Allelic diversity and haplotype structure of HLA loci in the Chinese Han population living in the Guanzhong region of the Shaanxi province

The allele and haplotype frequencies of HLA-A, -B and -DRB1 loci in 10,000 healthy unrelated Han individuals living in the Guanzhong region of the Shaanxi Province were analyzed with the methods of SSO, SSP and SBT. Subsequently, these data were compared with results obtained in Han populations living in other regions as well as to other ethnic groups, using genetic distance measurements, neighbor-joining dendrograms and principal component analysis. In total 18 alleles were detected at the HLA-A locus, 46 alleles at the HLA-B locus and 14 alleles at the HLA-DRB1 locus. HLA-A02 was the most common HLA-A allele (29.70%), followed by A11 (18.70%), and A24 (15.75%); whereas at the HLA-B locus, the allele with the highest frequency was HLA-B13 (10.76 %), followed by B46 (7.93%), B51 (7.68%). At the HLA-DRB1 locus, the most common alleles were HLA-DRB115 (15.54%), DRB109 (13.18%) and DRB104 (11.21%). Three-loci haplotype analysis revealed that HLA A30- B13- DRB107 (4.11%), A02 -B46 -DRB109 (2.57%) and A33 -B58 -DRB117 (1.32%) were the most common haplotypes in this population. Four two-loci haplotypes, including HLA-A30-B43, A30-B53, B43-DRB107 and B73-DRB104 had significant linkage disequilibrium (relative linkage disequilibrium parameter equals to 1). Compared with other populations, our results indicated that the Han populations in different regions had a similar allelic diversity of HLA -A, -B, and -DRB1 loci. The Han population in the Guanzhong region of the Shaanxi Province had a close genetic relationship with the Northern and Southern Han populations. In summary, the similarities and differences of the HLA allelic diversity and haplotype structure between the Han population in the Guanzhong region and related populations, regarding HLA genotype distribution, provide basic information for further studies of the HLA heterogeneity and anthropological studies.