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

ABSTRACT: 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 h

SUBMITTER: Thun GA 

PROVIDER: S-EPMC6934450 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature