Identification of a novel IRGM promoter single nucleotide polymorphism associated with tuberculosis |
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| Authors: | Nanying Che Song Li Tiejie Gao Zhiguo Zhang Yuefei Han Xuxia Zhang Yong Sun Yi Liu Zhaogang Sun Jianyuan Zhang Weicong Ren Miao Tian Yan Li Wensheng Li Jun Cheng Chuanyou Li |
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| Institution: | 1. Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea;2. School of Biological Sciences, College of Natural Science, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-747, Republic of Korea;1. State Key Laboratory of Earthquake Dynamics, Institute of Geology, China Earthquake Administration, Beijing 100029, China;2. Earth Observatory of Singapore, Nanyang Technological University, 639798, Singapore;3. Earthquake Administration of Shaanxi Province, Xi''an 710068, China;4. School of Earth Science and Geological Engineering, Sun Yat-Sen University, Guangzhou 510275, China;5. Center for Neotectonics Studies, University of Nevada, Reno 89557, USA |
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| Abstract: | BackgroundHuman immunity-related GTPase M (IRGM) is found to play an important role in defense against intracellular pathogen Mycobacterium tuberculosis in vitro by regulating autophagy. To verify whether single nucleotide polymorphisms (SNPs) in the promoter region of IRGM gene are associated with tuberculosis (TB) 1.7 kb IRGM promoter region was sequenced and SNP analysis was conducted in TB patients and healthy controls.MethodsA simple and rapid procedure for extracting DNA from clotted-blood was developed in this study. A 1.7 kb IRGM promoter region was amplified and sequenced for nucleotide polymorphism search. Then, 3 SNPs were selected and analyzed in 216 TB patients and 275 healthy subjects by ligase detection reaction technique.ResultsDNA extracted by our method was of high quality and suitable for PCR, sequencing, and genotyping. We identified 29 polymorphisms in the 1.7 kb IRGM promoter region, including 11 novel polymorphisms not yet reported. Large population analysis showed that frequencies of ? 1208A allele (P = 0.031), ? 1208AA genotype (P = 0.042), and ? 1208A/?1161C/?947C (P = 0.035) and ? 1208G/?1161C/?947C (P = 0.030) haplotypes in cases were significantly different from those in controls.ConclusionsIn 1.7 kb IRGM promoter region, only ? 1208A/G polymorphism is associated with susceptibility to TB. |
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