Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 Jan 13;15(1):105-118.
doi: 10.1158/2159-8290.CD-24-0393.

Early Detection of Ovarian Cancer Using Cell-Free DNA Fragmentomes and Protein Biomarkers

Jamie E Medina #  1 , Akshaya V Annapragada #  1 , Pien Lof  2 , Sarah Short  1 , Adrianna L Bartolomucci  1 , Dimitrios Mathios  1 , Shashikant Koul  1 , Noushin Niknafs  1 , Michaël Noë  1 , Zachariah H Foda  1 , Daniel C Bruhm  1 , Carolyn Hruban  1 , Nicholas A Vulpescu  1 , Euihye Jung  3 , Renu Dua  1 , Jenna V Canzoniero  1 , Stephen Cristiano  1 , Vilmos Adleff  1 , Heather Symecko  4 , Daan van den Broek  5 , Lori J Sokoll  1 , Stephen B Baylin  1 , Michael F Press  6 , Dennis J Slamon  7 , Gottfried E Konecny  7 , Christina Therkildsen  8 , Beatriz Carvalho  9 , Gerrit A Meijer  9 , Claus Lindbjerg Andersen  10   11 , Susan M Domchek  3   4 , Ronny Drapkin  3   4 , Robert B Scharpf  1 , Jillian Phallen  1 , Christine A R Lok  2 , Victor E Velculescu  1
Affiliations

Early Detection of Ovarian Cancer Using Cell-Free DNA Fragmentomes and Protein Biomarkers

Jamie E Medina et al. Cancer Discov. .

Abstract

There is an unmet need for effective ovarian cancer screening and diagnostic approaches that enable earlier-stage cancer detection and increased overall survival. We have developed a high-performing accessible approach that evaluates cfDNA fragmentomes and protein biomarkers to detect ovarian cancer.

PubMed Disclaimer

Conflict of interest statement

J.E. Medina reports a patent for 63/574,641 pending, a patent for 63/558,893 pending, and a patent for 63/621,749 pending. A.V. Annapragada reports a patent for 63/532,642 pending and licensed to DELFI Diagnostics, a patent for PCT/US2023/078857 pending, licensed, and with royalties paid from DELFI Diagnostics, a patent for 63/574,641 pending, and a patent for 63/558,893 pending. D. Mathios reports other support from Belay Diagnostics outside the submitted work; in addition, D. Mathios has a patent for “Detection of lung cancer with cfDNA fragmentation” licensed to DELFI Diagnostics and a patent for “Detection of brain cancer with cfDNA fragmentation and repeat landscapes” pending; D. Mathios’ wife is founding member of DELFI Diagnostics and has shares from the company. Z.H. Foda reports personal fees from DELFI Diagnostics outside the submitted work; in addition, Z.H. Foda has a patent for “Detecting liver cancer using cell-free DNA fragmentation” issued, licensed, and with royalties paid from DELFI Diagnostics. D.C. Bruhm reports patent applications related to early detection of cancer pending, issued, licensed, and with royalties paid from DELFI Diagnostics. N.A. Vulpescu reports grants from National Institute of General Medical Sciences during the conduct of the study. J.V. Canzoniero reports nonfinancial support from Foundation Medicine and personal fees from Illumina, AstraZeneca, MJH Life Sciences, and Conexient outside the submitted work; in addition, J.V. Canzoniero has a patent for 63/548,318 pending. S. Cristiano reports a patent for US20200131571A1 licensed and a patent for US20240060141A1 licensed. V. Adleff reports grants and personal fees from DELFI Diagnostics during the conduct of the study; in addition V. Adleff has a patent for 62/673,516 pending and licensed to DELFI Diagnostics and is an inventor on patent applications submitted by Johns Hopkins University related to cancer genomic analyses and cfDNA for cancer detection that have been licensed to one or more entities, including DELFI Diagnostics and LabCorp. Under the terms of these license agreements, the university and inventors are entitled to fees and royalty distributions. S.B. Baylin reports personal fees from MSP (Methylation Specific PCR) outside the submitted work; in addition, S.B. Baylin has a patent for US-20240156850-A1 with royalties paid, a patent for US-20210161928-A1 with royalties paid, a patent for US-20200239962-A1 with royalties paid, a patent for US-20150031022-A1 with royalties paid, and a patent for US-10363264-B2 with royalties paid. M.F. Press reports personal fees from Zymeworks Inc., Novartis Pharmaceuticals, AstraZenecca, Eli Lilly and Company, Merck & Co., Curio SciencePhysicians’ Education Resource, LLC (PER, and Medscape and other support from Jazz Pharmaceuticals and TORL Biotherapeutics, LLC outside the submitted work. D.J. Slamon reports nonfinancial support and other support from BioMarin, grants, nonfinancial support, and other support from Pfizer and Novartis, personal fees from Eli Lilly, and other support from Amgen, Seattle Genetics, 1200 Pharma, and TORL BioTherapeutics outside the submitted work. G.E. Konecny reports Speakers’ Bureau–AstraZeneca; Merck; GSK; Abbvie/Immunogen Research Funding–Lilly (Inst); Merck (Inst); Consulting–GOG Foundation; Travel, Accommodations, and Expenses–TORL Biotherapeutics; and Expert Testimony–Foundation Medicine. G.A. Meijer reports grants from Stand Up to Cancer–Dutch Cancer Society International Translational Cancer Research Dream Team Grant (SU2C-AACR-DT1415) and nonfinancial support from DELFI Diagnostics during the conduct of the study and nonfinancial support from DELFI Diagnostics outside the submitted work. C.L. Andersen reports grants from the Danish Council for Strategic Research during the conduct of the study and nonfinancial support from Natera Inc., and C2i Genomics outside the submitted work. R. Drapkin reports personal fees from Repare Therapeutics and Light Horse Therapeutics outside the submitted work; in addition, R. Drapkin has a patent for “Methods for detecting ovarian cancer” issued to Dana-Farber Cancer Institute. R.B. Scharpf reports grants and personal fees from DELFI Diagnostics outside the submitted work and is under a license agreement between DELFI Diagnostics and the Johns Hopkins University; the university and R.B. Scharpf are entitled to royalty distributions related to technology described in the study. Additionally, the university owns equity in DELFI Diagnostics. R.B. Scharpf is a founder of and holds equity in DELFI Diagnostics. He also serves as DELFI’s Head of Data Science. This arrangement has been reviewed and approved by the Johns Hopkins University in accordance with its conflict-of-interest policies. J. Phallen reports other support from DELFI Diagnostics during the conduct of the study; in addition, J. Phallen has a patent for 63/574,641 pending and a patent for 62/673,516 pending and licensed to DELFI Diagnostics. V.E. Velculescu reports grants, personal fees, and other support from DELFI Diagnostics during the conduct of the study and personal fees and other support from Viron Therapeutics and Epitope outside the submitted work; in addition, V.E. Velculescu has a patent for 63/574,641 pending and a patent for 62/673,516 pending and licensed to DELFI Diagnostics. V.E. Velculescu is a founder of DELFI Diagnostics, serves on the board of directors, and owns DELFI Diagnostics stock, which is subject to certain restrictions under university policy. In addition, Johns Hopkins University owns equity in DELFI Diagnostics. V.E. Velculescu divested his equity in Personal Genome Diagnostics to LabCorp in February 2022. V.E. Velculescu is an inventor on patent applications submitted by Johns Hopkins University related to cancer genomic analyses and cfDNA for cancer detection that have been licensed to one or more entities, including DELFI Diagnostics, LabCorp, QIAGEN, Sysmex, Agios, Genzyme, Esoterix, Ventana, and ManaT Bio. Under the terms of these license agreements, the university and inventors are entitled to fees and royalty distributions. V.E. Velculescu is an advisor to Viron Therapeutics and Epitope. These arrangements have been reviewed and approved by the Johns Hopkins University in accordance with its conflict-of-interest policies. No disclosures were reported by the other authors.

Figures

Figure 1.
Figure 1.
Schematic of ovarian cancer detection in screening and diagnostic models combining DELFI and protein biomarkers. Individuals undergo blood collection, plasma is extracted, and constructed genomic libraries undergo WGS at low coverage (∼2×). Using blood samples from the same collection, proteins are quantified enabling the combined assessment of genome-wide fragmentation profiles and protein biomarkers. These features are evaluated in a machine learning model that classifies cancer and noncancer individuals.
Figure 2.
Figure 2.
Characteristics of cfDNA fragmentation for ovarian cancer detection. A, Fragmentation profiles in which each line represents one participant and is colored according to that participant’s correlation to the median genome-wide profile for women without cancer. B, Heatmap of fragmentation and protein features show marked heterogeneity in the cfDNA fragmentome among individuals with ovarian cancer compared with those with benign lesions or without disease. In the heatmap, individuals are split into disease groups and then successively ordered by DELFI-Pro, CA-125, and HE4, and cancers are categorized according to stage and subtype. Fragmentation features are clustered in columns. The top bar indicates the feature family containing the short to long ratio of fragment sizes (ratio) and chromosomal arm representation (z-scores). C, Chromosomal gains (red) and losses (blue) characteristic of ovarian cancer tumor tissue evaluated in TCGA were observed in cfDNA fragmentation data in patients with ovarian cancer and absent from those with benign lesions or without disease (red represents gains, whereas losses are blue, and purple indicates no changes in chromosomal representation, respectively). D, Feature importance, as measured by scaled coefficients from the PLR locked screening model for ovarian cancer, demonstrates contributions of cfDNA fragmentation (fragment length and aneuploidy) and proteins (CA-125 and HE4) to high performance.
Figure 3.
Figure 3.
DELFI-Pro detects ovarian cancer with high sensitivity and specificity. A, In the discovery cohort, patients with ovarian cancer across all stages have elevated DELFI-Pro scores in HGSOC as well as other ovarian subtypes. B, ROC analyses of the discovery cohort show high performance across stages and in HGSOC. C and D, The locked DELFI-Pro model at locked thresholds (e.g., for 99% specificity, DELFI-Pro score >0.66) showed similar performance in the validation cohort.
Figure 4.
Figure 4.
Modelling the implementation of DELFI for ovarian cancer screening. A, The proposed approach integrates the use of cfDNA fragmentation and protein analyses from a blood draw. Women with a positive result would undergo a transvaginal ultrasound and if positive would subsequently have a diagnostic cancer workup. A negative result at any step in this continuum would remove patients from subsequent steps and lead to annual screening. B, Modeling a theoretical population of 100,000 women based on existing performances for CA-125 and HE4, as well those observed for DELFI-Pro. Predictive distributions for the (C) PPV and (D) FPR highlight the potential benefit of implementing DELFI-Pro as compared with existing biomarkers. JHU, Johns Hopkins University; TVUS, transvaginal ultrasound.
See this image and copyright information in PMC

References

    1. Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, et al. . Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin 2021;71:209–49. - PubMed
    1. Siegel RL, Giaquinto AN, Jemal A. Cancer statistics, 2024. CA Cancer J Clin 2024;74:12–49. - PubMed
    1. American Cancer Society . Ovarian cancer survival rates. Ovarian cancer early detection, diagnosis, and staging [Internet]. [cited 2024 Mar 12]. Available from:https://www.cancer.org/cancer/types/ovarian-cancer/detection-diagnosis-s....
    1. Ruhl J, Callaghan C, Schussler N. Summary stage 2018: codes and coding instructions. Bethesda (MD): National Cancer Institute; 2023.
    1. Prorok PC, Andriole GL, Bresalier RS, Buys SS, Chia D, Crawford ED, et al. . Design of the prostate, lung, colorectal and ovarian (PLCO) cancer screening trial. Control Clin Trials 2000;21:273S–309S. - PubMed