Copy number signatures in cervical samples enable early detection of high-grade serous ovarian carcinoma

Background Ovarian cancer is often diagnosed in advanced stages, resulting in poor outcomes. There is an unmet need for a sensitive and specific screening tool for early-stage detection of ovarian cancer.

Recognizing that high-grade serous ovarian carcinoma (HGSC) is driven by copy number alterations (CNAs) and that tumor DNA can be detected in cervical samples, we analyzed CNAs from shallow whole genome sequencing of 212 cervical samples from 128 women with/without HGSC, including 29 germline BRCA1/2 mutation carriers. Using a machine-learning classifier, we developed High-grade serous ovarian cancer Cervical copy number signature (HCsig), a predictor for HGSC detection.

HGSC-derived CNAs were detectable with HCsig in cervical samples collected several years before diagnosis. Importantly, HCsig correctly identified HGSC in 79% of archival cervical samples, including 91% stage I-II (0-27 months pre-diagnosis), and 77% stage III-IV (0-65 months pre-diagnosis). Among patients with HGSC who had multiple pre-diagnostic samples collected during the pre-symptomatic phase, 85% had at least one HCpositive cervical sample before surgery (up to 65 months before diagnosis). Detection rates were 90% and 76% for BRCA1/2-mutated and wildtype HGSC, respectively. Validation in 172 independent samples (0-98 months pre-diagnosis) showed 76% sensitivity and 94% specificity (AUC=0.83), including high sensitivity for early-stage cancers.

We show that applying the HCsig classifier to cervical samples, including from non-symptomatic women several years before diagnosis, holds promise for early-stage detection and secondary prevention of HGSC. Moreover, it may serve as a screening tool to aid decision-making regarding timing of risk-reducing surgery in high-risk populations. Competing Interest Statement The authors have declared no competing interest. Funding Statement This study was funded by: The Swedish Cancer Society grants 21 1684 Pj and 24 3839 Pj (IH) The Sjoberg Foundation grant 2023-639 (IH) The Berta Kamprad Foundation grant FBKS-2023-36 (IH) The Cancer and Allergy Foundation grants 10381, 10672 and 11002 (IH) The King Gustaf V Jubilee Foundation grant 197011 (IH) Governmental funding of clinical research within the national health services (ALF) grant 40615 (IH) Fondazione Alessandra Bono and AIRC grants IG 2024 ID30972 and ID30381 (MD, SM) Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The ethics committee of Lund University gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Footnotes Correction of Figure 5 (labeling of axes) URL for data availability changed Data Availability The data presented in this paper contain sensitive human information (whole genome sequencing) that cannot be shared openly. Processed data files and metadata necessary to reproduce the key findings are available at Mendeley under doi: 10.17632/d45hf6nxfv.2, in accordance with data-sharing and ethical guidelines. ABBREVIATIONS - ACE - Absolute Copy-number Estimation - ASCAT - Allele-Specific Copy Number Analysis of Tumors - BRCA1/2 - Breast and Ovarian Cancer Susceptibility Protein 1/2 - CA-125 - Cancer Antigen 125 (Mucin 16) - cfDNA - cell-free DNA - CNA - Copy Number Alteration - FGA - Fraction of Genome Altered - FIGO - International Federation of Gynecology and Obstetrics - HCsig - High-grade serous ovarian cancer Cervical copy number signature - HE4 - Human Epididymis Protein 4 - HGSC - High-Grade Serous Cancer - HRD - Homologous Recombination Deficiency - RRSO - Risk-Reducing Salpingo-Oophorectomy - STIC - Serous Tubal Intraepithelial Carcinoma - sWGS - shallow Whole Genome Sequencing - TP53 - Tumor Protein P53