Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer

Abstract

PURPOSE Circulating tumor DNA (ctDNA) detection is a minimally invasive technique that offers dynamic molecular snapshots of genomic alterations in cancer. Although ctDNA markers can be used for early detection of cancers or for monitoring treatment efficacy, the value of ctDNA in guiding treatment decisions in solid cancers is controversial. Here, we monitored ctDNA to detect clinically actionable alterations during treatment of high-grade serous ovarian cancer, the most common and aggressive form of epithelial ovarian cancer with a 5-year survival rate of 43%. PATIENTS AND METHODS We implemented a clinical ctDNA workflow to detect clinically actionable alterations in more than 500 cancer-related genes. We applied the workflow to a prospective cohort consisting of 78 ctDNA samples from 12 patients with high-grade serous ovarian cancer before, during, and after treatment. These longitudinal data sets were analyzed using our open-access ctDNA-tailored bioinformatics analysis pipeline and in-house Translational Oncology Knowledgebase to detect clinically actionable genomic alterations. The alterations were ranked according to the European Society for Medical Oncology scale for clinical actionability of molecular targets. RESULTS Our results show good concordance of mutations and copy number alterations in ctDNA and tumor samples, and alterations associated with clinically available drugs were detected in seven patients (58%). Treatment of one chemoresistant patient was changed on the basis of detection of ERBB2 amplification, and this ctDNA-guided decision was followed by significant tumor shrinkage and complete normalization of the cancer antigen 125 tumor marker. CONCLUSION Our results demonstrate a proof of concept for using ctDNA to guide clinical decisions. Furthermore, our results show that longitudinal ctDNA samples can be used to identify poor-responding patients after first cycles of chemotherapy. We provide what we believe to be the first comprehensive, open-source ctDNA workflow for detecting clinically actionable alterations in solid cancers.

Circulating Tumor DNA (ctDNA) in Precision Oncology of Ovarian Cancer

“…We recently published a paper on the use of ctDNA in management of high-grade serous ovarian cancer (HGSOC) 2 . HGSOC is the most frequent and lethal subtype of epithelial ovarian cancer with five-year survival of only 43%.…”

Prediction of the treatment response in ovarian cancer: a ctDNA approach

“…One chemo resistant patient therapy has changed based on the detection of ERBB2 amplification and ctDNA-guided decision. These results can be considered as a proof of using ctDNA concept to guide the clinical decisions during the cycles of chemotherapy in ovarian cancers [118]. In addition, Noguchi et al [119] compared the variant allele frequency (VAF) of the measured ctDNA mutations during neoadjuvant chemotherapy in 10 plasma samples.…”

Comparison of Somatic Mutation Profiles Between Formalin-Fixed Paraffin Embedded Tissues and Plasma Cell-Free DNA from Ovarian Cancer Patients Before and After Surgery

“…Some studies reported 68-100% concordance of mutations detected in plasma and tumor tissues. 10,11,43 Our gene panel sequencing method differed vastly to the number of genes examined by the abovementioned researchers. Phallen et al 10 analyzed 58 genes in various cancers, Oikkonen et al 11 investigated over 500 genes in ovarian cancer patients with different NGS approaches and Kim et al 43 examined genetic changes in only one gene using different mutation analysis.…”

“…10,11,43 Our gene panel sequencing method differed vastly to the number of genes examined by the abovementioned researchers. Phallen et al 10 analyzed 58 genes in various cancers, Oikkonen et al 11 investigated over 500 genes in ovarian cancer patients with different NGS approaches and Kim et al 43 examined genetic changes in only one gene using different mutation analysis. In contrast, other NGS analysis of BRCA1/2 mutations in ovarian cancer demonstrated 100% concordance between the tumor and ctDNA germline variants, but this was not observed in the case of somatic variants, indicating the intratumor heterogeneity.…”

“…This may reflect the genomic landscape of the primary tumor and metastases. [9][10][11][12][13][14] Circulating tumor DNA (ctDNA) originate from apoptotic or necrotic cancer cells, perhaps even from active cellular secretion, and its fragment size is most commonly less than 180 bp. [15][16][17][18][19][20] Moreover, ctDNA usually constitutes a small fraction (<20%) of total cfDNA concentration that is generally low.…”