Introduction and objectives Circulating cell-free tumour DNA (cfDNA) can be detected in patients with solid organ malignancies and has the potential to be used as a non-invasive biomarker. Specific mutational events can be identified in biopsies using targeted next-generation sequencing and individualised microdroplet digital PCR (mdPCR) assays designed to detect and monitor the individualised biomarker in plasma. This can inform the timing (and sometimes mechanism) of disease progression or treatment failure.
To date this has been demonstrated in patients with EGFR and KRAS mutations.
Our objective was to determine if this approach could be applied to an unselected cohort of patients with advanced non-small cell lung cancer (adenocarcinoma subtype).
Methods Unselected treatment-naive patients with lung cancer were recruited from thoracic oncology clinics. Paired DNA from tumour biopsies and baseline/longitudinal plasma samples was obtained. Targeted next-generation sequencing (NGS) was performed using a 26-gene panel on biopsy-derived DNA. Primer sets and probes for identified mutations were optimised and validated on a the BioRad-QX100 mdPCR system.
Results The NGS data is summarised in Table 1.
20 patients in our test cohort had stage IIIB/IV lung adenocarcinoma. These included cytology specimens – EBUS, lymph node FNA and pleural effusion, percutaneous biopsies, pleural biopsies and a brain biopsy. The mean quantity of DNA used for targeted resequencing was 23 ng. The lowest read depth for the identified mutations was 1639; in general coverage was >10,000.
19/20 patients had mutations identified in their diagnostic specimen.
12 of 20 samples had >1 mutation detected and 8 had more than 2 mutations detected at a mutant allele frequency (MAF) >10%.
CtDNA from plasma has been tested for specific mutations including in PIK3CA, TP53, and BRAF as well as KRAS and EGFR in these patients. In 16 of the 19 patients in which mutations were identified the mutation has also been detected in the plasma. The range of detected MAFs was between <0.1–49.6%.
It was noteworthy that there was discordance between the biomarker response and RECIST1.1 criteria in some patients.
Conclusion It is feasible to perform a targeted NGS analysis on DNA from standard fixed diagnostic lung adenocarcinoma specimens and then validate and use individualised molecular biomarkers for use in a microdroplet digital PCR assay of cell-free circulating tumour DNA. There is potential for this approach to inform clinical decision-making.
This is a robust and low cost means of monitoring treatment response non-invasively and merits further evaluation in a clinical trial.