Current Applications and Challenges of Next-Generation Sequencing in Plasma Circulating Tumour DNA of Ovarian Cancer

Simple Summary Circulating tumour DNA (ctDNA) corresponds to fragments of cancer genetic material circulating in body fluids, such as blood. Its isolation and analysis have made it a prominent biomarker in all types of human cancer. Ovarian cancer needs better biomarkers to help predict prognosis, treatment response, and early recurrence, and therefore there is an increasing interest in determining the real utility of ctDNA in each phase of the disease. With the advent of next-generation sequencing, ctDNA-based studies have greater potential to facilitate monitoring tumour genetic alterations across all metastatic sites and longitudinally through time, overcoming the need for an invasive tissue biopsy. This follow-up can be informative for clinicians regarding resistance mechanisms and new therapeutic options for cancer treatment. Therefore, in this review, we will address and group the current knowledge on ctDNA as a biomarker in ovarian cancer, focusing on studies using sequencing methods. We aimed to identify the paucity of scientific knowledge on the subject and highlight more adequate methodologies for biomarker research in order to motivate and guide future studies in the field.Abstract Circulating tumour DNA (ctDNA) facilitates longitudinal study of the tumour genome, which, unlike tumour tissue biopsies, globally reflects intratumor and intermetastatis heterogeneity. Despite its costs, next-generation sequencing (NGS) has revolutionised the study of ctDNA, ensuring a more comprehensive and multimodal approach, increasing data collection, and introducing new variables that can be correlated with clinical outcomes. Current NGS strategies can comprise a tumour-informed set of genes or the entire genome and detect a tumour fraction as low as 10-5. Despite some conflicting studies, there is evidence that ctDNA levels can predict the worse outcomes of ovarian cancer (OC) in both early and advanced disease. Changes in those levels can also be informative regarding treatment efficacy and tumour recurrence, capable of outperforming CA-125, currently the only universally utilised plasma biomarker in high-grade serous OC (HGSOC). Qualitative evaluation of sequencing shows that increasing copy number alterations and gene variants during treatment may correlate with a worse prognosis in HGSOC. However, following tumour clonality and emerging variants during treatment poses a more unique opportunity to define treatment response, select patients based on their emerging resistance mechanisms, like BRCA secondary mutations, and discover potential targetable variants. Sequencing of tumour biopsies and ctDNA is not always concordant, likely as a result of clonal heterogeneity, which is better captured in the plasma samples than it is in a large number of biopsies. These incoherences may reflect tumour clonality and reveal the acquired alterations that cause treatment resistance. Cell-free DNA methylation profiles can be used to distinguish OC from healthy individuals, and NGS methylation panels have been shown to have excellent diagnostic capabilities. Also, methylation signatures showed promise in explaining treatment responses, including BRCA dysfunction. ctDNA is evolving as a promising new biomarker to track tumour evolution and clonality through the treatment of early and advanced ovarian cancer, with potential applicability in prognostic prediction and treatment selection. While its role in HGSOC paves the way to clinical applicability, its potential interest in other histological subtypes of OC remains unknown.