MassARRAY analysis of twelve cancer related SNPs in esophageal squamous cell carcinoma in J&K, India

Abstract

Background MassARRAY (Agena Bioscience™) combines competitive PCR with MALDI-TOF mass spectrometry (MS) analysis that gives highly accurate, sensitive, and high-throughput methods for the quantitative analysis of variation of gene expression in multiple samples. SNPs (Single Nucleotide Polymorphisms) have a very high potential of discovering disease-gene relationships. SNP-genotyping through MassARRAY is not only a cost-effective genotyping method but also provides a platform to validate variants observed through a high-throughput Next-generation sequencing (NGS). Methods In the present study, we have incorporated the use of matrix-assisted laser desorption/ionization-time of flight, mass spectrometry (MALDI-TOF) as a tool for differentiating genotypes based on the mass of variant. We have performed multiplex PCR and genotyped 12 SNPs in 758 samples (166 cases and 592 controls). The 12 studied SNPs were chosen with a rationale for their association with multiple cancers in literature. Results This is the first study to explore these SNPs with esophageal cancer within the J&K population. Out of 12 SNPs, two SNPs rs12190287 of TCF21 and rs10046 of CYP19A1 were significantly associated with esophageal cancer with Odds Ratio (OR) 1.412 (1.09–1.8 at 95% CI, p = 0.008) and 1.54 (1.21–2.072 at 95% CI, p = 0.0007) within the population of Jammu and Kashmir. Conclusion We explored 12 SNPs that were found to be associated with multiple cancers in literature with esophageal cancer within the population of J&K. This is the first study to find the relation of these SNPs with ESCC within the studied population. This study explores the relation of genetic and environmental factors with the ESCC susceptibility.

The relevance analysis of GSTP1 rs1695 and lung cancer in the Chinese Han population

“…The results in different races and geographic locations are inconsistent, which may be due to the fact that most studies are local studies with small sample sizes. [18][19][20][21][22][23][24][25][26] Recently, a large-scale prospective study of a homogenous white population from 66 races showed that the GSTP1 Ile105Val (rs1695) genotype is associated with improved lung function and can prevent lung cancer and tobacco-related cancers, 19 which is consistent with the conclusion for the Caucasian population in the Cote et al study. 20 We also assessed the relationship between the GSTP1 Ile105Val gene polymorphism and lung cancer susceptibility through our case-control study of 1979 individuals from the Chinese population, and showed that the GSTP1 rs1695 A > G polymorphism is associated with a reduced risk of lung cancer, especially among smokers.…”

“…Since Ryberg et al reported that GSTP1 rs1695 A > G polymorphism was related to lung cancer in 1997, 17 many studies have explored the effects of the GSTP1 rs1695 A > G polymorphisms on the risk of lung cancer. [18][19][20][21][22][23][24][25][26] However, there are few studies on the Chinese population, and the results are inconclusive; therefore, it is not enough to draw definite conclusions about the impact of this mutation on the development of lung cancer.…”

Analysis of Genetic Variation in Circadian Rhythm Genes and Risk of Ovarian Cancer.

“…51206). All these subjects were genotyped by the (Sequenom Mass ARRAY platform) using the 384 well chip according to the standardized protocol which were replicated from the study [21].…”

REV3L Gene Variants rs1002481, rs462779, and rs465646 Lead to Increased Susceptibility Towards Non-Small Cell Lung Cancer in the Population of Jammu and Kashmir.

“…One recent study has put lung cancer as the second most common cancer in the J&K region with 23.5% of all new cases in 2017 [3]. Although several studies have evaluated mutations in key genes, such as genes involved in cell cycle and cell growth regulation, in DNA damage repair pathways and many other pathways with reference to different cancer types in the population of J&K [4][5][6][7], none has evaluated the role of Translesion Synthesis (TLS) polymerase in any cancer type. The DNA sequence can get altered as the result of replication error and by the environmental agents such as tobacco smoking, mutagenic chemicals, and certain types of radiation, which may lead to cancer [8][9][10].…”