BRCA1, RASSF1A and PTEN Methylation in Breast Lesions of Uncertain Malignant Potential

February 23, 2026 updated by: Institute of Oncology Ljubljana

Diagnostic Significance of BRCA1, RASSF1A and PTEN Methylation in Breast Lesions of Uncertain Malignant Potential

This prospective interventional diagnostic study evaluates the clinical utility of methylation analysis of BRCA1, RASSF1A and PTEN genes in breast lesions of uncertain malignant potential (B3 lesions).

Women with suspicious non-palpable breast lesions undergo standard diagnostic procedures including clinical examination, imaging assessment, and image-guided core needle biopsy when indicated.

As part of the study protocol, breast tissue samples are prospectively assigned to additional molecular diagnostic testing using methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA).

The study evaluates whether gene promoter methylation status improves diagnostic assessment by comparing methylation results with final histopathological diagnosis.

Study Overview

Status

Completed

Conditions

Intervention / Treatment

Detailed Description

Breast cancer is the most common malignancy in women. Epigenetic alterations, particularly DNA promoter methylation of tumor suppressor genes, play an important role in breast carcinogenesis and may occur early in disease development.

This single-center prospective interventional diagnostic study is conducted at the Institute of Oncology Ljubljana. Participants are women with suspicious non-palpable breast lesions referred through the Slovenian national screening program DORA or other diagnostic pathways.

All participants undergo standard diagnostic work-up, including:

  • clinical breast examination,
  • breast imaging (mammography and/or ultrasound),
  • image-guided core needle biopsy when indicated.

Breast tissue samples obtained during biopsy or surgical excision are prospectively assigned to additional molecular testing using MS-MLPA to determine methylation status of BRCA1, RASSF1A and PTEN.

Histopathological classification includes:

  • benign lesions,
  • lesions of uncertain malignant potential (B3 lesions),
  • malignant lesions.

The primary objective is to evaluate the diagnostic performance of methylation analysis compared with histopathological diagnosis.

Statistical analysis will be performed using SPSS and GraphPad Prism. Sensitivity, specificity, positive predictive value, and negative predictive value will be calculated. Group comparisons will be performed using chi-square test or Fisher's exact test. Statistical significance is defined as p < 0.05.

Study Type

Interventional

Enrollment (Actual)

301

Phase

  • Not Applicable

Contacts and Locations

This section provides the contact details for those conducting the study, and information on where this study is being conducted.

Study Locations

  • Slovenia
      • Ljubljana, Slovenia, 1000
        • Institute of Oncology Ljubljana

Participation Criteria

Researchers look for people who fit a certain description, called eligibility criteria. Some examples of these criteria are a person's general health condition or prior treatments.

Eligibility Criteria

Ages Eligible for Study

  • Adult
  • Older Adult

Accepts Healthy Volunteers

No

Description

Inclusion Criteria:

  • Female participants aged 40 years or older
  • Suspicious non-palpable breast lesion referred for diagnostic evaluation at the Institute of Oncology Ljubljana
  • Undergoing image-guided core needle biopsy or surgical excision as part of standard diagnostic work-up
  • Availability of sufficient breast tissue sample for methylation analysis Signed written informed consent

Exclusion Criteria:

  • Contraindications to standard diagnostic procedures
  • Insufficient tissue sample for molecular analysis
  • Withdrawal of informed consent

Study Plan

This section provides details of the study plan, including how the study is designed and what the study is measuring.

How is the study designed?

Design Details

  • Primary Purpose: Diagnostic
  • Allocation: N/A
  • Interventional Model: Single Group Assignment
  • Masking: None (Open Label)

Arms and Interventions

Participant Group / Arm
Intervention / Treatment
Experimental: MS-MLPA Methylation Analysis
Participants undergo standard diagnostic evaluation for suspicious non-palpable breast lesions. Breast tissue samples obtained during image-guided core needle biopsy or surgical excision are prospectively assigned to additional molecular testing using methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) to determine promoter methylation status of BRCA1, RASSF1A and PTEN.
Diagnostic test: MS-MLPA Methylation Analysis
Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) is performed on breast tissue samples obtained during routine diagnostic procedures. The assay determines promoter methylation status of BRCA1, RASSF1A and PTEN. Results are compared with the final histopathological diagnosis to evaluate diagnostic performance.

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Diagnostic Performance of BRCA1, RASSF1A and PTEN Methylation Analysis
Time Frame: Up to June 2025
Sensitivity (%), specificity (%), positive predictive value (%) and negative predictive value (%) of methylation status determined by MS-MLPA for detection of malignant breast lesions compared with histopathological diagnosis.
Up to June 2025

Other Outcome Measures

Outcome Measure
Measure Description
Time Frame
Association of BRCA1, RASSF1A and PTEN Methylation Status With Histopathological Diagnosis
Time Frame: Up to June 2025
Methylation status of BRCA1, RASSF1A and PTEN will be determined in breast tissue samples using MS-MLPA and correlated with histopathological classification of breast lesions, including lesions of uncertain malignant potential (B3 lesions).
Up to June 2025

Collaborators and Investigators

This is where you will find people and organizations involved with this study.

Sponsor

Institute of Oncology Ljubljana

Study record dates

These dates track the progress of study record and summary results submissions to ClinicalTrials.gov. Study records and reported results are reviewed by the National Library of Medicine (NLM) to make sure they meet specific quality control standards before being posted on the public website.

Study Major Dates

Study Start (Actual)

September 1, 2024

Primary Completion (Actual)

June 30, 2025

Study Completion (Actual)

June 30, 2025

Study Registration Dates

First Submitted

February 10, 2026

First Submitted That Met QC Criteria

February 10, 2026

First Posted (Actual)

February 18, 2026

Study Record Updates

Last Update Posted (Actual)

February 25, 2026

Last Update Submitted That Met QC Criteria

February 23, 2026

Last Verified

February 1, 2026

More Information

Terms related to this study

Keywords

Additional Relevant MeSH Terms

Other Study ID Numbers

  • OI-B3METH-2024-01
  • 0120-215/2024-2711-4 (Other Identifier: Ethics Committee Approval Number)

Plan for Individual participant data (IPD)

Plan to Share Individual Participant Data (IPD)?

NO

Drug and device information, study documents

Studies a U.S. FDA-regulated drug product

No

Studies a U.S. FDA-regulated device product

No

This information was retrieved directly from the website clinicaltrials.gov without any changes. If you have any requests to change, remove or update your study details, please contact register@clinicaltrials.gov. As soon as a change is implemented on clinicaltrials.gov, this will be updated automatically on our website as well.

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