Genomic Profiling of Bronchoalveolar Lavage Fluid in Lung Cancer

? ABSTRACT Genomic profiling of bronchoalveolar lavage (BAL) samples may be useful for tumor profiling and diagnosis in the clinic. Here, we compared tumor-derived mutations detected in BAL samples from subjects with non-small cell lung cancer (NSCLC) to those detected in matched plasma samples. Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq) was used to genotype DNA purified from BAL, plasma, and tumor samples from patients with NSCLC. The characteristics of cell-free DNA (cfDNA) isolated from BAL fluid were first characterized to optimize the technical approach. Somatic mutations identified in tumor were then compared with those iden-tified in BAL and plasma, and the potential of BAL cfDNA analysis to distinguish lung cancer patients from risk-matched controls was explored. In total, 200 biofluid and tumor samples from 38 cases and 21 controls undergoing BAL for lung cancer evaluation were profiled. More tumor variants were identified in BAL cfDNA than plasma cfDNA in all stages (P < 0.001) and in stage Ito II disease only. Four of 21 controls harbored low levels of cancer-associated driver mutations in BAL cfDNA [mean variant allele frequency (VAF) 1/4 0.5%], suggesting the presence of somatic mutations in nonmalignant airway cells. Finally, using a Random Forest model with leave-one-out cross -validation, an exploratory BAL genomic classifier identified lung cancer with 69% sensitivity and 100% specificity in this cohort and detected more cancers than BAL cytology. Detecting tumor-derived mutations by targeted sequencing of BAL cfDNA is technically feasible and app-ears to be more sensitive than plasma profiling. Further studies are required to define optimal diagnostic applications and clinical utility. Significance: Hybrid-capture, targeted deep sequencing of lung cancer mutational burden in cell-free BAL fluid identifies more tumor-derived mutations with increased allele frequencies com-pared with plasma cell-free DNA.

Automated summary

This study compared tumor-derived mutations in bronchoalveolar lavage (BAL) samples to matched plasma samples from non-small cell lung cancer (NSCLC) patients. The results showed that more tumor variants were detected in BAL cell-free DNA (cfDNA) than in plasma cfDNA, especially in early-stage disease. The study also found low levels of cancer-associated driver mutations in BAL cfDNA from controls, suggesting the presence of somatic mutations in nonmalignant airway cells. Targeted sequencing of BAL cfDNA is technically feasible and appears to be more sensitive than plasma profiling for detecting tumor-derived mutations.