Determining Minimal Residual Disease Using ctDNA Deep Sequencing

NCT07660627 | Recruiting DMC

• 1 other identifier: A2/23
• Study Type: interventional
• Target: 34
• Locations: 1 country
• Sites: 1

Brief Summary

Preoperative neoadjuvant chemotherapy is the standard treatment for locally advanced gastrointestinal tumours. However, not all patients respond to preoperative treatment. Early identification of progression during neoadjuvant chemotherapy or diagnosis of early disease relapse during adjuvant treatment is essential to modify the treatment strategy. The aim of this project is to validate ctDNA as a biomarker of molecular relapse/progression of disease.

Conditions

Esophageal Adenocarcinoma; Gastric Cancer; Pancreatic Cancer

Keywords

Minimal residual disease; NGS sequencing; gastrointestinal tumors; Preoperative neoadjuvant chemotherapy

Outcome Measures

Primary Outcomes (1)

• Sensitivity of targeted NGS assay for ctDNA mutation detection

  Proportion of tumor-confirmed driver mutations detected in plasma cfDNA using the developed targeted NGS assay. Unit of Measure: Percentage (%)

  Through study completion, an average of 24 months.

Secondary Outcomes (2)

• Monitoring ctDNA levels

  Through study completion, an average of 24 months.

• Variant allele frequency (VAF) of detected driver mutations in cfDNA

  Through study completion, an average of 24 months.

Study Arms (2)

Interventional

EXPERIMENTAL

Participants with locally advanced potentially resectable esophageal, gastric, or pancreatic cancer receiving neoadjuvant/perioperative treatment will undergo serial blood sampling for plasma isolation and circulating tumor DNA (ctDNA) analysis. Samples will be collected prior to initiation of neoadjuvant therapy, at the time of surgery, and subsequently at approximately 3-month intervals for 1-2 years after surgery or until disease progression. ctDNA analyses will be performed using a targeted next-generation sequencing (NGS) approach to evaluate longitudinal changes in tumor-specific genomic alterations and their association with treatment response and disease recurrence.

Diagnostic Test: NGS sequencing of mutations selected based on sequencing of primary tumors

Control

ACTIVE COMPARATOR

Participants with esophageal, gastric, or pancreatic cancer receiving first-line palliative systemic therapy will undergo serial blood sampling for plasma isolation and ctDNA analysis. Samples will be collected prior to initiation of systemic treatment and subsequently at approximately 3-month intervals during first-line therapy. ctDNA analyses will be performed using the same targeted NGS methodology to assess longitudinal changes in tumor-specific genomic alterations during systemic treatment.

Diagnostic Test: NGS sequencing of mutations selected based on sequencing of primary tumors

Interventions

NGS sequencing of mutations selected based on sequencing of primary tumors DIAGNOSTIC_TEST

Sequencing of the primary tumor will be performed on a MiSeq instrument using the Accel-Amplicon panel, which covers the most common mutations. For deep sequencing of ctDNA, 2-3 genomic regions carrying mutations in the primary tumor will be selected for the patient. For these regions, sets of universal primers will be designed to amplify the mutations most commonly found in solid tumors (RAS, BRAF, TP53, EGFR, APC, etc.). Another set of universal primers will contain a sequence for indexing individual samples, enabling the parallel sequencing of up to 96 samples simultaneously. The sequencing library will be analyzed on a NextSeq 500 instrument, which allows for up to 400 million reads in a single sequencing run. The sequencing results will then be correlated with the clinical course of the disease.

Control; Interventional

Eligibility Criteria

• Sex: all
• Healthy Volunteers: No
• Age Groups: Child (0-17), Adult (18-64), Older Adult (65+)

You may qualify if:

• Consent to participate in the study
• Patients with esophageal, gastric, or pancreatic cancer, stage 0-2
• Patients with locally advanced, potentially operable disease treated with systemic perioperative chemotherapy or chemoradiotherapy
• Patients with metastatic disease treated with first- to third-line palliative systemic therapy

You may not qualify if:

• not specified

Sponsors & Collaborators

• Masaryk Memorial Cancer Institute: lead

Study Sites (1)

Masaryk Memorial Cancer Institute

Brno, 65653, Czechia

RECRUITING

MeSH Terms

Conditions

Adenocarcinoma Of Esophagus; Stomach Neoplasms; Pancreatic Neoplasms; Neoplasm, Residual; Digestive System Neoplasms

Condition Hierarchy (Ancestors)

Gastrointestinal Neoplasms; Neoplasms by Site; Neoplasms; Digestive System Diseases; Gastrointestinal Diseases; Stomach Diseases; Endocrine Gland Neoplasms; Pancreatic Diseases; Endocrine System Diseases; Neoplastic Processes; Pathologic Processes; Pathological Conditions, Signs and Symptoms

Study Officials

• Petr Müller, MD, PhD

  Masaryk Memorial Cancer Institute

  STUDY DIRECTOR

• Radka Lordick Obermannová, MD, Doc, PhD

  Masaryk Memorial Cancer Institute

  PRINCIPAL INVESTIGATOR

Central Study Contacts

Martina Lojová, PhD

CONTACT

+420543136232; martina.lojova@mou.cz

Tereza Štěpánková, PhD

CONTACT

+420543136223; tereza.stepankova@mou.cz

Study Design

• Study Type: interventional
• Phase: not applicable
• Allocation: NON RANDOMIZED
• Masking: NONE
• Purpose: DIAGNOSTIC
• Intervention Model: PARALLEL
• Sponsor Type: OTHER
• Responsible Party: SPONSOR

Study Record Dates

• First Submitted: June 10, 2026
• First Posted: June 22, 2026
• Study Start: August 22, 2022
• Primary Completion (Estimated): December 31, 2026
• Study Completion (Estimated): December 31, 2026
• Last Updated: June 24, 2026

Record last verified: 2026-06

Data Sharing

• IPD Sharing: Will share
• Shared Documents: CSR
• Time Frame: after study completion
• Access Criteria: During the study, data will be managed in pseudonymized form in a protected database environment, available only for study team. After completion of the study, the data will be fully anonymized for publication purposes. All publication outputs of the study will be carried out by a team of researchers led by the principal investigator. The submission of each publication is subject to the approval of the principal investigator. The results of this study may be published or presented at scientific meetings after approval by the PI and always after anonymization of the subjects' personal data in accordance with Act No. 101/2000 Coll., on the protection of personal data.

Locations

CZ (1)