Tumor-informed liquid biopsy detection of structural variants in high grade serous ovarian cancer
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https://doi.org/10.18632/oncoscience.645
Jian Li1, Shiro Takamatsu1, Allison L. Brodsky1, Thomas Welte1, Katherine Calzoncinth1, Veena K. Vuttaradhi1, Joseph Celestino1, Barrett Lawson2 and R. Tyler Hillman3
1 Department of Gynecologic Oncology and Reproductive Medicine, Division of Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
2 Department of Pathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
3 Department of Obstetrics, Rebecca and John Moores Cancer Center, Gynecology and Reproductive Sciences, Division of Gynecologic Oncology, University of California San Diego, La Jolla, CA 92093, USA
Correspondence to:
R. Tyler Hillman, email: tyhillman@health.ucsd.edu
Keywords: ovarian cancer; ctDNA; biomarker; liquid biopsy; structural variant
Received: August 5, 2025 Accepted: January 16, 2026 Published: March 5, 2026
ABSTRACT
Background: High grade serous ovarian cancer (HGSOC) recurs frequently and commercial tests have emerged for tumor-informed, cell-free DNA (cfDNA)-based detection of minimal residual disease. These tests are based on somatic single nucleotide variants prevalent in many cancers and thus are not well matched to HGSOC, which is dominated by structural genomic rearrangements. The purpose of this study was to evaluate the feasibility of a structural-variant (SV)-informed, cfDNA-based method for detecting clonal and subclonal HGSOC disease burden.
Methods: A method was developed for detecting patient-specific SV breakpoints using digital droplet PCR (ddPCR) with custom tumor-informed primer/probe pairs. Test parameters were first estimated using synthetic cfDNA generated by ultrasonication of genomic DNA from ovarian cancer cell lines. The optimized workflow was implemented in which whole genome sequencing of multisite pre-treatment HGSOC biopsies performed and high confidence SVs were called by multiple published SV callers. Real-time PCR and ddPCR were used for assay development.
Results: Following the optimized workflow, tumor-specific SV breakpoint-spanning primers/probe sets of four HGSOC patients’ multisite biopsies were designed and validated by real-time PCR and ddPCR. Together with four HGSOCs, a total of 29 SVs breakpoints-spanning tumor-informed primers/probe sets were designed and validated in multisite biopsies. 15 validated tumor-specific SVs were selected for quantification in their corresponding liquid biopsies using the validated ddPCR, and 9 had measurements in liquid biopsies.
Conclusions: Our result shows the detection of SVs from pre-treatment cfDNA using tumor-informed breakpoints-spanning ddPCR is feasible and may enable a novel and sensitive method for monitoring on-treatment disease burden.
PII: 645
