Difference of copy number variation in blood of patients with lung cancer

Abstract

Background: Lung cancer is the leading cause of cancer-related deaths worldwide. Copy number variation (CNV) in several genetic regions correlate with cancer susceptibility. Hence, this study evaluated the association between CNV and non-small cell lung cancer (NSCLC) in the peripheral blood. Methods: Blood samples of 150 patients with NSCLC and 150 normal controls were obtained from a bioresource center (Seoul, Korea). Through an epigenome-wide analysis using the MethylationEPIC BeadChip method, we extracted CNVs by using an SVS8 software-supplied multivariate method. We compared CNV frequencies between the NSCLC and controls, and then performed stratification analyses according to smoking status. Results: We acquired 979 CNVs, with 582 and 967 copy-number gains and losses, respectively. We identified five nominally significant associations (ACOT1, NAA60, GSDMD, HLA-DPA1, and SLC35B3 genes). Among the current smokers, the NSCLC group had more CNV losses and gains at the GSDMD gene in chromosome 8 ( P=0.02) and at the ACOT1 gene in chromosome 14 ( P=0.03) than the control group. It also had more CNV losses at the NAA60 gene in chromosome 16 ( P=0.03) among non-smokers. In the NSCLC group, current smokers had more CNV gains and losses at the ACOT1 gene in chromosome 14 ( P=0.003) and at HLA-DPA1 gene in chromosome 6 ( P=0.02), respectively, than non-smokers. Conclusion: Five nominally significant associations were found between the NSCLC and CNVs. CNVs are associated with the mechanism of lung cancer development. However, the role of CNVs in lung cancer development needs further investigation.

Genome-Wide Copy Number Variant and High-Throughput Transcriptomics Analyses of Placental Tissues Underscore Persisting Child Susceptibility in At-Risk Pregnancies Cleared in Standard Genetic Testing

“…In our cohort, cases presented with overall more duplications, but not more deletions, as compared to controls (burden analysis, based on all CNVs with at most 10% frequency, 823 called duplications in 297 cases versus 626 called duplications in 277 controls, p = 0.01, based on 10,000 permutations, see Figure 2 ). This range of CNV counts is in line with previous studies using similar technology and sample sizes [ 12 , 13 ].…”

Identification of gene variation feature for targeted therapy of non-small cell lung cancer through combined method of DNA and RNA sequencing

“…In this study, we found that CNV including CCND1, FGF3/4/19 genes in male, smoking and LUSC cases was significantly enhanced than female, no-smoking and LUAD, respectively. Consistently, Heo and the colleagues have reported significant associations between CNV and smoking, such as acyl-CoA thioesterase 1 (ACOT1), N-terminal acetyltransferase F (NAA60), gasdermin-D (GSDMD) and HLA-DPA1 genes [ 18 ].…”

Identification of Subtypes Associated with Pyroptosis and Immune Cell Death, Prediction using Prognostic Models, and Analysis of Tumor Microenvironment in Head and Neck Squamous Cell Carcinoma

“…As a result, 47 PRGs and 33 ICDGs were identi ed 14,16 . Gene mutations and copy number variations reportedly promote the progression of cancer [17][18][19] . Therefore, the gene mutation frequency and copy number variation frequency of PRGs and ICDGs in HNSCC were investigated in the present study.…”