The polymorphism of HLA-A, -C, -B,-DRB3/4/5,-DRB1,-DQB1 loci in Zhejiang Han population, China using NGS technology

The distributions of HLA allele and haplotype are various in the populations. Currently, the data for HLA alleles and haplotypes at three fields resolution level in Chinese Han population is rare. Here, the HLA alleles and haplotypes of the 1734 cord blood samples from Zhejiang Han population, China were reported at three fields resolution. All samples were randomly collected from the Zhejiang Cord Blood Bank, China. HLA-A, -B, -C, -DRB1, -DQB1, -DRB3/4/5 loci was genotyped using next generation sequencing method. The genotypes of the samples were assigned using the HLA TypeStream Visual Software version 1.2.0. The frequency of alleles, haplotype estimation and linkage disequilibrium analysis were performed with the Arlequin software 3.5.2.2. It was found that the top three frequent alleles of HLA-A, -B, -C, -DRB1, -DQB1, -DRB3/4/5 loci were A*11:01:01 (25.81%), A*24:02:01 (16.70%), A*02:01:01 (10.61%); B*40:01:02 (15.97%), B*46:01:01 (11.48%), B*58:01:01 (7.96%); C*07:02:01 (19.03%), C*01:02:01 (17.65%), C*03:04:01 (10.41%); DRB1*09:01:02G (17.96%), DRB1*12:02:01 (9.57%), DRB1*08:03:02 (9.54%); DQB1*03:01:01G (21.05%), DQB1*03:03:02 (19.15%), DQB1*06:01:01G (12.08%); DRB4*01:03:01 (25.72%), DRB3*02:02:01 (20.27%), DRB5*01:01:01 (10.96%), respectively. A total of 1528 distinct A similar to C similar to B similar to DRB3/4/5 similar to DRB1 similar to DQB1 haplotypes were estimated, and the top three most common haplotypes were A*33:03:01 similar to C*03:02:02 similar to B*58:01:01 similar to DRB3*02:02:01 similar to DRB1*03:01:01 similar to DQB1*02:01:01 (4.02%), A*30:01:01 similar to C*06:02:01 similar to B*13:02:01 similar to DRB4*01:03:01 similar to DRB1*07:01:01 similar to DQB1*02:02:01 (3.11%) and A*02:07:01 similar to C*01:02:01 similar to B*46:01:01 similar to DRB4*01:03:01 similar to DRB1*09:01:02G similar to DQB1*03:03:02 (3.05%). Some alleles of different HLA loci were shown strong linkage disequilibrium. In conclusion, the data of allele and haplotype of HLA-A, -B, -C, -DRB1, -DQB1 and -DRB3/4/5 loci at three fields resolution level were obtained in Zhejiang Han population, thus contributing to analyze the HLA ploymorphism in the populations.

Automated summary

The study reported the three-field resolution analysis of HLA allele and haplotype in cord blood samples of the Han population in Zhejiang, China. It identified high-frequency alleles and haplotypes, as well as strong linkage disequilibrium between different HLA loci.