Optimization of high resolution melting method for genotyping and estimating the frequency of snp RS 1219648 on the FGFR2 gene in Vietnamese breast cancer patients

Abstract

Breast cancer is the most frequent malignancy and the leading cause of cancer death among females. SNPs linked to the breast cancer have been identified in Genome Wide Association studies. Among those, SNPs in FGFR2 gene are found to be important markers for breast cancer susceptibility. In this study, High resolution melting analysis was designed for screening the A and G alleles of SNP rs1219648 in FGFR2 gene in a group of 108 breast cancer blood samples. DNA is extracted by the Salting-out method. The HRM method was optimized based on the concentration of PCR reagents such as DNA, Mg2+, and primer to get the optimal condition. Despite some disadvantages and limits during employing HRM method, this study showed that the HRM analysis is a reliable, simple tool and effective cost method for identifying the SNP rs1219648 in FGFR2 gene. Analysis of 109 breast cancer samples revealed that the frequency of A allele was 57% and the frequency of G allele was found to be 43%. The frequency of minor G allele supports to the further association study to identify the genetic markers for early diagnosis of breast cancer for the Vietnamese. Key words: Breast cancer FGFR2 gene SNP rs1219648 HRM method