MassARRAY-based single nucleotide polymorphism analysis in breast cancer of north Indian population

Abstract

Background Breast Cancer (BC) is associated with inherited gene mutations. High throughput genotyping of BC samples has led to the identification and characterization of biomarkers for the diagnosis of BC. The most common genetic variants studied are SNPs (Single Nucleotide Polymorphisms) that determine susceptibility to an array of diseases thus serving as a potential tool for identifying the underlying causes of breast carcinogenesis. Methods SNP genotyping employing the Agena MassARRAY offers a robust, sensitive, cost-effective method to assess multiple SNPs and samples simultaneously. In this present study, we analyzed 15 SNPs of 14 genes in 550 samples (150 cases and 400 controls). We identified four SNPs of genes TCF21, SLC19A1, DCC, and ERCC1 showing significant association with BC in the population under study. Results The SNPs were rs12190287 (TCF21) having OR 1.713 (1.08–2.716 at 95% CI) p-value 0.022 (dominant), rs1051266 (SLC19A1) having OR 3.461 (2.136–5.609 at 95% CI) p-value 0.000000466 (dominant), rs2229080 (DCC) having OR 0.6867 (0.5123–0.9205 at 95% CI) p-value 0.0116 (allelic) and rs2298881 (ERCC1) having OR 0.669 (0.46–0.973 at 95% CI), p-value 0.035 (additive) respectively. The in-silico analysis was further used to fortify the above findings. Conclusion It is further anticipated that the variants should be evaluated in other population groups that may aid in understanding the genetic complexity and bridge the missing heritability.

Von Hippel-Lindau gene single nucleotide polymorphism (rs1642742) may be related to the occurrence and metastasis of HBV-related hepatocellular carcinoma

“…Our results suggested that there was correlation between rs1642742 and metastasis and the allele A might be associated with tumor metastasis. Of course, the correlation between SNP and tumor metastasis had been reported in previous literatures, including lung cancer, breast cancer, gastric cancer, prostate cancer, and so on [42–45] . Rs1642742 is residing in the 3′UTR of the VHL , which plays an important role in mRNA translocation, stability and translational regulation.…”

“…Of course, the correlation between SNP and tumor metastasis had been reported in previous literatures, including lung cancer, breast cancer, gastric cancer, prostate cancer, and so on. [42][43][44][45] Rs1642742 is residing in the 3 0 UTR of the VHL, which plays an important role in mRNA translocation, stability and translational regulation. The variant allele of rs1642742 may affect the ability of miRNA to bind to its sequence, which in turn affects the VHL gene expression and may lead to tumor metastasis.…”

Evaluation of 17 genetic variants in association with leukemia in the north Indian population using MassARRAY Sequenom

“…For SNP genotyping, the Agena MassARRAY platform was used and the whole protocol and conditions were replicated from our previous studies. [ 11,12 ] DNA sample of 1 μl at 10 ng/μl concentration was loaded in 384‐well PCR plates, which was dried at 85°C for 10 min. The reaction mixture consists of dNTPs, primer pool (forward and reverse primers pool) reaction buffers, and DNA polymerase.…”

“…11 rs2494752 AKT1 Hepatocellular carcinoma [60] BHAT ET AL. ATM/ATR pathway [63,64] step in exploring genetic factors associated with leukemia, functional studies are now necessary to exemplify the exact biological function of these genes in leukemia for validation. Thus, the study needs to be replicated in the large cohorts for functional validation.…”

“…T A B L E 5 The variants that are not associated with leukemia in the studied population 11 rs2494752 AKT1 Hepatocellular carcinoma [60] Our study is the first study that provides the preliminary data that highlights these variants in association with leukemia from the Jammu ATM/ATR pathway [63,64]…”