Optimizing the PCR HRM for initial study of the association between SNP rs10941679 and breast cancer in Vietnamese population

Abstract

As the second most popular cancer in the world, breast cancer affects millions of people and causes a large number of deaths every year. Identifying the genetic marker is one of approaches of early diagnosis for following cancer and give a correct treatment. Many recent studies have shown several SNPs including rs10941679 (located at the uptream of MRPS30 gene) are strongly associated with breast cancer in European and other populations. The association between rs10941679 and breast cancer in Vietnamese population has been investigated in this study using High Resolution Melt (HRM) method as a tool for genotyping. HRM was designed on Umelt sofware and was optimized based on annealing temperature and MgCl₂ concentration gradient in order to have 3 distinct melting curves from 3 genotypes of rs10941679. The optimal HRM conditions were selected with Tm=58 ^oC and MgCl₂=3.0 mM and 100 Cases/control samples were genotyped by the optimimal HRM condition. The results showed that the frequency of the risk allele G in case and control group were 48.5 % and 54.0 %, respectively. Regression analysis on the presense of the risk allele and risk allele-containing genotypes has shown no association between rs10941679 and breast cancer in Vietnamese population (OR = 0.80; 95% CI =  [0.54 – 1.19]; P_G = 0.27; PGG/GA = 0.56). The power of this result was estimated to be 12.02 %. To obtain the power up to 90 %, the sample size up to 1691 cases/controls is needed. Due to its low posibility in the assocation with breast cancer in Vietnamese population, rs1094169 is not recommended for further study in finding the genetic for markers cancer in Vietnamese population.