Copy Number Variation (CNV) in Chronic Obstructive Pulmonary Disease (COPD) with and without ongoing smoking

Abstract

Background: Chronic Obstructive Pulmonary Disease (COPD) development may be associated with CNV in susceptible genomic regions. CNV also contributes to COPD heritability.CNVs in COPD smokers (CS) and COPD former smokers (CFS) have not been deciphered so far.

Objective: To study the genome wide CNV to identify the vulnerable candidate genes for genetic susceptibility by performing array based comparative genomic hybridization (aCGH).Methods:COPD smokers (n=6) and COPD former smokers (n=9) were recruited from the Pulmonary Critical Care and Sleep Medicine OPD donated blood samples with prior informed consents. DNA was isolated from each sample using Qiagen DNeasy kit. aCGH was performed using Agilent two-colour microarray protocol to evaluate CNV. Agilent Cytogenomics software was used for analysis. Thresholds for gain, loss, amplification and deletion were set at log-ratios of 0.3, -0.3, 0.8 and -0.8, respectively.

Results: Copy loss and deletion of 15q11.1-q11.2 was only detected in COPD smokers but not in COPD former smokers. Copy gain and deletion of 1q31.3 was only detected in COPD smokers, but not in COPD former smokers.Copy loss of four genes (CHECKP2, HERC2P3, GOLGA6L6 and GOLGA8CP) in all the samples of CS. Copy loss and gain of Xq28 and 22q11.21 was observed only in CFS. LICAM, LCA10, AVPR2 and GD11 were found to be associated with copy gain in all samples of COPD former smokers.

Conclusion: The CNV located in 15q11.1-q11.2 region of CS might be associated with both smoking and COPD, while the CNVs located in Xq28 and 22q11.21 were observed only in samples from CFS suggesting their association in reversal to baseline after quitting smoking.