Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer

Jaana Oikkonen; Kaiyang Zhang; Liina Salminen; Ingrid Schulman; Kari Lavikka; Noora Andersson; Erika Ojanperä; Sakari Hietanen; Seija Grénman; Rainer Lehtonen; Kaisa Huhtinen; Olli Carpén; Johanna Hynninen; Anniina Färkkilä; Sampsa Hautaniemi

doi:10.1200/PO.18.00343

Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer

JCO Precis Oncol. 2019 May 3:3:PO.18.00343. doi: 10.1200/PO.18.00343. eCollection 2019.

Authors

Jaana Oikkonen¹, Kaiyang Zhang¹, Liina Salminen², Ingrid Schulman¹, Kari Lavikka¹, Noora Andersson¹, Erika Ojanperä¹, Sakari Hietanen², Seija Grénman², Rainer Lehtonen¹, Kaisa Huhtinen³, Olli Carpén^{1

3

4}, Johanna Hynninen², Anniina Färkkilä^{1

4

5}, Sampsa Hautaniemi¹

Affiliations

¹ Research Program in Systems Oncology, University of Helsinki, Finland.
² Turku University Hospital, Turku, Finland.
³ Institute of Biomedicine, University of Turku, Turku, Finland.
⁴ Helsinki University Hospital, Helsinki, Finland.
⁵ Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.

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.