High degree of polyclonality hinders somatic mutation calling in lung brush samples of COPD cases and controls

• Published in: Scientific reports 2019-12, Vol.9 (1), p.20158-12, Article 20158
• Main Authors: Thun, Gian-Andri, Derdak, Sophia, Castro-Giner, Francesc, Apunte-Ramos, Katherine, Águeda, Lidia, Wjst, Matthias, Boland, Anne, Deleuze, Jean-François, Kolsum, Umme, Heiss-Neumann, Marion S., Nowinski, Adam, Gorecka, Dorota, Hohlfeld, Jens M., Welte, Tobias, Brightling, Christopher E., Parr, David G., Prasse, Antje, Müller-Quernheim, Joachim, Greulich, Timm, Stendardo, Mariarita, Boschetto, Piera, Barta, Imre, Döme, Balázs, Gut, Marta, Singh, Dave, Ziegler-Heitbrock, Loems, Gut, Ivo G.
• Format: Article
• Language: English
• Subjects: 45; 45/23; 631/208/726; 692/699/1785/4037; Aged; Biochemistry, Molecular Biology; Biomarkers; Biopsy; Chronic obstructive pulmonary disease; Cigarette smoking; Cigarette Smoking - adverse effects; Computational Biology; DNA Mutational Analysis; Female; Genetic Association Studies; Genetic Predisposition to Disease; Genetics; Genomes; Genomics; Humanities and Social Sciences; Humans; Life Sciences; Lung - metabolism; Lung - pathology; Lung cancer; Lung diseases; Male; Middle Aged; multidisciplinary; Mutation; Obstructive lung disease; Pulmonary Disease, Chronic Obstructive - diagnosis; Pulmonary Disease, Chronic Obstructive - etiology; Reproducibility of Results; Respiratory Function Tests; Respiratory tract; Risk Factors; Science; Science (multidisciplinary); Severity of Illness Index; Whole Genome Sequencing
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-019-56618-1

Chronic obstructive pulmonary disease (COPD) is induced by cigarette smoking and characterized by inflammation of airway tissue. Since smokers with COPD have a higher risk of developing lung cancer than those without, we hypothesized that they carry more mutations in affected tissue. We called somatic mutations in airway brush samples from medium-coverage whole genome sequencing data from healthy never and ex-smokers (n = 8), as well as from ex-smokers with variable degrees of COPD (n = 4). Owing to the limited concordance of resulting calls between the applied tools we built a consensus, a strategy that was validated with high accuracy for cancer data. However, consensus calls showed little promise of representing true positives due to low mappability of corresponding sequence reads and high overlap with positions harbouring known genetic polymorphisms. A targeted re-sequencing approach suggested that only few mutations would survive stringent verification testing and that our data did not allow the inference of any difference in the mutational load of bronchial brush samples between former smoking COPD cases and controls. High polyclonality in airway brush samples renders medium-depth sequencing insufficient to provide the resolution to detect somatic mutations. Deep sequencing data of airway biopsies are needed to tackle the question.