Cell-free DNA from ascites identifies clinically relevant variants and tumour evolution in patients with advanced ovarian cancer

Background The emergence of targeted therapies and predictive biomarkers is transforming the ovarian cancer treatment paradigm. However, the demand for high quality, tumour-enriched samples for biomarker profiling can be limited by access to adequate tissue samples. The use of cell-free DNA (cfDNA) in ascites presents a potential solution to this clinical challenge. Methods A unique set of sequential ascites-derived cfDNA samples (26 samples from 15 human participants) were collected from people with ovarian cancer (age range 36-82 years). cfDNA was sequenced using targeted next-generation sequencing, along with matched DNA from ascites-derived tumour cells (n=5) and archived FFPE-tissue from surgery (n=5). Results Similar tumour purity, variant detection and reference alignment were achieved with cfDNA when compared to FFPE and ascites derived tumour cell DNA, as well as improved coverage. No artefactual single-base mutation signatures were identified in cfDNA. Combined analysis of large-scale genomic alterations, loss of heterozygosity and tumour mutation burden identified 6 cases of high genomic instability (including 4 with pathogenic variants in BRCA1 and BRCA2). Copy number profiles and subclone prevalence changed between sequential ascites samples, particularly in a case study where deletions and chromothripsis in Chr17p13.1 and Chr8q resulted in changes in clinically relevant TP53 and MYC variants over time. Conclusions Ascites cfDNA successfully identified clinically actionable information, concordant to tissue biopsies, enabling opportunistic molecular profiling. These findings advocate for analysis of ascites cfDNA in lieu of accessing tumour tissue via biopsy.