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OpenTrials
Completed

NCT Number: NCT07428733

Gene Methylation for Diagnosis of Breast Lesions

Breast lesions of uncertain malignant potential represent a diagnostic challenge, as conventional histopathological assessment does not always reliably distinguish between benign and malignant changes.

The purpose of this prospective diagnostic study is to evaluate whether methylation patterns of selected breast cancer-related genes (BRCA1, RASSF1A, and PTEN) can help differentiate benign from malignant breast lesions.

Tissue samples obtained during diagnostic needle biopsy, and when applicable during surgical excision, will be analyzed for gene methylation status. The results will be compared with standard histopathological findings.

The study aims to improve diagnostic accuracy in breast lesions of uncertain malignant potential and contribute to better clinical decision-making in breast diagnostics.

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Key information

Conditions

Breast Lesions of Uncertain Malignant Potential PTEN

Age range

18 year and older

Sex eligibility

Female

Study type

Interventional

Phase

Not applicable

Primary location

Institute of Oncology Ljubljana

Ljubljana, 1000, Slovenia

About this study

Breast lesions of uncertain malignant potential (B3 category) pose a significant diagnostic challenge in clinical practice, as they carry a variable risk of malignancy and often lead to surgical excision despite a substantial proportion of benign outcomes.

Epigenetic alterations, particularly DNA methylation of tumor suppressor genes, are recognized as early events in breast carcinogenesis and may provide additional diagnostic information beyond conventional histopathology.

This prospective interventional diagnostic study investigates the diagnostic significance of methylation status of BRCA1, RASSF1A, and PTEN genes in breast lesions of uncertain malignant potential. Participants undergoing diagnostic evaluation for suspicious breast lesions will be enrolled after providing written informed consent.

Tissue samples obtained during diagnostic needle biopsy will be analyzed using molecular methods to determine gene methylation status. In cases where surgical excision is performed, methylation findings from needle biopsy specimens will be compared with those from surgical samples and correlated with final histopathological diagnosis.

The primary objective is to assess whether gene methylation patterns can distinguish benign from malignant breast lesions. Secondary objectives include evaluating concordance between needle biopsy and surgical specimens and analyzing differences in methylation profiles across histopathological lesion categories.

The study is conducted at the Institute of Oncology Ljubljana and does not influence clinical decision-making. All diagnostic and therapeutic procedures follow standard clinical practice.

Who can participate

Healthy volunteers accepted: No

Only the study team can determine whether someone qualifies for participation.

Inclusion criteria

  • Female patients aged 18 years or older.
  • Patients referred for diagnostic evaluation of breast lesions of uncertain malignant potential.
  • Availability of breast tissue samples obtained by diagnostic needle biopsy.
  • Written informed consent for participation in the study.

Exclusion criteria

  • Male patients.
  • Patients younger than 18 years.
  • Patients without breast lesions or without indication for diagnostic biopsy.
  • Inadequate or insufficient tissue material for molecular analysis.
  • Withdrawal of informed consent.

Treatment and study plan

Gene Methylation Analysis of BRCA1, RASSF1A and PTEN

Diagnostic Test

Molecular analysis of BRCA1, RASSF1A, and PTEN gene methylation performed on breast tissue samples obtained during diagnostic procedures.

Primary outcomes

  1. Diagnostic Accuracy (Sensitivity and Specificity) of BRCA1, RASSF1A and PTEN Methylation for Malignancy Detection in B3 Breast Lesions

    Time frame: Baseline (needle biopsy) to final histopathological diagnosis (up to 12 months)

    Diagnostic accuracy of BRCA1, RASSF1A and PTEN gene methylation status measured in diagnostic needle biopsy tissue samples for predicting malignancy (malignant vs benign final diagnosis), using final histopathological diagnosis as the reference standard. Diagnostic performance will be reported as sensitivity and specificity (%), with additional diagnostic accuracy measures (PPV, NPV and AUC).

Secondary outcomes

  1. Concordance of BRCA1, RASSF1A and PTEN Methylation Status Between Needle Biopsy and Surgical Specimens

    Time frame: Up to 12 months after needle biopsy

    Agreement of BRCA1, RASSF1A and PTEN methylation status between diagnostic needle biopsy tissue samples and matched surgical excision specimens. Concordance will be assessed using percentage agreement (%) and Cohen's kappa coefficient (κ).

Sponsors and collaborators

Lead sponsor

Institute of Oncology Ljubljana

Other

Registry information

Official study title

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

Important dates

Study start
2024
Primary completion
2025
Study completion
2026
First posted
Feb 24, 2026
Registry last updated
Feb 24, 2026

OpenTrials presents study information sourced from ClinicalTrials.gov. The official registry record should be consulted for the latest information.

View the official ClinicalTrials.gov record (opens in a new tab)

This listing is for discovery and informational purposes only. It is not medical advice, does not guarantee that a study is recruiting, and does not determine eligibility. Contact the study team and a qualified healthcare professional when considering participation.

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