Exhaled Breath Condensate (EBC) analysis of circulating tumour DNA (ctDNA) using a lung cancer specific UltraSEEK oncogene panel

•Exhaled Breath (EBC) and plasma were analysed for 5 genetic alterations using ultrasensitive PCR in lung cancer patients.•Results were compared to corresponding diagnostic tissue samples analysed using targeted NextGeneration Sequencing (NGS).•Higher failure rates owing to unamplifiable DNA were noted in tissue NGS compared to EBC and Plasma.•Significantly higher numbers of mutations in EGFR, KRAS and PIK3CA were identified in EBC and plasma than tissue NGS.•Overlap and divergence was noted in the mutation profiles between EBC and plasma. Small diagnostic tissue samples can be inadequate in testing an expanding list of validated oncogenic driver alterations and fail to reflect intratumour heterogeneity (ITGH) in lung cancer. Liquid biopsies are non-invasive and may better reflect ITGH. Most liquid biopsies are performed in the context of circulating tumour DNA (ctDNA) in plasma but Exhaled Breath Condensate (EBC) shows promise as a lung-specific liquid biopsy. In this prospective, proof-of-concept study we carried out targeted Next Generation Sequencing (NGS) on diagnostic tissue samples from 125 patients with lung cancer and compared results to plasma and EBC for 5 oncogenic driver mutations (EGFR, KRAS, PIK3CA, ERBB2, BRAF) using an ultrasensitive PCR technique (UltraSEEK™ Lung Panel on the MassARRAY® System, Agena Bioscience, San Diego, CA, USA). There was a significantly higher failure rate due to unamplifiable DNA in tissue NGS (57/125, 45.6%) compared to plasma (27/125, 21.6%, p