Mapping of PARK2 and PACRG overlapping regulatory region reveals LD structure and functional variants in association with leprosy in unrelated indian population groups.

Leprosy is a chronic infectious disease caused by Mycobacterium Leprae, where the host genetic background plays an important role toward the disease pathogenesis. Various studies have identified a number of human genes in association with leprosy or its clinical forms. However, non-replication of results has hinted at the heterogeneity among associations between different population groups, which could be due to differently evolved LD structures and differential frequencies of SNPs within the studied regions of the genome. A need for systematic and saturated mapping of the associated regions with the disease is warranted to unravel the observed heterogeneity in different populations. Mapping of the PARK2 and PACRG gene regulatory region with 96 SNPs, with a resolution of 1 SNP per 1 Kb for PARK2 gene regulatory region in a North Indian population, showed an involvement of 11 SNPs in determining the susceptibility towards leprosy. The association was replicated in a geographically distinct and unrelated population from Orissa in eastern India. In vitro reporter assays revealed that the two significantly associated SNPs, located 63.8 kb upstream of PARK2 gene and represented in a single BIN of 8 SNPs, influenced the gene expression. A comparison of BINs between Indian and Vietnamese populations revealed differences in the BIN structures, explaining the heterogeneity and also the reason for non-replication of the associated genomic region in different populations.

Coding and non-coding polymorphisms in VDR gene and susceptibility to pulmonary tuberculosis in tribes, castes and Muslims of Central India.

Vitamin D receptor (VDR) plays an important role in activating immune response against various infectious agents. This study was aimed to investigate the association between VDR gene polymorphisms and different clinical forms of pulmonary tuberculosis (TB) in different population groups. Four common polymorphisms (TaqI, ApaI, BsmI and FokI) of VDR gene were studied in clinically diagnosed TB patients and healthy controls from Sahariya tribe (n=377), Bhil tribe (n=95), Chhattisgarh tribe (n=33), general population from North-Central (NC) (n=1021) and South-Eastern (SE) region (n=646) and Muslims (n=217). Genotyping was carried out using PCR-RFLP method and re-confirmed by direct sequencing. The haplotype analysis was performed on Haploview 4.1 and statistical analysis was done using SPSS 13.0 software. We found that bb genotype of BsmI polymorphism conferred significant risk to smear positive and multiple drug resistant (MDR) TB in tribes [OR (CI)=3.7 (1.5-9.2), p=0.002], SE population [OR (CI)=2.1 (1.4-3.3), p=0.0004] and Muslims [OR (CI)=6.7 (1.1-39), p=0.01]. The subjects with FF genotype of FokI polymorphism appeared less likely (p=0.004) to develop MDR TB in NC population, whereas, those with Ff [OR (CI)=2.5 (1.3-5.0), p=0.004] and ff [OR (CI)=3.4 (1.2-9.3), p=0.01] genotypes were at high risk of MDR and smear positive disease, respectively. Similarly, tt genotype of TaqI polymorphism was found associated with high risk of smear positive TB in NC [OR (CI)=3.6 (0.9-14.2), p=0.05] as well as in SE [OR (CI)=4.7 (1.8-12.3), p=0.00003] population. Interestingly, tt genotype appeared strongly associated [OR (CI)=8.9 (2.7-29), p=0.00001] with high bacillary load outcome. In conclusion, genetic polymorphisms in VDR gene, alone or in combination (haplotypes) are associated with different clinical outcomes in pulmonary TB.