Type:Journal Article
- Keywords:
HLA class I;
long-read sequencing;
locus-specific sequence type;
nucleotide diversity;
Tajima′s D;
Ewens-Watterson test
- From:
Chinese Journal of Blood Transfusion
2026;39(6):743-749
- CountryChina
- Language:Chinese
-
Abstract:
Objective: To characterize the sequence polymorphism of HLA-A, -B, and -C loci in the northern Han Chinese population and to evaluate their selection signals and phylogenetic patterns based on long-read sequencing data. Methods: A total of 408 unrelated healthy blood donors were enrolled. Long-read sequencing of HLA-A, -B, and -C loci was performed using the PacBio Sequel II platform. The Ewens-Watterson neutrality test, sliding-window nucleotide diversity (π) and Tajima′s D analyses were conducted, together with genetic distance heatmaps, principal coordinates analysis (PCoA), and maximum likelihood phylogenetic analysis to assess polymorphism distribution, selection signals, and phylogenetic structure across the three loci. Results: The analyzed sequence lengths for the HLA-A, -B, and -C loci were 3 257 bp, 3 794 bp, and 3 831 bp, respectively; the numbers of locus-specific sequence types were 44, 82, and 56, with corresponding locus-specific sequence type diversities of 0.905 2, 0.964 9, and 0.939 8, respectively. The Ewens-Watterson test showed no significant deviation from neutrality (P>0.05). Sliding-window analysis revealed elevated π and Tajima′s D values in exons 2 and 3 as well as in certain intronic regions of HLA-A and HLA-B, whereas HLA-C exhibited relatively lower overall diversity. Genetic distance heatmaps, PCoA, and phylogenetic analysis consistently showed clear clustering in HLA-A and HLA-C, while HLA-B displayed the highest phylogenetic heterogeneity. Conclusion: HLA-A, -B, and -C gene sequences in the northern Chinese Han population exhibit high levels of polymorphism and marked regional heterogeneity. HLA-B shows greater diversity, stronger signals of selection, and more complex phylogenetic structure compared with HLA-A and HLA-C.
