Exploring a Breast Cancer Early Screening Model Based on cfDNA

Scientific Research on Exploring a Breast Cancer Early Screening Model Using cfDNA Multi-omics Liquid Biopsy Technology Based on Deep Learning

The goal of this observational study is to use cfDNA multi-omics technology to explore a new breast cancer early detection model to improve the accuracy of early diagnosis in breast cancer patients. The main questions it aims to answer are:

• Evaluate the sensitivity and specificity of the early detection model for breast cancer screening
• Evaluate participants' TeFei™ score Participants will be collected peripheral venous blood before surgery or systemic treatment. The blood will then be sent to the collaboration company for sequencing. The collaboration company will analyze the sequencing results and build a cfDNA multi-omics signature library. Finally, the collaboration company will use deep learning algorithms to train and optimize the feature library.

Researchers will compare the cancer group with a benign control group to determine the model's effectiveness in differentiating between them.

Study Overview

• Status: Completed
• Conditions: Breast Cancer; Breast Fibroadenoma; Breast Hypoplasia
• Intervention / Treatment: Genetic: cfDNA sequencing

• Study Type: Observational
• Enrollment (Actual): 839

Contacts and Locations

Study Locations

• China
  • Anhui
    • Bengbu, Anhui, China, 233000
      • The First Affiliated Hospital of Bengbu Medical University
  • Zhejiang
    • Hangzhou, Zhejiang, China, 310009
      • Second Affiliated Hospital of Zhejiang University School of Medicine
    • Hangzhou, Zhejiang, China, 310000
      • Women's Hospital School of Medicine Zhejiang University
    • Hangzhou, Zhejiang, China, 310000
      • Affiliated Hangzhou First People's Hospital ,Westlake University School of Medicine
    • Hangzhou, Zhejiang, China, 310000
      • Sir Run Run Shaw Hospital Affiliated with Zhejiang University School of Medicine
    • Hangzhou, Zhejiang, China, 310000
      • Wenhui Community Health Service center, Gongshu district, Hangzhou city
    • Hangzhou, Zhejiang, China, 310000
      • Zhejiang Provincial Hospital of Traditional Chinese Medicine
    • Ningbo, Zhejiang, China, 315046
      • Ningbo Medical Center Lihuili Hospital

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Adult; Older Adult
• Accepts Healthy Volunteers: No

• Sampling Method: Non-Probability Sample

Study Population

Breast cancer patients and patients with benign breast diseases.

Description

Inclusion Criteria:

1. Patients ≥18 years old and ≤70 years old;
2. Plasma of the participant can be obtained;
3. Willing to sign the informed consent;
4. Meet one of the following criteria:

4.1)Patients diagnosed with invasive breast cancer or carcinoma in situ of the breast for the first time; 4.2)Patients with breast fibroma or breast adenosis and breast fibrocystic hyperplasia;

Exclusion Criteria:

In any of the following situations, subjects should not participate in the trial:

1. Pregnant or lactating;
2. Unable to obtain the participant's plasma;
3. Patients with other types of malignant tumors diagnosed by pathology within 5 years before enrollment;
4. The patients had suspected imaging (B-ultrasound, CT, etc.) of other malignant tumors within the past 1 year after enrollment, but no pathological confirmation;
5. Received any blood product transfusion in the past 30 days;
6. Participants considered by the investigator to be inappropriate to participate in this research-type clinical trial.

Study Plan

How is the study designed?

Number of groups / cohorts

2

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
the cancer group; 503 cases of early breast cancer	Genetic: cfDNA sequencing; Multi-omics sequencing of cfDNA in peripheral venous blood.
the benign control group; 289 cases of control group	Genetic: cfDNA sequencing; Multi-omics sequencing of cfDNA in peripheral venous blood.

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Evaluate the sensitivity and specificity of the early detection model for breast cancer screening	Peripheral blood samples were collected during routine physical examinations for healthy volunteers and prior to surgery for cancer patients. The blood samples were drawn and placed into cfDNA preservation tubes (Ardent BioMed, Guangdong, China, Cat. # BY10240301). After collection, the fresh blood was subjected to an initial centrifugation at 1,600 × g for 10 minutes at 4°C, allowing the plasma supernatant to be carefully separated via pipetting. This plasma was then centrifuged again at 16,000 × g for 10 minutes at 4°C to remove any residual debris. The resulting plasma supernatant was then carefully collected and stored at -80°C. The preserved plasma samples were subsequently transported on dry ice to the central laboratory at OmixScience Research Institute (Hangzhou, China).	1 year from enrollment

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Evaluate participants' TeFei™ score	This test is based on the expression level of key genes in the cfDNA tumor of the participant's blood sample, and the relative expression level of these genes is calculated to obtain a score. This score is called the TeFei™ Score and usually ranges from 0 to 100, with a higher score indicating a higher tumor burden in the patient.	60 days

Collaborators and Investigators

• Sponsor: Second Affiliated Hospital, School of Medicine, Zhejiang University
• Collaborators: OmixScience Institute
• Investigators: Principal Investigator: Chao Ni, Second Affiliated Hospital of Zhejiang University School of Medicine

Publications and helpful links

General Publications

• Mathios D, Johansen JS, Cristiano S, Medina JE, Phallen J, Larsen KR, Bruhm DC, Niknafs N, Ferreira L, Adleff V, Chiao JY, Leal A, Noe M, White JR, Arun AS, Hruban C, Annapragada AV, Jensen SO, Orntoft MW, Madsen AH, Carvalho B, de Wit M, Carey J, Dracopoli NC, Maddala T, Fang KC, Hartman AR, Forde PM, Anagnostou V, Brahmer JR, Fijneman RJA, Nielsen HJ, Meijer GA, Andersen CL, Mellemgaard A, Bojesen SE, Scharpf RB, Velculescu VE. Detection and characterization of lung cancer using cell-free DNA fragmentomes. Nat Commun. 2021 Aug 20;12(1):5060. doi: 10.1038/s41467-021-24994-w.

Helpful Links

• Freenome, a privately held biotech company, announced the completion of enrollment for PREEMPT CRC, the company's large, prospective study to validate its blood test for colorectal cancer (CRC) screening among average-risk adults.

Study record dates

Study Major Dates

• Study Start (Actual): April 11, 2023
• Primary Completion (Actual): December 13, 2023
• Study Completion (Actual): October 31, 2024

Study Registration Dates

• First Submitted: August 22, 2023
• First Submitted That Met QC Criteria: August 28, 2023
• First Posted (Actual): August 30, 2023

Study Record Updates

• Last Update Posted (Actual): July 29, 2025
• Last Update Submitted That Met QC Criteria: July 28, 2025
• Last Verified: January 1, 2025

More Information

Terms related to this study

• Keywords: cfDNA; Deep learning
• Additional Relevant MeSH Terms: Neoplasms by Site; Neoplasms; Neoplasms by Histologic Type; Neoplasms, Glandular and Epithelial; Skin Diseases; Breast Diseases; Neoplasms, Connective and Soft Tissue; Neoplasms, Connective Tissue; Neoplasms, Fibrous Tissue; Neoplasms, Fibroepithelial; Breast Neoplasms; Fibroadenoma
• Other Study ID Numbers: ZE-OMIX-001

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: NO
• IPD Plan Description: Because the database is related to the products of the cooperative company, in order to protect the intellectual property rights of the cooperative company, IPD will not be shared.

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No
• product manufactured in and exported from the U.S.: No