Abstract
Various Genome-wide association studies (GWAS) have reported the association of variant rs2494938 with lung cancer. However, genetic association of LRFN2 genetic variation with non-small cell lung cancer (NSCLC) in North Indian population remained unexplored. We conducted a case–control association study using TaqMan-based chemistry in which a total of 619 individuals, 189 NSCLC cases and 430 controls, were genotyped to explore the association of rs2494938 genetic variant of the LRFN2 gene with NSCLC patients from North India. The allele ‘G’ (risk allele) of the genetic variant rs2494938 was significantly associated with the NSCLC [OR = 1.51 (1.18–1.93 at 95% CI); p value = 0.0009]. Genetic association was also explored by applying different genetic models (Dominant, Additive). These results suggest that rs2494938 polymorphism of the LRFN2 gene is a risk factor in the North Indian populations to develop NSCLC. The LD (Linkage Disequilibrium) plot demonstrates the variant and its LD SNPs (r2 > 0.8) and the variant has direct regulatory effect, which could affect the overall physiology of the gene. These findings could be used as diagnostic and prognostic markers in clinical studies of lung cancer patients in North Indian population groups. The present study also provides an important evidence on the genetic etiology of NSCLC in North Indian populations and further expounds GWAS findings on the role of LRFN2 in lung cancer risk. This study provides the holistic view about the non-small cell lung cancer in Jammu and Kashmir, North Indian population and it can be a hallmark of cancer if verified on a very large sample size (cohort).
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RK and GRB acknowledge Department of science & technology, Government of India project (DST/SSTP/J&K/459) for financial assistance.
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13205_2020_2403_MOESM1_ESM.tif
Supplementary file1 Supplementary Fig1: Showing the interaction of LRFN2 with other important genes using String Software (https://string-db.org/) v.11.0. The interaction among the genes depends upon the thickness of the nodes. Greater the thickness of nodes, greater is the relationship among the genes. LRFN2 strongly interacts with DLG3 and DLG4. (TIF 235 kb)
13205_2020_2403_MOESM2_ESM.tif
Supplementary file2 Supplementary figure 2: showing the LD of the genetic variant rs2494938 of LRFN2 using genetic variant centered annotation browser SNIPA 3.0. Linkage disequilibrium plot shows the amount of correlation between a sentinel variant (blue coloured) and its surrounding variants (red coloured). The plot demonstrates the variant and its LD SNP’s (r2 > 0.8) and the variant has direct regulatory effect, which could affect the overall physiology of the gene. (TIF 73 kb)
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Bhat, G.R., Verma, S., Bhat, A. et al. Genetic variant rs2494938 of LRFN2 gene is associated with non-small cell lung cancer risk in North-Indian population. 3 Biotech 10, 410 (2020). https://doi.org/10.1007/s13205-020-02403-1
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DOI: https://doi.org/10.1007/s13205-020-02403-1