Genetic variant rs2494938 of LRFN2 gene is associated with non-small cell lung cancer risk in North-Indian population
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ORIGINAL ARTICLE
Genetic variant rs2494938 of LRFN2 gene is associated with non‑small cell lung cancer risk in North‑Indian population Gh. Rasool Bhat1 · Sonali Verma1 · Amrita Bhat1 · Ruchi Shah2 · Itty Sethi2 · Khursheed A. Dar3 · Deepak Abrol4 · Audesh Bhat5 · Rakesh Raina6 · Rakesh Kumar1 Received: 15 July 2020 / Accepted: 19 August 2020 / Published online: 28 August 2020 © King Abdulaziz City for Science and Technology 2020
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). Keywords Taqman genotyping chemistry · Non-small cell lung cancer · North India
Introduction Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13205-020-02403-1) contains supplementary material, which is available to authorized users. * Rakesh Kumar [email protected] 1
Cancer Genetics Research Group, ICMR, Centre for Advanced Research, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K UT, India
2
Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, J&K UT, India
3
Chest Disease Hospital, Government Medical College, Srinagar, J&K UT, India
4
Department of Radiotherapy, Govt. Medical College Kathua, Jammu, J&K UT, India
5
Central University of Jammu, Jammu, J&K UT, India
6
Siddhi Vinayak Dental and Health Care Centre, Roop Nagar Jammu, Jammu, J&K UT, India
Lung cancer is a heterogeneous disease and a major global
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