Circulating biomarkers and tumour molecular profiling in patients with non-small cell lung cancer

Abstract

Background & aims: Targeted therapy has transformed the care of lung cancer patients by incorporating tumour genotyping into therapeutic decision making. Improvements in sequencing technology have allowed for a rapid/broad snapshot of a tumour9s genetic landscape. Circulating cell-free tumour DNA (cfDNA) can be detected in patients with solid organ malignancies and can be used as a non-invasive biomarker (“liquid biopsy”). By integrating the two approaches, it is possible to detect specific mutational events in diagnostic samples, assess tumour burden, longitudinally monitor the response to therapeutic intervention and detect disease recurrence. Methods: 20 unselected treatment-naive patients with lung cancer were recruited. Paired DNA from tumour biopsies and plasma was obtained. Targeted next-generation sequencing (NGS) was performed on the tumour biopsy DNA. Primer sets and probes for identified mutations were optimised and validated on a microdroplet digital PCR (mdPCR) system. Results: 19 of 20 patients in our test cohort had stage IIIB/IV non-small cell lung cancer. 95% of patients had mutations identified in their diagnostic biopsy. The corresponding mutation was then assayed in cfDNA. We successfully detected and quantified EGFR, KRAS, BRAF, PIK3CA and p53 mutations in cfDNA from 90% of patients, which we then tracked during treatment. There was complete concordance between mutations identified as part of the clinical standard-of-care and our NGS data. Conclusion: It is feasible to perform a targeted NGS analysis on DNA from standard diagnostic lung cancer specimens and design generic and patient-specific biomarkers for use in a mdPCR assay of cfDNA.