Dataset Information

A rare variant at 11p13 is associated with tuberculosis susceptibility in the Han Chinese population.

ABSTRACT: Genome-wide association studies (GWASs) have yet to be conducted for tuberculosis (TB) susceptibility in China. Two previously identified single nucleotide polymorphisms (SNPs) from tuberculosis GWASs, rs2057178 and rs4331426, were evaluated for TB predisposition. The associations between SNPs and gene expression levels were analyzed using the genomic data and corresponding whole-genome expression of the Han Chinese in Beijing, China. Genotyping was successfully completed for 763 pulmonary TB patients and 763 healthy controls. The T allele of the rare variant rs2057178 was significantly associated with TB predisposition (?(2)?= 14.07, P = 0.0002). Meanwhile, the CT genotype of rs2057178 was associated with a decreased risk of TB (adjusted OR = 0.52, 95% CI, 0.34-0.78). The CT genotype of rs2057178 was also associated with decreased expression levels of infection-related gene, suppressor of cytokine signaling 2 (SOCS2), and increased expression levels of v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog B (MAFB). No gene expression levels were found to be associated with the genotype of rs4331426. We found that the rare variant rs2057178 was significantly associated with TB in the Han Chinese population. Moreover, the expression levels of MAFB and SOCS2 correlated with rs2057178 and might be potential candidates for assessing TB susceptibility.

SUBMITTER: Chen C

PROVIDER: S-EPMC4817510 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

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A rare variant at 11p13 is associated with tuberculosis susceptibility in the Han Chinese population.

Chen Cheng C Zhao Qi Q Hu Yi Y Shao Yan Y Li Guoli G Zhu Limei L Lu Wei W Xu Biao B

Scientific reports 20160401

Genome-wide association studies (GWASs) have yet to be conducted for tuberculosis (TB) susceptibility in China. Two previously identified single nucleotide polymorphisms (SNPs) from tuberculosis GWASs, rs2057178 and rs4331426, were evaluated for TB predisposition. The associations between SNPs and gene expression levels were analyzed using the genomic data and corresponding whole-genome expression of the Han Chinese in Beijing, China. Genotyping was successfully completed for 763 pulmonary TB pa ...[more]

PMID: 27035414

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Project description:Tuberculosis (TB) is an important public health problem. Studies indicated that TAP plays a key role in the presentation and transport of antigenic peptides during anti-M.tb infection. Given the important biological role of the TAP gene involved in anti-M.tb infection, a family-based case-control study including 133 tuberculosis patients, 107 healthy household contacts, and 173 healthy controls was conducted to assess the association between TAP gene polymorphisms and TB susceptibility. The basic information of subjects and their blood samples were collected. Four SNPs including rs1135216, rs1057141, rs241447, and rs3819721 were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Our results suggested that BMI, residence, bedroom crowding, indoor humidity, fitness activities, history of smoking, and TB exposure history were associated with the occurrence of tuberculosis (P < 0.05). A significant association was observed between the TAP1 rs1135216 CT/CC genotype and increased TB risk, and the ORs were 2.56 (95% CI 1.31-4.99) and 6.73 (95% CI 1.33-34.02), respectively. TAP2 rs3819721 GG genotype carriers also showed an increased risk of TB when compared TB patients to healthy household contacts. Haplotype analysis revealed that the haplotype CT at rs1057141 and rs1135216 (OR = 11.34, 95% CI 1.49-86.56; OR = 7.45, 95% CI 1.43-38.76), as well as TA at rs241447 and rs3819721 (OR = 2.20, 95% CI 1.07-4.56) had a significantly increased risk of TB. The genetic risk scores (GRS) analysis of the four loci indicated that the risk of tuberculosis increased with increasing GRS scores in TB vs HHC (Ptrend = 0.010) and in TB vs HC (Ptrend = 0.001). In conclusion, our findings suggested that the SNPs of rs1135216 and rs3819721 were associated with TB susceptibility among the tuberculosis-prone families in the Chinese Han population and the risk of developing tuberculosis increases with the number of risk alleles, which could help identify high-risk groups in time and take scientific preventive measures. Further cohort studies with large samples are needed to validate the role of TAP gene variants on TB susceptibility.

Dataset Information

A rare variant at 11p13 is associated with tuberculosis susceptibility in the Han Chinese population.

Publications

A rare variant at 11p13 is associated with tuberculosis susceptibility in the Han Chinese population.

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