Fast and Accurate Breast Cancer Diagnosis Using Nanopore Sequencing in Tanzania (Fast-ABCD Sequencing)

Recruiting

• Conditions: Breast Cancer Invasive

• Registration Number: NCT06633276
• Lead Sponsor: University of Bonn

Brief Summary

This pilot study will test the feasibility of using nanopore sequencing for breast cancer diagnosis in Tanzania. It aims to show that nanopore sequencing is non-inferior to the current standard of care, with the potential for faster and more cost-efficient results. By enhancing the speed and accuracy of diagnosis, this approach could improve treatment planning and outcomes for patients in resource-limited settings.

Detailed Description

Excess fresh tissue samples from patients with suspected breast cancer will undergo nanopore sequencing alongside the current standard of care (SoC), which includes histopathology and biomarker analysis for estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 (HER2) status.

Low-pass whole genome sequencing and DNA methylation-based classification will potentially enable the diagnosis of invasive ductal breast cancer in a cost-efficient and highly accurate manner. Additionally, breast cancer subtypes can be determined using methylation signatures and HER2 focal amplification, with results available within hours in a point-of-care setting.

The primary outcome measures are non-inferiority compared to SoC, turnaround time, and overall feasibility. Treatment is not altered due to results of the nanopore sequencing.

Study Timeline

• Study First Submitted: 2024-10-01
• Study First Submitted QC: 2024-10-07
• Study First Posted: 2024-10-09
• Status Verified: 2025-05
• Study Start: 2025-05
• Last Update Submitted: 2025-05-08
• Last Update Posted: 2025-05-14
• Primary Completion: 2026-04
• Study Completion: 2026-05

Recruitment & Eligibility

• Status: RECRUITING
• Sex: All
• Target Recruitment: 100

Inclusion Criteria

• Patient with suspected diagnosis of breast cancer undergoing biopsy or surgical resection after specialist consultation as per institutional guidelines
• Excess fresh tumor sample
• Written informed consent

Exclusion Criteria

• Unable to provide informed consent
• Patients who have already commenced therapy for BC (except for treatment other than biomedicine, e.g. herbal medicines)

Study & Design

• Study Type: OBSERVATIONAL
• Study Design: Not specified

Primary Outcome Measures

Name	Time	Method
Non-inferiority of nanopore-based biomarker evaluation	Concordance will be assessed after the enrollment of each cohort of 25 patients, with the final evaluation after study completion, approximately 12 months from enrollment start.	Concordance of invasive breast cancer diagnosis using nanopore sequencing vs. IHC HR/HER2 status as standard of care. The concordance will be expressed as the percentage agreement between the two methods across 100 patients.
Feasibility	The ratio will be assessed continuously after the sequencing of each batch of samples, with the final evaluation at study completion, approximately 12 months from enrollment start.	Feasibility will be measured by calculating the ratio of samples that are successfully sequenced and analyzed using nanopore sequencing technology, compared to the total number of samples processed.
Turnaround time	Through study completion, an average of 1 year	Turnaround time will be measured as the time (in days) from biopsy to the availability of the nanopore sequencing report, compared to the time from biopsy to the finalized pathology report.

Secondary Outcome Measures

Name	Time	Method
Patient Reported Experiences (PREs) with diagnostic procedures using a custom questionnaire	Administered within 24-48 hours post-biopsy.	Patient-reported experiences related to the diagnostic procedures, including the ease of sample collection, the perceived length of time for results, and overall comfort during procedures, will be assessed using a custom questionnaire.
Quality of Life (QoL) as assessed by the EORTC-QLQ BR-45 questionnaire	Administered at baseline, 6 months and 12 months.	Quality of Life (QoL) will be measured using the EORTC-QLQ BR-45 questionnaire. The questionnaire will be administered at baseline and at multiple time points during the study, with changes in QoL scores compared over time. It is available in Swahali and in case of illiteracy will be read to the patient.

Trial Locations

Locations (1)

Kilimanjaro Christian Medical Centre; 🇹🇿 Moshi, Tanzania