Hla-c Distribution Of Sichuan Han Population In Cmdp

ObjectiveTo investigate the allelic distribution of HLA-C locus in Han individuals from Sichuan branch of Chinese Marrow Donor Program (CMDP).MethodsA total of 244 peripheral blood DNA samples, consecutively collected from unrelated donors during Dec.2008 and Mar.2009, were randomly chosen. Exon 2,3 and 4 of each sample were sequenced using PCR-SBT. Additional exon sequencing and group-specific sequencing were performed to resolve the allele ambiguities. Allele frequencies were calculated by direct counting and the chi-square values of allele frequencies from different populations were also analyzed. Haplotype frequencies of HLA-A-C, HLA-C-B and HLA-A-C-B-DRB1 were calculated by expectation-maximization method, and the linkage disequilibrium for two-locus haplotypes was analyzed.ResultsOf the 244 samples,68 showed conclusive typing results, and the remaining 176 samples showed ambiguity results. As to the 176 inconclusive samples,90 samples were resolved by group-specific sequencing and additional exon sequencing both, and 59 were resolved just by additional exon sequencing, and 27 were resolved by group-specific sequencing, including one sample with a novel HLA-C allele. In our study, a total of 24 different HLA-C alleles and a novel allele were identified. The most common alleles, with the allele frequency of more than 10%, were C*01:02 (21.93%), C*07:02 (18.65%) and C*03:04 (13.11%), which comprised 53.68% of the total alleles identified in our study. And 12 kinds of allele were detected with the allele frequency of more than 1%, which comprised 95.69% of the total alleles identified in our study. Comparison of the HLA-C allelic distribution with different populations showed that little difference was observed between Sichuan Han and southern Chinese population, whereas there were many significant differences between Sichuan Han and Eastern European American /African American populations. Expectation-maximization revealed 100 kinds of HLA-A-C,96 of HLA-C-B and 302 of HLA-A-C-B-DRB1 haplotypes, and the most frequent haplotype for A-C, C-B and A-C-B-DRB1 haplotype was A*02:07-C*01:02 (9.7125%), C*01:02-B*46:01 (15.1043%) and A*02:07-C*01:02-B*46:01-DRB1*09:01 (5.1708%), respectively. Linkage disequilibrium estimation of the association of two alleles from different two loci showed that 9 of HLA-A-C, and 23 of HLA-C-B had significant LD. In additional, a novel HLA-C allele C*06:45 was found in our study. This novel allele differed from the closet matching allele C*06:02 by a missense nucleotide substitution at the first position of codon 39(GAC>TAC), resulting in an amino acid changed from Asp to Tyr. Interestingly, no substitution at this conserved codon had ever been found before.ConclusionA reliable HLA-C SBT technique, from exon 2 through exon 4, has been established in our study. In additional, all the allele ambiguities are resolved by group-specific sequencing and additional exon sequencing. The HLA-C allelic distribution and haplotype analysis demonstrate that the Sichuan Han population share HLA patterns with southern Chinese, while it also retains unique characteristics.