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Objective The present study is aimed to investigate potential association of SNPs in exon 7 of the MRC1 gene with pulmonary tuberculosis (TB) in Chinese Han and Kazak populations. Methods Six SNPs (G1186A, G1195A, T1212C, C1221G, C1303T and C1323T) of the MRC1 gene were genotyped using the PCR and DNA sequencing methods in 454 Chinese Han and 595 Uygur subjects. Linkage disequilibrium analysis was performed to determine any linkage between the polymorphic sites. Results In a Chinese Han population, we found that the allele frequency of G1186A had a significant difference in frequency distribution between the two groups ( P =0.037; OR=0.76; 95% CI, 0.58-0.98). The AG genotypes were significantly correlated with pulmonary TB ( EM>P /EM><0.01; OR=0.57; 95% CI, 0.37-0.87). After adjustment for age and gender, G1186A site was found to be dominant ( EM>P /EM><0.01; OR=0.59; 95% CI, 0.40-0.87), over-dominant ( EM>P/EM> =0.045; OR=0.69; 95% CI, 0.47-0.99) and additive models (EM> P/EM> =0.041; OR=0.76; 95% CI, 0.59-0.99) in association with pulmonary TB. In the Chinese Uygur population, we found that the allele frequency of G1186A was a significant difference between the two groups ( EM>P/EM> =0.031; OR=1.29; 95% CI=1.02-1.62). The AA genotype was significantly correlated with pulmonary TB ( EM>P /EM>=0.033; OR=1.64; 95% CI=1.04-2.60). After adjustment for age and gender, G1186A site was found to be additive models ( EM>P/EM> =0.033; OR=1.28; 95% CI=1.02-1.61) in association with pulmonary TB. By calculating the pairwise LD between 6 SNPs in the Chinese Uygur population, we found that the frequency of the haplotype GGTCCT ( EM>P /EM>=0.032; OR=0.75; 95% CI=0.57-0.97) and GGTCCC (EM> P/EM> =0.044; OR=0.57; 95% CI=0.33-0.99) was significantly associated with pulmonary TB. No association was found between the other 5 SNPs and TB ( EM>P /EM>>0.05) in the Chinese population. Conclusion This study reports that genetic variants in the MRC1 gene may be associated with pulmonary TB in a Chinese population.