Personalised analysis of cell-free circulating tumour DNA for detection of molecular residual disease and recurrence in patients with head and neck squamous cell carcinoma

Abstract

Early relapse and development of metastatic disease are some of the primary reasons for the poor prognosis of patients with head and neck squamous cell carcinoma (HNSCC). The recent advent of personalised assays capable of detecting circulating cell-free tumour DNA (ctDNA) has enabled detection of molecular residual disease and recurrence following curative therapy. We conducted LIONESS, a single-centre prospective cohort study to assess ctDNA in plasma and saliva from 77 HNSCC patients receiving primary surgery with curative intent. Samples were collected pre- and postoperatively and during clinical follow-up. Whole exome sequencing was performed on FFPE tumour tissue. Tumour-specific variants for personalised assay design (RaDaR​, Inivata Ltd) were selected and used in the analysis of serial samples for evidence of molecular residual disease. Plasma ctDNA levels were correlated to tumour volumes from staging CT and other clinical parameters. In 530 longitudinal plasma samples collected preoperatively and during clinical follow-up, ctDNA was detected at levels ranging from 11.2% estimated variant allele fraction (eVAF) to as low as 0.0005% eVAF. Increased plasma ctDNA levels were detected postoperatively in all cases with confirmed clinical recurrences (12/12) with lead times up to 449 days. All cases with detectable ctDNA prior to treatment which remained ctDNA-negative thereafter have not recurred to date. ctDNA was also detected in baseline saliva samples from patients with tumours of various anatomical locations. The use of ctDNA measurements in this HNSCC patient cohort has significant potential to guide treatment decisions, improve disease outcome and potentially spare patients unnecessary, partially invasive interventions during clinical follow-up.