Developing a high resolution melting method for genotyping and predicting association of SNP rs353291 with breast cancer in the Vietnamese population

Authors

  • Luan Huu Huynh Faculty of Biology and Biotechnology, University of Science, VNUHCM, Ho Chi Minh City, Vietnam
  • Phuong Thi-Kim Bui School of Biotechnology, International University, VNUHCM, Ho Chi Minh City, Vietnam
  • Thanh Thi-Ngoc Nguyen Faculty of Biology and Biotechnology, University of Science, VNUHCM, Ho Chi Minh City, Vietnam
  • Hue Thi Nguyen Faculty of Biology and Biotechnology, University of Science, VNUHCM, Ho Chi Minh City, Vietnam

DOI:

https://doi.org/10.15419/bmrat.v4i12.387

Keywords:

Breast cancer, HRM, miRNA, SNP rs353291, Cancer

Abstract

Introduction: Breast cancer is the one of the most common types of cancer as well as the second leading cause of cancer death in women in the world. In recent studies, microRNAs (miRNAs) have been demonstrated to play a crucial role as a new potential biomarker in the association with breast cancer. Single Nucleotide Polymorphisms (SNPs) located on specific miRNA may result in breast cancer. Among the SNPs, SNP rs353291 has shown to be associated with breast cancer in individuals of Caucasian background. Furthermore, this SNP is observed in a high percentage of mutant alleles in the Vietnamese population. Thus, SNP rs353291 was selected as a candidate SNP for investigation in this study. The frequency of SNP rs353291 was evaluated by High Resolution Melting (HRM) method, which is a highly powerful method to detect variants in DNA sequence, especially for SNP genotyping.

Methods: In this study, the association between this SNP and risk of breast cancer in the Vietnamese population was evaluated in 90 cases and 96 healthy controls via genotyping using an optimized HRM protocol.

Result: The genotyping results revealed that SNP rs353291 is a polymorphism in the Vietnamese population. We have successfully identified frequencies of AA, AG and GG to be 40%, 42.2% and 17.8%, respectively. In particular, the calculated frequencies of allele G was 61.1% while risk allele A was 38.9%. The association between this SNP and breast cancer in Vietnam revealed that there is an obvious decreased risk of breast cancer among Vietnamese population when comparing G allele to A allele (G vs A: OR=0.92, 95% CI: 0.62-1.36, p= 0.677); the results also showed that heterozygote model had a reduced risk of breast cancer compared to dominant model (GA+GG vs AA: OR=0.94, 95% CI: 0.52-1.70, p=0.839).

Conclusion: However, since the p-values were >0.05, our results only show a correlation rather than a significant association between SNP rs353291 and breast cancer risk in the Vietnamese population.

Author Biography

  • Hue Thi Nguyen, Faculty of Biology and Biotechnology, University of Science, VNUHCM, Ho Chi Minh City, Vietnam
    nthue@hcmus.edu.vn

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<li>Chacon-Cortes, D., Smith, R. A., Haupt, L. M., Lea, R. A., Youl, P. H., &amp; Griffiths, L. R. (2015). Genetic association analysis of miRNA SNPs implicates MIR145 in breast cancer susceptibility. BMC Medical Genetics, 16(1), 107.&nbsp;<a href="https://doi.org/10.1186/s12881-015-0248-0">https://doi.org/10.1186/s12881-015-0248-0</a> </li>
<li>Chen, Q.-H., Wang, Q.-B., &amp; Zhang, B. (2014). Ethnicity modifies the association between functional microRNA polymorphisms and breast cancer risk: A HuGE meta-analysis. Tumour Biology, 35(1), 529–543.&nbsp;<a href="https://doi.org/10.1007/s13277-013-1074-7">https://doi.org/10.1007/s13277-013-1074-7</a> </li>
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<li>GLOBOCAN (2012). GLOBOCAN 2012: Estimated Incidence, Mortality and Prevalence Worldwide in 2012.</li>
<li>Hue, N. T., Chan, N. D. H., Phong, P. T., Linh, N. T. T., &amp; Giang, N. D. (2012). Extraction of human genomic DNA from dried blood spots and hair roots. International Journal of Bioscience, Biochemistry, Bioinformatics, 2, 21–26.&nbsp;<a href="https://doi.org/10.7763/IJBBB.2012.V2.62">https://doi.org/10.7763/IJBBB.2012.V2.62</a> </li>
<li>Jovanovic, M., &amp; Hengartner, M. (2006). miRNAs and apoptosis: RNAs to die for. Oncogene, 25(46), 6176–6187.&nbsp;<a href="https://doi.org/10.1038/sj.onc.1209912">https://doi.org/10.1038/sj.onc.1209912</a> </li>
<li>Kim, S.-J., Oh, J.-S., Shin, J.-Y., Lee, K.-D., Sung, K. W., Nam, S. J., &amp; Chun, K.-H. (2011). Development of microRNA-145 for therapeutic application in breast cancer. Journal of Controlled Release, 155(3), 427–434.&nbsp;<a href="https://doi.org/10.1016/j.jconrel.2011.06.026">https://doi.org/10.1016/j.jconrel.2011.06.026</a> </li>
<li>Kong, Y. W., Ferland-McCollough, D., Jackson, T. J., &amp; Bushell, M. (2012). microRNAs in cancer management. The Lancet. Oncology, 13(6), e249–e258.&nbsp;<a href="https://doi.org/10.1016/S1470-2045(12)70073-6">https://doi.org/10.1016/S1470-2045(12)70073-6</a> </li>
<li>O’Day, E., &amp; Lal, A. (2010). MicroRNAs and their target gene networks in breast cancer. Breast Cancer Research, 12(2), 201.&nbsp;<a href="https://doi.org/10.1186/bcr2484">https://doi.org/10.1186/bcr2484</a> </li>
<li>Onay, V. Ü., Briollais, L., Knight, J. A., Shi, E., Wang, Y., Wells, S., . . . Ozcelik, H. (2006). SNP-SNP interactions in breast cancer susceptibility. BMC Cancer, 6(1), 114.&nbsp;<a href="https://doi.org/10.1186/1471-2407-6-114">https://doi.org/10.1186/1471-2407-6-114</a> </li>
<li>Qi, P., Wang, L., Zhou, B., Yao, W., Xu, S., Zhou, Y., &amp; Xie, Z. (2015). Associations of miRNA polymorphisms and expression levels with breast cancer risk in the Chinese population. Genetics and Molecular Research, 14(2), 6289–6296.&nbsp;<a href="https://doi.org/10.4238/2015.June.11.2">https://doi.org/10.4238/2015.June.11.2</a> </li>
<li>Song, F.-J., &amp; Chen, K.-X. (2011). Single-nucleotide polymorphisms among microRNA: Big effects on cancer. Chinese Journal of Cancer, 30(6), 381–391.&nbsp;<a href="https://doi.org/10.5732/cjc.30.0381">https://doi.org/10.5732/cjc.30.0381</a> </li>
<li>Spizzo, R., Nicoloso, M., Lupini, L., Lu, Y., Fogarty, J., Rossi, S., . . . Liu, X. (2010). miR-145 participates with TP53 in a death-promoting regulatory loop and targets estrogen receptor-α in human breast cancer cells. Cell Death and Differentiation, 17(2), 246–254.&nbsp;<a href="https://doi.org/10.1038/cdd.2009.117">https://doi.org/10.1038/cdd.2009.117</a> </li>
<li>Sun, G., Yan, J., Noltner, K., Feng, J., Li, H., Sarkis, D. A., . . . Rossi, J. J. (2009). SNPs in human miRNA genes affect biogenesis and function. RNA (New York, N.Y.), 15(9), 1640–1651.&nbsp;<a href="https://doi.org/10.1261/rna.1560209">https://doi.org/10.1261/rna.1560209</a> </li>
<li>Takahashi, R., Miyazaki, H., &amp; Ochiya, T. (2015). The roles of microRNAs in breast cancer. Cancers (Basel), 7(2), 598–616.&nbsp;<a href="https://doi.org/10.3390/cancers7020598">https://doi.org/10.3390/cancers7020598</a> </li>
<li>Trieu, P. D. Y., Mello-Thoms, C., &amp; Brennan, P. C. (2015). Female breast cancer in Vietnam: A comparison across Asian specific regions. Cancer Biology &amp; Medicine, 12, 238.</li>
<li>van Schooneveld, E., Wildiers, H., Vergote, I., Vermeulen, P. B., Dirix, L. Y., &amp; Van Laere, S. J. (2015). Dysregulation of microRNAs in breast cancer and their potential role as prognostic and predictive biomarkers in patient management. Breast Cancer Research, 17(1), 21.&nbsp;<a href="https://doi.org/10.1186/s13058-015-0526-y">https://doi.org/10.1186/s13058-015-0526-y</a> </li>
<li>Vuong, D. A., Velasco-Garrido, M., Lai, T. D., &amp; Busse, R. (2010). Temporal trends of cancer incidence in Vietnam, 1993-2007. Asian Pacific Journal of Cancer Prevention, 11, 739–745.</li>
<li>Wang, S., Bian, C., Yang, Z., Bo, Y., Li, J., Zeng, L., . . . Zhao, R. C. (2009). miR-145 inhibits breast cancer cell growth through RTKN. International Journal of Oncology, 34, 1461.</li>
<li>Zhang, J., Sun, Q., Zhang, Z., Ge, S., Han, Z., &amp; Chen, W. (2013). Loss of microRNA-143/145 disturbs cellular growth and apoptosis of human epithelial cancers by impairing the MDM2-p53 feedback loop. Oncogene, 32(1), 61–69.&nbsp;<a href="https://doi.org/10.1038/onc.2012.28">https://doi.org/10.1038/onc.2012.28</a> </li>
</ol>

Published

2017-12-08

Issue

Section

Methodology

How to Cite

Developing a high resolution melting method for genotyping and predicting association of SNP rs353291 with breast cancer in the Vietnamese population. (2017). Biomedical Research and Therapy, 4(12), 1812-1831. https://doi.org/10.15419/bmrat.v4i12.387

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