Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease.
Reduced lung function in patients with chronic obstructive pulmonary disease (COPD) is likely due to both environmental and genetic factors. We report here a targeted high-throughput DNA sequencing approach to identify new and previously known genetic variants in a set of candidate genes for COPD.



Exons in 22 genes implicated in lung development as well as 61 genes and 10 genomic regions previously associated with COPD were sequenced using individual DNA samples from 68 cases with moderate or severe COPD and 66 controls matched for age, gender and smoking. Cases and controls were selected from the Obstructive Lung Disease in Northern Sweden (OLIN) studies.



In total, 37 genetic variants showed association with COPD (p < 0.05, uncorrected). Several variants previously discovered to be associated with COPD from genetic genome-wide analysis studies were replicated using our sample. Two high-risk variants were followed-up for functional characterization in a large eQTL mapping study of 1,111 human lung specimens. The C allele of a synonymous variant, rs8040868, predicting a p.(S45=) in the gene for cholinergic receptor nicotinic alpha 3 (CHRNA3) was associated with COPD (p = 8.8 x 10-3). This association remained (p = 0.003 and OR = 1.4, 95 % CI 1.1-1.7) when analysing all available cases and controls in OLIN (n = 1,534). The rs8040868 variant is in linkage disequilibrium with rs16969968 previously associated with COPD and altered expression of the CHRNA5 gene. A follow-up analysis for detection of expression quantitative trait loci revealed that rs8040868-C was found to be significantly associated with a decreased expression of the nearby gene cholinergic receptor, nicotinic, alpha 5 (CHRNA5) in lung tissue.



Our data replicate previous result suggesting CHRNA5 as a candidate gene for COPD and rs8040868 as a risk variant for the development of COPD in the Swedish population.
Department of Biosciences and Nutrition, Karolinska Institutet, 7-9, SE-141 83, Huddinge, Sweden. hans.matsson@ki.se.|Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden. hans.matsson@ki.se.
Hans
0000-0002-8193-4029
H
Matsson
Department of Biosciences and Nutrition, Karolinska Institutet, 7-9, SE-141 83, Huddinge, Sweden.|Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
Cilla
C
Söderhäll
Department of Biosciences and Nutrition, Karolinska Institutet, 7-9, SE-141 83, Huddinge, Sweden.|Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland.
Elisabet
E
Einarsdottir
Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada.
Maxime
M
Lamontagne
Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
Sanna
S
Gudmundsson
Department of Public Health and Clinical Medicine, Division of Occupational and Environmental Medicine, Umeå University, Umeå, Sweden.
Helena
H
Backman
Department of Public Health and Clinical Medicine, Division of Medicine, Umeå University, Umeå, Sweden.
Anne
A
Lindberg
Department of Public Health and Clinical Medicine, Division of Occupational and Environmental Medicine, Umeå University, Umeå, Sweden.
Eva
E
Rönmark
Department of Biosciences and Nutrition, Karolinska Institutet, 7-9, SE-141 83, Huddinge, Sweden.|Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland.
Juha
J
Kere
The University of British Columbia Center for Heart Lung Innovation, St-Paul's Hospital, Vancouver, Canada.
Don
D
Sin
Center Groningen, GRIAC research institute, University of Groningen, Groningen, The Netherlands.
Dirkje S
DS
Postma
Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada.|Department of Molecular Medicine, Laval University, Québec, Canada.
Yohan
Y
Bossé
Krefting Research Centre, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.
Bo
B
Lundbäck
Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
Joakim
J
Klar
D000368:Aged; D016022:Case-Control Studies; D005260:Female; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D015810:Linkage Disequilibrium; D008168:Lung / Q000503:physiopathology*; D008297:Male; D008875:Middle Aged; D009419:Nerve Tissue Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D029424:Pulmonary Disease, Chronic Obstructive / Q000235:genetics*; D011978:Receptors, Nicotinic / Q000235:genetics*; D013548:Sweden
C447158:CHRNA5 protein, human; D009419:Nerve Tissue Proteins; D011978:Receptors, Nicotinic
Association; CHRNA5; COPD; Lung development; Sequencing; eQTL