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NCT Number: NCT06633276

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

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.

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Key information

Conditions

Breast Cancer Invasive Breast Diseases Breast Neoplasms Neoplasms Neoplasms by Site Skin Diseases Skin and Connective Tissue Diseases

Age range

18 year and older

Sex eligibility

All sexes

Study type

Observational

Primary location

About this study

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.

Who can participate

Healthy volunteers accepted: No

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

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)

Treatment and study plan

Primary outcomes

  1. Non-inferiority of nanopore-based biomarker evaluation

    Time frame: 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.

  2. Feasibility

    Time frame: 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.

  3. Turnaround time

    Time frame: 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 outcomes

  1. Quality of Life (QoL) as assessed by the EORTC-QLQ BR-45 questionnaire

    Time frame: 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.

  2. Patient Reported Experiences (PREs) with diagnostic procedures using a custom questionnaire

    Time frame: 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.

Study contacts

Contact information is provided by the study sponsor or research team.

Maximilian Rost, MD

CONTACT

[email protected]

+49 (0) 228 287 51521

Oliver Henke, MD

CONTACT

[email protected]

+49 (0) 228 287 51521

Sponsors and collaborators

Lead sponsor

University of Bonn

Other

Collaborators

  • German Cancer Research Center
  • Kilimanjaro Christian Medical Centre,Moshi,Tanzania

Registry information

Official study title

Nanopore Sequencing for Accelerating Breast Cancer Diagnosis in Tanzania: A Prospective Observational Study

Important dates

Study start
2025
Primary completion
2026
Study completion
2026
First posted
Oct 9, 2024
Registry last updated
May 14, 2025

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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