Molecular profiling of cell free DNA in patients with paediatric solid tumours

Abstract

Tumour tissue profiling studies show that a substantial proportion of paediatric cancer patients have potentially actionable alterations and minimally invasive molecular profiling test using cell free DNA (cfDNA) could provide a powerful platform to guide clinical decision-making and to deliver precision treatments. Clinical diagnostic sequencing of cfDNA is well advanced for adult patients, but application to paediatric cancer patients lags behind. To fill this gap, in this thesis I have described the development and validation of a clinically relevant pan-paediatric solid tumour NGS capture panel optimised for cfDNA analysis and an accompanying workflow with low coverage WGS (lcWGS) to molecularly profile paediatric patients with solid tumours. I applied this wrokflow to cfDNA samples from multiple clinical trials and showed that it is informative and yields comparable results to tissue biopsy molecular profiling in patients with extracranial tumours. Additionally, high numbers of cfDNA unique variants detected in patients at relapse showed the potential to complement tissue biopsy testing in many clinical diagnostics situations by allowing detection of tumour heterogeneity and identifying variants missed by tissue biopsy profiling, some of which are potentially targetable or aiding enrolment to clinical trials. In patients with CNS tumours plasma based cfDNA profiling was of limited success, however I showed potential to use cerebrospinal fluid cfDNA instead. Significant changes were observed between diagnostic and primary tissue biopsies with accumulation of SNVs and copy number changes at relapse and the ability to detect these changes in cfDNA was shown in patients with good purity ctDNA, highlighting the potential of cfDNA profiling to monitor tumour evolution in a minimally invasive way. Finally, several case studies showed the potential to track disease progress and identify relapse earlier than conventional methods using longitudinal cfDNA sampling. Overall, in this thesis I have shown that cfDNA is a good biomarker in paediatric cancer care and future molecularly enriched biomarker-driven interventional clinical trials utilising cfDNA are warranted.