Optimization of high resolution melting method for genotyping and estimating the frequency of SNP rs11568820 on VDR Gene in Vietnamese breast cancer patient

Abstract

Breast cancer is the most popular cancer and it is acknowledged as the second cause of death in women worldwide. Many researchers have concluded that breast cancer is the cumulative result of multiple environmental factors and genetic factors. Numerous studies have found that vitamin D and its analogues reduce cell proliferation in breast cancer cell lines and tumor samples and may hence play a protective role against breast cancer development. The active form of vitamin D [1,25 (OH)2D3] will bind with vitamin D receptor (VDR). This ligand-receptor complex will then act as a transcription factor to regulate transcription of more than 60 genes involved in anti-proliferative, differentiating, anti-metastatic and pro-apoptotic effects on cells and the cell cycle. Cdx2 (rs11568820), which was considered as a popular single nucleotide polymorphisms (SNP) in VDR gene, hampered its effect on lowering VDR expression and could associate with increased susceptibility to breast cancer risk. This SNP varies in both frequency and the way it associates with breast cancer risk in diverse populations, but among all VDR polymorphisms, limited data was available on VDR-Cdx2 polymorphism and breast cancer susceptibility. These genotypic distributional properties might contribute to this SNP’s specificity for each ethnic group even for Vietnamese and became the target of our study. This study aimed to investigate the frequency of SNP Cdx2 in Vietnamese population using optimized HRM method. Therefore, within the scope of this research, the frequency of SNP Cdx2 was estimated by performing High Resolution Melting (HRM) technique on 100 extracted DNA samples from Vietnamese breast cancer cases. The association between this SNP and risk of breast cancer in Vietnamese breast cancer patients was performed by comparing the frequency of SNP alleles in 100 cases and control which obtained data from 1000 Genome Database. The result showed that SNP Cdx2 was not associated with risk of breast cancer since P value > 0.05 in all genetic models. Due to a small sample size, the power of this study is relatively low (19.2%) and thus the result of the test for association was unsupported. Therefore, a further study, which performs in larger and more reliable sample size and additional examination on other SNPs in VDR are required to assess their relationships with breast cancer. Keywords: Breast cancer Vitamin D polymorphisms Cdx2 (rs11568820) High resolution melting (HRM)