Correlation between single nucleotide polymorphisms in long non-coding RNA and survival in patients with laryngeal squamous cell carcinoma

Objective To identify single nucleotide polymorphisms (SNPs) in long non-coding RNA (LncRNA) that influences the survival of laryngeal squamous cell carcinoma (LSCC) patients. Methods We performed a genome wide association study (GWAS) on the survival of 98 LSCC patients who were previously recruited from the Cancer Hospital,the Chinese Academy of Medical Sciences from January 2000 to December 2012,and screened out 57 promising SNPs located in LncRNAs,which were replicated in the samples of 537 LSCC patients.The 537 LSCC patients were recruited from January 2009 to March 2018 in Chinese PLA General Hospital,the First Affiliated Hospital of Anhui Medical University and Shandong Provincial ENT Hospital.Genotyping analysis was performed using Sequenom MassARRAY system.The Kaplan-Meier survival curves of different genotypes were compared using log-rank tests.Hazard ratios (HRs) and their 95% confidence intervals (CIs) of the different genotypes were estimated through multivariate Cox proportional hazard models. Results The loci of rs17059513,rs10208830 and rs2901182 were significantly associated with the overall survival of LSCC patients.The risk of death in patients with rs17059513 AG genotype increased compared with rs17059513 AA genotype,with the HR (95% CI) being 2.23 (1.46-3.39).The risk of death in patients with rs10208830 CC genotype was lower compared with rs10208830 GG genotype,with the HR (95% CI) being 0.75 (0.61-0.92).The risk of death in patients with rs2901182 CT genotype increased compared with rs2901182 CC genotype,with the HR (95% CI) being 2.10 (1.11-4.00).Multivariate Cox regression analysis revealed the HRs (95% CIs) of 1.95 (1.34-2.83) for rs17059513 and 0.77 (0.63-0.93) for rs10208830 using the additive model,the HRs (95% CIs) of 2.19 (1.45-3.32) for rs17059513 and 0.74 (0.56-0.98) for rs10208830 using the dominant model,and the HR (95% CI) of 1.59 (1.10-2.30) for rs10208830 using the recessive model.We identified three SNPs having a joint effect on survival through accumulation of risk alleles or risk genotypes.Patients with 3 risk alleles or 2-3 risk genotypes had a higher risk of death,with the HRs (95% CI) being 3.11 (1.71-5.65) and 3.24 (1.97-5.32),respectively.Conclusions We have identified three new SNPs closely related to the prognosis for LSCC patients.These variations may serve as potential biomarkers for predicting the survival of LSCC patients.