Pre-analytical Factors Affecting ctDNA Analysis in Early and Locally Advanced Breast Cancer

Recruiting

• Conditions: Early Stage Breast Carcinoma; Locally Advanced Breast Carcinoma; Anatomic Stage I Breast Cancer AJCC v8; Anatomic Stage III Breast Cancer AJCC v8; Anatomic Stage II Breast Cancer AJCC v8
• Interventions: Procedure: Biospecimen Collection; Other: Electronic Health Record Review

• Registration Number: NCT05945290
• Lead Sponsor: Mayo Clinic

Brief Summary

This study evaluates pre-analytical factors affecting circulating tumor deoxyribonucleic acid (ctDNA) analysis in breast cancer that not spread beyond the breast and or lymph nodes (early and locally advanced). ctDNA refers to freely circulating tumor DNA fragments found in the blood plasma. Pre-analytical factors such as blood collection tubes, delays in separation of plasma, centrifugation speeds, storage conditions, shipping and DNA extraction methods can all affect ctDNA measurements. Inappropriate processing can cause breaking down of the membrane (lysis) of peripheral blood cells that release background wild-type DNA and may also cause degradation of circulating tumor-specific DNA fragments. Both mechanisms will dilute levels of ctDNA in plasma and make it more difficult to detect. Evaluating the pre-analytical factors of the collection of blood and left over tissue samples for the research of cancer may help researchers to evaluate the impact of the blood collection/processing and long-term storage from patients with locally advanced breast cancer.

Detailed Description

PRIMARY OBJECTIVES:

I. To evaluate the impact of blood collection/processing. II. To evaluate the impact of long-term storage of plasma and extracted DNA.

OUTLINE: This is an observational study.

Patients undergo blood sample collection throughout the study. Patients also undergo collection of leftover tissue samples from standard of care (SOC) procedures and have medical records reviewed.

Study Timeline

• Study Start: 2022-07-07
• Study First Submitted: 2023-07-06
• Study First Submitted QC: 2023-07-06
• Study First Posted: 2023-07-14
• Status Verified: 2025-05
• Last Update Submitted: 2025-05-16
• Last Update Posted: 2025-05-21
• Primary Completion: 2030-07
• Study Completion: 2030-12

Recruitment & Eligibility

• Status: RECRUITING
• Sex: Female
• Target Recruitment: 120

Inclusion Criteria

• All women > 18 years of age
• Stage I-III breast cancer
• Subject has consented to IRB 2130-00 Tissue Registry

Exclusion Criteria

• Stage IV breast cancer
• Unwilling or unable to give consent
• Unable to participate for 1 year
• No one with a concurrent cancer except those diagnosed with an in situ cancer or non-melanoma skin cancer

Study & Design

• Study Type: OBSERVATIONAL
• Study Design: Not specified

Arm && Interventions

Group	Intervention	Description
Observational (Biospecimen collection, medical record)	Electronic Health Record Review	Patients undergo blood sample collection throughout the study. Patients also undergo collection of leftover tissue samples from SOC procedures and have medical records reviewed.
Observational (Biospecimen collection, medical record)	Biospecimen Collection	Patients undergo blood sample collection throughout the study. Patients also undergo collection of leftover tissue samples from SOC procedures and have medical records reviewed.

Primary Outcome Measures

Name	Time	Method
Change in tumor specific circulating tumor deoxyribonucleic acid (ctDNA) levels	Baseline to 5 years	Will be measured as tumor fraction (%), using TARgeted DIgital Sequencing (TARDIS).

Secondary Outcome Measures

Name	Time	Method
Change in total cell-free DNA concentration	Baseline to 5 years	Will be measured in genome copies/ml of plasma, using the Quality Assessment (QA) assay.
Background error rate	Baseline to 5 years	Will be measured as errors per bp sequenced, measured using TARgeted DIgital Sequencing (TARDIS).
Change in tumor-specific circulating tumor deoxyribonucleic acid (ctDNA) fragment size profile	Baseline to 5 years	Will be measured as average fragment size, using TARgeted DIgital Sequencing (TARDIS).
Change in total cell-free DNA fragment size profile	Baseline to 5 years	Will be measured as % fragmented, using the Quality Assessment (QA) assay.

Trial Locations

Locations (1)

Mayo Clinic in Arizona; 🇺🇸 Scottsdale, Arizona, United States