Liquid biopsy assay for lung carcinoma using centrifuged supernatants from fine-needle aspiration specimens

• Published in: Annals of oncology Vol. 30; no. 6; pp. 963 - 969
• Main Authors: Hannigan, B., Ye, W., Mehrotra, M., Lam, V., Bolivar, A., Zalles, S., Barkoh, B.A., Duose, D., Hu, P.C., Broaddus, R., Stewart, J., Heymach, J., Medeiros, L.J., Wistuba, I., Luthra, R., Roy-Chowdhuri, S.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.06.2019
• Subjects: fine-needle aspiration; liquid biopsy; lung cancer; mutation profiling; next-generation sequencing; supernatant; lung cancer; fine-needle aspiration; mutation profiling; next-generation sequencing; supernatant; liquid biopsy
• ISSN: 0923-7534; 1569-8041
• DOI: 10.1093/annonc/mdz102

Tumor mutation profiling is standard-of-care in lung carcinoma patients. However, comprehensive molecular profiling of small specimens, including core needle biopsy (CNB) and fine-needle aspiration (FNA) specimens, may often be inadequate due to limited tissue. Centrifuged FNA supernatants, which are typically discarded, have emerged recently as a novel liquid-based biopsy for molecular testing. In this study, we evaluate the use of lung carcinoma FNA supernatants for detecting clinically relevant mutations. Supernatants from lung carcinoma FNA samples (n=150) were evaluated. Samples were further analyzed using next-generation sequencing (NGS) and ultrasensitive droplet digital PCR (ddPCR). Mutation profiles in a subset of samples were compared with results derived from paired tissue samples from the same patient (n=67) and available plasma liquid biopsy assay (n=45). All 150 samples yielded adequate DNA and NGS were carried out successfully on 104 (90%) of 116 selected samples. Somatic mutations were detected in 82% of the samples and in 50% of these patients a clinically relevant mutation was identified that would qualify them for targeted therapy or a clinical trial. There was high overall concordance between the mutation profiles of supernatants and the corresponding tissue samples, with 100% concordance with concurrent FNA and 96% with concurrent CNB samples. Comparison of actionable driver mutations detected in supernatant versus plasma samples showed 84% concordance. FNA supernatants can provide a valuable specimen source for genotyping lung carcinoma especially in patients with insufficient tumor tissue, thereby reducing multigene mutation profiling failure rates, improving turnaround times, and avoiding repeat biopsies.