Single nucleotide polymorphisms in an indian cohort and association of CNTN4, MMP2 and SNTB1 variants with oral cancer

Publication date: Available online 23 March 2017
Source:Cancer Genetics
Author(s): Subuhi Yete, Sultan Pradhan, Dhananjaya Saranath
Oral cancer is a high incidence cancer in India primarily due to the prevalent tobacco/areca nut chewing habits and hence a major health concern. India constitutes 26% of the global oral cancer burden. Besides the well-established risk factors, the genomic constitution of an individual plays a role in oral cancer. The aim of the current study was to analyse genomic variants represented as single nucleotide polymorphisms (SNPs), analyse their prevalence and investigate risk association of allelotypes/genotypes to oral cancers. Eleven SNPs in genes associated with biological functions were analysed in an Indian cohort (n=1000) comprising 500 oral cancer patients and 500 long term tobacco habitués as controls, using Allelic discrimination Real-Time PCR assay with SYBR Green dye. Fisher's exact test and Odds Ratio was used for statistical analysis. Increased risk was observed for rs9849237 CC [P=0.008; OR 1.412 (1.09-1.82)] and rs243865 CT [P=0.004; OR 1.469 (1.13-1.90)] genotypes, whereas rs9849237 CT [P=0.034; OR 0.755 (0.58-0.97)], rs243865 CC [P=0.002; OR 0.669 (0.51-0.86)] and rs10090787 CC [P=0.049; OR 0.774 (0.60-0.99)] genotypes indicated decreased risk to oral cancer. The other SNPs showed equidistribution in both groups. Our data indicated genotypes and alleles in specific SNPs rs9849237, rs243865 and rs10090787 with increased/decreased risk to oral cancer.



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