Four Distinct HLA Amino-acid Variants And Two HLA Alleles Associate With Risk Of Leprosy In The Han Chinese Population

Background Leprosy is a chronic inflammatory skin disease caused by Mycobacterium leprosy infection.It affects the skin and peripheral nerve can cause irreversible neurological impairment and subsequent irreversible chronic disability.The host genetic factor is considered to affect the susceptibility to infection and the progression of the disease.The risk of leprosy is strongly related to the variation in the major histocompatibility complex(MHC)region,especially the human leukocyte antigen HLA-DRβ1.In 2009,we carried out genome-wide association analysis(GWAS)for 706 leprosy patients and 1225 controls in China.We found that HLA-DR area is significantly correlated with leprosy susceptibility,but it is still not yet clear in HLA region.HLA is located in 6p21.3 and plays an important role in genetics and immunology in organisms.The area has been identified to be associated with more than 200 diseases or traits,including primary immunodeficiency,autoimmune diseases,infections,malignancies and mental disorders.At present,the HLA region will be divided into three categories,HLA-I gene,HLA-II gene,HLA-III gene,the classical HLA-I gene,including HLA-A HLA-B,and HLA-C,the classical HLA-II gene contains HLA-DR,HLA-DP,HLA-DQ,The genetic characteristics of HLA region include haplotype inheritance,co-dominant inheritance and linkage disequilibrium.Due to the high complexity of HLA region,it is a difficult problem to further determine the association between HLA region and many diseases.Imputation refers to the technology of using known genotyping data to predict the loci that have not been genotyped and the absence of genotyping data,and is a widely used fine locating method.Imputation can increase the density of single-nucleotide polymorphisms(SNPs)in GWAS data,making it possible to find disease sites around the associated sites that have been found,as well as can improve the performance of SNP loci that have been labeled with unsuitable tag SNPs.Han-MHC reference panel is our research team extracted from the total genetic variation of MHC database in 2016 minor allele frequency of 0.5% or more mutation loci constructed,compared with the usual research institute with the related variation of spectrum,it has a deeper sequencing depth,with a more complete accurate information.Objectives 1)Impute the GWAS data of leprosy in previous studies;2)Found the leprosy related independent loci by stepwise regression analysis;3)Identificate theleprosy susceptibility genes in HLA region.Methods We conducted a large-scale fine-mapping study of leprosy risk(706 leprosy cases and 1225 controls were included)by imputing class I and II HLA genes and corresponding amino acid variation sites from previously reported GWAS data together with a Han population-specific reference panel,then selected the potential HLA variant for stepwise regression analysis,and protein spatial composition analysis.Results This research uses early leprosy GWAS data,the Han population-specific reference panel as a reference platform,made by the SNP2 HLA genotype in the HLA area to fill the analysis by the quality control after the discovery of 23,508 SNP,found a total of 30 HLA alleles and 184 amino acid sites reached genome-wide association level,among them the P value of the most significant allele for HLA-DRB1*15(P=1.28 * 10-42,OR=2.71,95%CI=2.34-3.14),which have been reported the association with leprosy by a number of studies.In order to further determine the correlation of leprosy independent loci using stepwise regression analysis,further analysis of the data after quality control,showed that there are six independent sites reach the significant threshold(P<1.67 * 10-6),HLA-DRβ1 amino acid position 71(P=1.28 * 10-42,OR=2.71,95%CI=2.34-3.19),HLA-DPβ1 amino acid position 35(P= 1.75 * 10-14,OR=0.60,95%CI=0.52-0.68),HLA-C amino acid position 116(P= 5.12 * 10-11,OR=1.68,95%CI=1.44-1.96),HLA-A amino acid position 152(P=1.16 * 10-11,OR=2.24,95%CI=2.83-6.79),HLA-DRB1*13:02(P=8.58 * 10-7,OR=2.28,95%CI=1.64-3.17),HLA-B*07:02(P=9.14 * 10-6,OR=2.40,95%CI=1.61-3.41).By analyzing the spatial conformation of four amino acid variats,it was found that the amino acid residues of the four HLA molecules were all located in the antigen binding regionConclusions In this study,we fine mapping the variants in HLA region and revealed 6 independent signals related to leprosy,which increased the risk variants of leprosy and provided a new direction for the prevention,diagnosis and treatment of leprosy.