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

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

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.

Study Overview

• Status: Recruiting
• Conditions: Breast Cancer Invasive

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 Type: Observational
• Enrollment (Estimated): 100

Contacts and Locations

• Study Contact: Name: Oliver Henke, MD; Phone Number: +49 (0) 228 287 51521; Email: Oliver.Henke@ukbonn.de
• Study Contact Backup: Name: Maximilian Rost, MD; Phone Number: +49 (0) 228 287 51521; Email: maximilian.rost@ukbonn.de

Study Locations

• Tanzania
  • Moshi, Tanzania, P.O. Box 3010
    • Recruiting
    • Kilimanjaro Christian Medical Centre
    • Contact: Oliver Henke; Phone Number: +255 (0) 76 1511227; Email: Oliver.Henke@ukbonn.de

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Adult; Older Adult
• Accepts Healthy Volunteers: No

• Sampling Method: Non-Probability Sample

Study Population

All patients with suspected invasive breast cancer undergoing diagnostic workup will be offered to participate.

Description

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 Plan

How is the study designed?

Number of groups / cohorts

1

Cohorts and Interventions

Group / Cohort
Nanopore sequencing; All adult patients at with suspected diagnosis of breast cancer undergoing biopsy or surgical resection will be offered to participate in the study. After informed written consent excess tissue is preserved for DNA extraction using commercial spin column kits and will be further analyzed.

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Non-inferiority of nanopore-based biomarker evaluation	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.	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.
Feasibility	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.	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.
Turnaround time	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.	Through study completion, an average of 1 year

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Patient Reported Experiences (PREs) with diagnostic procedures using a custom questionnaire	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.	Administered within 24-48 hours post-biopsy.
Quality of Life (QoL) as assessed by the EORTC-QLQ BR-45 questionnaire	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.	Administered at baseline, 6 months and 12 months.

Collaborators and Investigators

• Sponsor: University of Bonn
• Collaborators: German Cancer Research Center; Kilimanjaro Christian Medical Centre,Moshi,Tanzania
• Investigators: Principal Investigator: Oliver Henke, MD, Section Global Health, University Hospital Bonn

Study record dates

Study Major Dates

• Study Start (Estimated): May 1, 2025
• Primary Completion (Estimated): April 1, 2026
• Study Completion (Estimated): May 1, 2026

Study Registration Dates

• First Submitted: October 1, 2024
• First Submitted That Met QC Criteria: October 7, 2024
• First Posted (Actual): October 9, 2024

Study Record Updates

• Last Update Posted (Actual): May 14, 2025
• Last Update Submitted That Met QC Criteria: May 8, 2025
• Last Verified: May 1, 2025

More Information

Terms related to this study

• Keywords: breast cancer; Nanopore sequencing
• Additional Relevant MeSH Terms: Neoplasms by Site; Neoplasms; Skin Diseases; Breast Diseases; Breast Neoplasms
• Other Study ID Numbers: 23Ac03011

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: UNDECIDED

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No
• product manufactured in and exported from the U.S.: No