CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
Helmholtz-Zentrum München, National Research Centre for Environmental Health, Institute of Lung Biology and Disease, Neuherberg, Germany.
Sci Rep. 2019 Dec 27;9(1):20158. 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.
慢性阻塞性肺疾病（COPD）由吸烟引起，其特征是气道组织炎症。由于 COPD 吸烟者比不吸烟者患肺癌的风险更高，我们假设他们在受影响的组织中携带更多的突变。我们对来自健康从不吸烟者和戒烟者（n=8）以及有不同程度 COPD 的戒烟者（n=4）的中等覆盖全基因组测序数据的气道刷样本进行了体细胞突变分析。由于应用工具之间的结果调用一致性有限，我们构建了一个共识，该策略在癌症数据中具有很高的准确性验证。然而，由于相应序列读取的可映射性低且与已知遗传多态性位置重叠，共识调用几乎没有希望代表真正的阳性。靶向重测序方法表明，只有少数突变能够通过严格的验证测试，并且我们的数据不允许推断支气管刷样本中 COPD 病例和对照之间的突变负荷有任何差异。气道刷样本中的高度多克隆性使得中等深度测序不足以提供检测体细胞突变的分辨率。需要对气道活检的深度测序数据进行处理以解决该问题。
