ARTICLE ABSTRACT
Purpose To evaluate the use of blood cell-free DNA (cfDNA) to identify emerging mechanisms of resistance to PARP inhibitors (PARPi) in high grade serous ovarian cancer (HGSOC). Patients and Methods We used targeted sequencing (TS) to analyse 78 longitudinal cfDNA samples collected from 30 patients with HGSOC enrolled in a phase II clinical trial evaluating cediranib (VEGF inhibitor) plus olaparib (PARPi) after progression on PARPi alone. cfDNA was collected at baseline, before treatment cycle 2, and at end of treatment. These were compared to whole exome sequencing (WES) of baseline tumour tissues. Results At baseline (time of initial PARPi progression), cfDNA tumour fractions were 0.2-67% (median 3.25%) and patients with high ctDNA levels (>15%) had a higher tumour burden (sum of target lesions; p = 0.043). Across all timepoints, cfDNA detected known from tumour WES with 74.4% sensitivity, and detected 3 of 5 expected BRCA1/2 reversion mutations. In addition, cfDNA identified 10 novel mutations not detected by WES, including 7 TP53 mutations annotated as pathogenic by ClinVar. cfDNA fragmentation analysis attributed 5 of these novel TP53 mutations to clonal hematopoiesis of indeterminate potential (CHIP). At baseline, samples with significant differences in mutant fragment size distribution had shorter time to progression (p = 0.001). Conclusions Longitudinal testing of cfDNA by TS provides a non-invasive tool for detection of tumour-derived mutations and mechanisms of PARPi resistance that may aid in directing patients to appropriate therapeutic strategies. With cfDNA fragmentation analyses, CHIP was identified in several patients and warrants further investigation.
