Introduction Somatic molecular profiling is more important than ever, as precision treatment for ovarian cancer advances. Tumour material for profiling can be accessed via malignant ascites, however cancer cells are often sparse in ascites and cell-free DNA (cfDNA) is not well studied.

Methods Ascites-derived cfDNA from 14 patients (36–82 years), including 11 patients with sequential samples, was sequenced with the Illumina TSO-500 panel. Matched DNA from ascites-derived tumour cells (n=5) and archived FFPE-tissue from surgery (n=4) was sequenced using the same panel. cfDNA from one patient was additionally sequenced using an Oxford Nanopore Technology R9.4.1 MinION.

Results Abundant cfDNA was identified in all ascites samples (up to 660 ng/mL), achieving similar read alignment and improved coverage compared to cell or FFPE-derived DNA. Somatic driver mutations were detected in 100% of cfDNA samples at mutation fractions of up to 79%. All clinically known variants were identified in ascites cfDNA (including 6 in BRCA1 or BRCA2), except for one case, where a TP53 mutation identified in FFPE-DNA was absent in ascites due to the clonal loss of chromosome 17 p-arm in tumour evolution; indicated by a decrease in Oxford Nanopore sequencing reads per kilobase over 17p relative to 17q (p=0.0015). Tumour evolution was also indicated by an increase in tumour mutational burden in samples collected subsequent to multiple cycles of chemotherapy (p=0.043).

Conclusion/Implications We demonstrate the reliability of sequencing cfDNA from ascites for molecular profiling. This approach provides opportunistic access to tumour DNA, allowing a liquid biopsy of ovarian cancer in lieu of a traditional biopsy.