The Use of High Resolution Melting (HRM) Method to Detect rs1800629 of Tumor Necrosis Factor-alpha (TNF-alpha) Gene among Tuberculosis Patients
DOI:
https://doi.org/10.31964/mltj.v7i1.362Keywords:
High resolution melting, genotyping, TNF-α gene, tuberculosis, rs1800629Abstract
The rs1800629 polymorphism plays a crucial role in the pathogenesis of infectious and autoimmune diseases. Meanwhile, tuberculosis (TB) remains a health primary infectious disease in Indonesia. The purpose of this study is to evaluate the HRM method in detecting the rs1800629 genotype, in the TNF-α gene’s promoter region, within TB patients. The benefit of this study is to accelerate the detection of rs1800629 with a simple, rapid, and cost-effective method for genotyping and mutation screening that does not include the use of a fluorescent probe. In this experimental study, the rs1800629 genotyped in a total of 25 tuberculosis patients using KAPA HRM kit in MyGo Mini PCR, and all amplified PCR products subsequently dispatched for direct DNA sequencing to Macrogen Inc, South Korea. Based on the results, a 100% concordance find in the genotyping of rs1800629 between HRM and sequencing. The authors provided evidence to use HRM in detecting rs1800629 within the TNF-α promotor region. This application as a genotyping assay in tuberculosis patients is a low-cost, rapid, and accurate detection. However, further studies using the HRM method in case-control samples of tuberculosis are required to evaluate the method’s effectiveness and to obtain more information regarding the genotype’s susceptibility to tuberculosis and its adverse effect treatment, including anti-tuberculosis drug, induced liver injury (AT-DILI), and multidrug-resistant TB (MDR-TB), within the Indonesian population.References
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Chen, C., Li, S., Lu, X., Tan, B., Huang, C., & Qin, L. (2014). High resolution melting method to detect single nucleotide polymorphism of VKORC1 and CYP2C9. International Journal of Clinical and Experimental Pathology, 7(5), 2558–2564.
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Tucker, E. J., & Huynh, B. L. (2014). Genotyping by high-resolution melting analysis. Methods in Molecular Biology, 1145(3), 59–66. https://doi.org/10.1007/978-1-4939-0446-4_5
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Wu, S., Wang, M. G., Wang, Y., & He, J. Q. (2019). Polymorphisms of cytokine genes and tuberculosis in two independent studies. Scientific Reports, 9(1), 1–11. https://doi.org/10.1038/s41598-019-39249-4
Yang, G., Chen, J., Xu, F., Bao, Z., Yao, Y., & Zhou, J. (2014). Association between Tumor Necrosis Factor-a rs1800629 Polymorphism and Risk of Asthma : A Meta-Analysis. PlosOne, 9(6), e99962. https://doi.org/10.1371/journal.pone.0099962
Applied Biosystem. (2010). A Guide to High Resolution Melting ( HRM ) Analysis. Foster City, CA, USA.
Bao, Y., Ma, X., Rasmussen, T. P., & Zhong, X. B. (2018). Genetic Variations Associated with Anti-Tuberculosis Drug-Induced Liver Injury. Current Pharmacology Reports, 4(3), 171–181. https://doi.org/10.1007/s40495-018-0131-8
Bikmaeva, A. R., Sibiryak, S. V., Valiakhmetova, D. K., & Khusnutdinova, E. K. (2002). Polymorphism of the tumour necrosis factor alpha gene in patients with infiltrative tuberculosis and from the Bashkortostan populations. Molecular Biology, 36, 631–633.
Chen, C., Li, S., Lu, X., Tan, B., Huang, C., & Qin, L. (2014). High resolution melting method to detect single nucleotide polymorphism of VKORC1 and CYP2C9. International Journal of Clinical and Experimental Pathology, 7(5), 2558–2564.
Chen, J., Wu, Y., Yu, J., & Shen, J. (2018). Association between tumor necrosis factor alpha rs1800629 polymorphism and risk of osteoarthritis in a Chinese population. Brazilian Journal of Medical and Biological Research, 51(8), e7311. https://doi.org/10.1590/1414-431X20187311
Chen, R., Wang, J., Zhang, Y., Tang, S., & Zhan, S. (2015). Key factors of susceptibility to anti-tuberculosis drug-induced hepatotoxicity. Archives of Toxicology, 89(6), 883–897. https://doi.org/10.1007/s00204-015-1473-1
Do, H. and Dobrovic, A. (2009). Limited copy number - high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies. Molecular Cancer, 8, 82. doi: 10.1186/1476-4598-8-82.
Elahi, M. M., Asotra, K., Matata, B. M., & Mastana, S. S. (2009). Tumor necrosis factor alpha - 308 gene locus promoter polymorphism: An analysis of association with health and disease. Biochimica et Biophysica Acta - Molecular Basis of Disease, 1792(3), 163–172. https://doi.org/10.1016/j.bbadis.2009.01.007
Erali, M., Voelkerding, K. V., & Wittwer, C. T. (2008). High Resolution Melting Applications for Clinical Laboratory Medicine. Exp Mol Phatol, 85(1), 50–58. https://doi.org/10.1016/j.yexmp.2008.03.012.High
Graham, R., Liew, M., Meadows, C., Lyon, E., & Wittwer, C. T. (2005). Distinguishing Different DNA Heterozygotes by High- Resolution Melting. Clinical Chemistry, 51(7), 1295–1298. https://doi.org/10.1373/clinchem.2004.046466
Islam, M. T., Sarkar, S. K., Sultana, N., Begum, M. N., Bhuyan, G. S., Talukder, S., … Mannoor, K. (2018). High resolution melting curve analysis targeting the HBB gene mutational hot-spot offers a reliable screening approach for all common as well as most of the rare beta-globin gene mutations in Bangladesh. BMC Genetics, 19(1), 1–12. https://doi.org/10.1186/s12863-017-0594-3
Khan, S., Mandal, R. K., Jawed, A., Dar, S. A., & Wahid, M. (2016). TNF-α -308 G > A (rs1800629) Polymorphism is Associated with Celiac Disease: A Meta-analysis of 11 Case-Control Studies. Scientific Reports, 6, 32677. https://doi.org/10.1038/srep32677
Kim, S. H., Kim, S. H., Yoon, H. J., Shin, D. H., Park, S. S., Kim, Y. S., … Jee, Y. K. (2012). TNF-α genetic polymorphism -308G/A and antituberculosis drug-induced hepatitis. Liver International, 32(5), 809–814. https://doi.org/10.1111/j.1478-3231.2011.02697.x
Li, M., Han, Y., Wu, T., Feng, Y., & Wang, H. (2013). Tumor Necrosis Factor Alpha rs1800629 Polymorphism and Risk of Cervical Lesions : A Meta-Analysis. PlosOne, 8(8), e69201. https://doi.org/10.1371/journal.pone.0069201
Qidwai, T., & Khan, F. (2011). Tumour Necrosis Factor Gene Polymorphism and Disease Prevalence. Scandinavian Journal of Immunology, 74, 522–547. https://doi.org/10.1111/j.1365-3083.2011.02602.x
Scola, L., Crivello, A., Marino, V., Gioia, V., Serauto, A., Candore, G., … Lio, D. (2003). IL-10 and TNF-alpha polymorphisms in a sample of Sicilian patients affected by tuberculosis: implication for ageing and life span expectancy. Mech Ageing Dev, 124(4), 569–572.
Sivangala, R., Ponnana, M., Thada, S., Joshi, L., Ansari, S., Hussain, H., … Gaddam, S. (2014). Association of Cytokine Gene Polymorphism in Patients with Tuberculosis and Their Houshold Contacs. Human Immunology, 79, 197–205.
Słomka, M., Sobalska-Kwapis, M., Wachulec, M., Bartosz, G., & Strapagiel, D. (2017). High resolution melting (HRM) for high-throughput genotyping-limitations and caveats in practical case studies. International Journal of Molecular Sciences, 18(11). https://doi.org/10.3390/ijms18112316
Tucker, E. J., & Huynh, B. L. (2014). Genotyping by high-resolution melting analysis. Methods in Molecular Biology, 1145(3), 59–66. https://doi.org/10.1007/978-1-4939-0446-4_5
World Health Organization(WHO). (2020). Global Tuberculosis Report 2020. Geneva.
Wu, S., Wang, M. G., Wang, Y., & He, J. Q. (2019). Polymorphisms of cytokine genes and tuberculosis in two independent studies. Scientific Reports, 9(1), 1–11. https://doi.org/10.1038/s41598-019-39249-4
Yang, G., Chen, J., Xu, F., Bao, Z., Yao, Y., & Zhou, J. (2014). Association between Tumor Necrosis Factor-a rs1800629 Polymorphism and Risk of Asthma : A Meta-Analysis. PlosOne, 9(6), e99962. https://doi.org/10.1371/journal.pone.0099962
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Published
2021-06-29
How to Cite
Prayuni, K., Razari, I., Nihayah, S., & Yuliwulandari, R. (2021). The Use of High Resolution Melting (HRM) Method to Detect rs1800629 of Tumor Necrosis Factor-alpha (TNF-alpha) Gene among Tuberculosis Patients. Medical Laboratory Technology Journal, 7(1), 66–72. https://doi.org/10.31964/mltj.v7i1.362
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