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NCT Number: NCT07416500

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.

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Key information

Conditions

Breast Cancer Breast Diseases Breast Lesions of Uncertain Malignant Potential (B3 Lesions) Breast Neoplasms Neoplasms Neoplasms by Site Skin Diseases Skin and Connective Tissue Diseases

Age range

40 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 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.

Who can participate

Healthy volunteers accepted: No

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

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

Treatment and study plan

MS-MLPA Methylation Analysis

Diagnostic Test

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.

Primary outcomes

  1. 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.

Other outcomes

  1. 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).

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
2025
First posted
Feb 18, 2026
Registry last updated
Feb 25, 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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