Esophageal AdenocarcinomaCIT-SEQNCT07660627
Determining Minimal Residual Disease Using ctDNA Deep Sequencing
A study testing NGS sequencing of mutations selected based on sequencing of primary tumors in people with Esophageal Adenocarcinoma and Gastric Cancer, run by Masaryk Memorial Cancer Institute at 1 site in Czechia.
Trial 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… Read more about this study
- Who is it for?
- Any age
- Conditions the study is for
- Esophageal Adenocarcinoma, Gastric Cancer, Pancreatic Cancer
- What is being tested?
- NGS sequencing of mutations selected based on sequencing of primary tumors
- Could I receive a placebo?
- No, everyone receives an active treatment
- How many people
- 34 participants
- Where
- 1 siteCzechia
- Study dates
- 22 Aug 2022to 31 Dec 2026
- Phase
- Interventional
- Are there results?
- Not yet: the study is under way
Key requirements
Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.
- Ages Any age
- All sexes
- No healthy volunteers
- Child, Adult, Older adult
Who may be able to join
- 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
Who cannot join
- not specified
Trial locations and contacts
1 site in 1 country. Contact the study team or a site near you to ask about taking part.
Czechia1 site, 1 recruiting
- Recruiting
Masaryk Memorial Cancer Institute
Brno, 65653
About this study
Official title: Determination of Minimal Residual Disease by Deep ctDNA Sequencing.
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.
Read the detailed description
Neoadjuvant chemotherapy is the standard of care for locally advanced gastrointestinal tumors. However, not all patients respond to preoperative treatment. Early identification of disease progression during neoadjuvant chemotherapy or diagnosis of early disease relapse during adjuvant therapy is essential for modifying the treatment strategy. The aim of the project is to validate ctDNA as a molecular biomarker of disease relapse/progression.
The persistence of tumor cells after primary treatment of cancer is a key prognostic indicator of the disease's future course. In solid tumors, minimal residual disease (MRD) may involve tumor cells in the blood, small metastases in the body, or a small portion of the primary tumor that remains after treatment. Detection of MRD at a stage when the tumor cannot be detected by morphological imaging techniques is becoming an important diagnostic indicator that could better stratify patients after primary treatment in the future. MRD determination should thus serve in the future both to indicate further treatment and to monitor treatment response. For the successful clinical application of MRD determination, it is crucial to establish a sufficiently sensitive and specific method based on the detection of circulating tumor DNA (ctDNA). Tumor ctDNA is a component of circulating free DNA (cfDNA), which is released into the plasma from apoptotic or necrotic cells in the form of fragments with an average length of approximately 170 bp. The release of DNA from cells into the bloodstream can be influenced by a number of factors, which is reflected in the high variability of total cfDNA concentration, which can range from 1 to 100,000 fragments per milliliter of plasma. Therefore, to quantify MRD, it is crucial to determine both the total concentration of cfDNA and the proportion of tumor ctDNA. To reliably distinguish tumor ctDNA from non-tumor cfDNA, the detection of mutations identified in the primary tumor is currently used. For this purpose, PCR or digital PCR detecting specific mutations using fluorescent probes can be used. An alternative to PCR is mutation detection using next-generation sequencing (NGS), which allows for the detection of multiple different mutations in parallel. A disadvantage of MRD determination using commercial NGS kits designed for liquid biopsies is the high financial cost and the time-consuming preparation of sequencing libraries. We hypothesize that deep sequencing of cfDNA targeting mutations identified in the primary tumor can significantly increase both the specificity and sensitivity of MRD detection from liquid biopsies. Deep sequencing of 2-3 genomic regions with known mutations should enable the parallel detection of MRD in multiple patients while reducing the cost of this type of testing compared to commercially available options.
- Conditions
- Esophageal Adenocarcinoma, Gastric Cancer, Pancreatic Cancer
- Being tested
- NGS sequencing of mutations selected based on sequencing of primary tumors
- Keywords
- Minimal residual disease, NGS sequencing, gastrointestinal tumors, Preoperative neoadjuvant chemotherapy
- Medical subject headings
- Adenocarcinoma Of Esophagus, Stomach Neoplasms, Pancreatic Neoplasms, Neoplasm, Residual, Digestive System Neoplasms
What participants receive
What participants receive. In a randomised study each person is assigned to one group by chance.
NGS sequencing of mutations selected based on sequencing of primary tumorsDiagnostic 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.
| Study group | Role | What they receive |
|---|---|---|
| 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. Receives: 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. Receives: Diagnostic Test: NGS sequencing of mutations selected based on sequencing of primary tumors |
What is being measured
The primary outcome is the main question the study is designed to answer.
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 (%)
Measured: Through study completion, an average of 24 months.
Secondary outcomes (2)
Monitoring ctDNA levels
A secondary objective is to monitor ctDNA levels throughout the patient's treatment and to determine appropriate intervals for plasma collection after surgery and during adjuvant therapy.
Measured: Through study completion, an average of 24 months.
Variant allele frequency (VAF) of detected driver mutations in cfDNA
Quantitative assessment of tumor-specific mutations detected in cfDNA using targeted NGS sequencing. Unit of Measure: Variant allele frequency (%)
Measured: Through study completion, an average of 24 months.
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted22 Jun 2026
- Study start22 Aug 2022
- Primary completion31 Dec 2026 (estimated)
- Study completion31 Dec 2026 (estimated)
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Other trials for Esophageal AdenocarcinomaStudies of the same condition, open and under way.
- What the trial phases meanHow a treatment moves from first tests in people to approval.
More details
For doctors and researchers: how the study is designed, who runs it, and its registry IDs.
Study design
- Study type
- Interventional
- Phase
- Phase N/A
- Primary purpose
- Diagnosis
- Allocation
- Non-randomised
- Intervention model
- Parallel groups
- Masking
- None (open label)
- Enrolment
- 34 participants (estimated)
Sponsor and investigators
- Lead sponsor
- Masaryk Memorial Cancer Institute
- Sponsor type
- University, hospital or other
- Responsible party
- Sponsor
- Investigators
- Petr Müller, MD, PhD, Study director, Masaryk Memorial Cancer InstituteRadka Lordick Obermannová, MD, Doc, PhD, Principal investigator, Masaryk Memorial Cancer Institute
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT07660627
- Sponsor's protocol ID
- A2/23
- Acronym
- CIT-SEQ
- Status last verified
- Jun 2026
- First submitted
- 10 Jun 2026
- Last updated
- 24 Jun 2026
- Results posted
- No
- Data monitoring committee
- Yes
- FDA-regulated drug
- No
- FDA-regulated device
- No
- Individual data sharing
- Yes: IPD to be shared in pseudonymized form during the study. IPD to be published in anonymized form.
Study at a glance
From the registry record, last updated by the sponsor on 24 Jun 2026. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- Determination of Minimal Residual Disease by Deep ctDNA Sequencing.
- ClinicalTrials.gov ID
- NCT07660627
- Acronym / sponsor ID
- CIT-SEQ / A2/23
- Conditions
- Esophageal Adenocarcinoma, Gastric Cancer, Pancreatic Cancer
- Keywords
- Minimal residual disease, NGS sequencing, gastrointestinal tumors, Preoperative neoadjuvant chemotherapy
- Study type
- Interventional
- Recruitment status
- Recruiting
- Enrolment
- 34 participants (estimated)
- Lead sponsor
- Masaryk Memorial Cancer InstituteUniversity, hospital or other
- Study start
- 22 Aug 2022 (actual)
- Primary completion
- 31 Dec 2026 (estimated)
- Study completion
- 31 Dec 2026 (estimated)
- First posted
- 22 Jun 2026 (actual)
- Results
- Not posted in the source record
Clinical summary
The research question as the sponsor registered it. This describes what the study plans to test, not what it found.
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.
Detailed description
Neoadjuvant chemotherapy is the standard of care for locally advanced gastrointestinal tumors. However, not all patients respond to preoperative treatment. Early identification of disease progression during neoadjuvant chemotherapy or diagnosis of early disease relapse during adjuvant therapy is essential for modifying the treatment strategy. The aim of the project is to validate ctDNA as a molecular biomarker of disease relapse/progression.
The persistence of tumor cells after primary treatment of cancer is a key prognostic indicator of the disease's future course. In solid tumors, minimal residual disease (MRD) may involve tumor cells in the blood, small metastases in the body, or a small portion of the primary tumor that remains after treatment. Detection of MRD at a stage when the tumor cannot be detected by morphological imaging techniques is becoming an important diagnostic indicator that could better stratify patients after primary treatment in the future. MRD determination should thus serve in the future both to indicate further treatment and to monitor treatment response. For the successful clinical application of MRD determination, it is crucial to establish a sufficiently sensitive and specific method based on the detection of circulating tumor DNA (ctDNA). Tumor ctDNA is a component of circulating free DNA (cfDNA), which is released into the plasma from apoptotic or necrotic cells in the form of fragments with an average length of approximately 170 bp. The release of DNA from cells into the bloodstream can be influenced by a number of factors, which is reflected in the high variability of total cfDNA concentration, which can range from 1 to 100,000 fragments per milliliter of plasma. Therefore, to quantify MRD, it is crucial to determine both the total concentration of cfDNA and the proportion of tumor ctDNA. To reliably distinguish tumor ctDNA from non-tumor cfDNA, the detection of mutations identified in the primary tumor is currently used. For this purpose, PCR or digital PCR detecting specific mutations using fluorescent probes can be used. An alternative to PCR is mutation detection using next-generation sequencing (NGS), which allows for the detection of multiple different mutations in parallel. A disadvantage of MRD determination using commercial NGS kits designed for liquid biopsies is the high financial cost and the time-consuming preparation of sequencing libraries. We hypothesize that deep sequencing of cfDNA targeting mutations identified in the primary tumor can significantly increase both the specificity and sensitivity of MRD detection from liquid biopsies. Deep sequencing of 2-3 genomic regions with known mutations should enable the parallel detection of MRD in multiple patients while reducing the cost of this type of testing compared to commercially available options.
Study design
- Primary purpose
- Diagnosis
- Allocation
- Non-randomised
- Intervention model
- Parallel groups
- Masking
- None (open label)
- Number of arms
- 2
| Arm | Type | Receives |
|---|---|---|
| Interventional | Experimental | Diagnostic Test: NGS sequencing of mutations selected based on sequencing of primary tumorsParticipants 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. |
| Control | Active comparator | Diagnostic Test: NGS sequencing of mutations selected based on sequencing of primary tumorsParticipants 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. |
Who may qualify
- Sex
- All
- Healthy volunteers
- Not accepted
- Age groups
- Child, Adult, Older adult
Key inclusion criteria (4 listed)
- 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
Key exclusion criteria (1 listed)
- not specified
Eligibility is decided by the study team after screening; this overview does not establish that a patient qualifies. Full inclusion and exclusion criteria.
Interventions
| Intervention | Type | Arms |
|---|---|---|
| NGS sequencing of mutations selected based on sequencing of primary tumorsSequencing 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. | Diagnostic test | Control, Interventional |
Primary outcome
Sensitivity of targeted NGS assay for ctDNA mutation detection
Time frame: Through study completion, an average of 24 months.
Proportion of tumor-confirmed driver mutations detected in plasma cfDNA using the developed targeted NGS assay. Unit of Measure: Percentage (%)
2 secondary outcomes
Monitoring ctDNA levels
Time frame: Through study completion, an average of 24 months.
Variant allele frequency (VAF) of detected driver mutations in cfDNA
Time frame: Through study completion, an average of 24 months.
Results and safety
This study is still under way. Results are not available in the source record yet.
Research links
- Official record on ClinicalTrials.govLast updated by the sponsor 24 Jun 2026.
- Individual participant dataSharing planned: Yes. IPD to be shared in pseudonymized form during the study. IPD to be published in anonymized form.
Related trials for Esophageal Adenocarcinoma
Active, not recruitingPhase 1
A Study of KK2269 in Adult Participants With Solid Tumors
Advanced Solid Tumor, Metastatic Solid Tumor
RecruitingPhase 1/2
A Study to Evaluate the Efficacy and Safety of Ifinatamab Deruxtecan (I-DXd) in Subjects With Recurrent or Metastatic Solid Tumors (IDeate-PanTumor02)
Recurrent or Metastatic Solid Tumors
RecruitingPhase 2/3
Adding Nivolumab to Usual Treatment for People With Advanced Stomach or Esophageal Cancer, PARAMUNE Trial
Advanced Esophageal Adenocarcinoma, Advanced Gastric Adenocarcinoma
Active, not recruitingPhase 2
Targeted Therapy Directed by Genetic Testing in Treating Patients With Advanced Refractory Solid Tumors, Lymphomas, or Multiple Myeloma (The MATCH Screening Trial)
Advanced Lymphoma, Advanced Malignant Solid Neoplasm
Not yet recruitingObservational study
Zanidatamab Outcomes and Lived Experiences in Advanced HER2+ GEA
Esophageal Cancer, GastroEsophageal Cancer
Referral and contact
AzTrials does not enrol participants or take referrals. Contact the study team or a site listed below; they decide who can take part.
Petr Müller, MD, PhD study director
Masaryk Memorial Cancer Institute
Radka Lordick Obermannová, MD, Doc, PhD principal investigator
Masaryk Memorial Cancer Institute
1 site in 1 country: see every site and its status.
Questions about this trial
What is this clinical trial studying?
A study testing NGS sequencing of mutations selected based on sequencing of primary tumors in people with Esophageal Adenocarcinoma and Gastric Cancer, run by Masaryk Memorial Cancer Institute at 1 site in Czechia.
The full registered description is in the About this study section and the official record.
Who may be eligible to take part?
The sponsor lists 4 inclusion and 1 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.
Is this clinical trial currently recruiting?
The record says: looking for participants now, as of the sponsor's last update on 24 Jun 2026. Status can change between updates, so confirm with the study contact before making plans.
Where is the study taking place?
The record lists 1 site in Czechia. Whether a site is taking part right now should be confirmed with that site. See every site.
What are the possible benefits and risks?
They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.
Are results available for this study?
This study is still under way. Results are not available in the source record yet.
How can a doctor refer a patient or contact the research team?
Contact Martina Lojová, PhD (+420543136232, martina.lojova@mou.cz), or a site near the patient. AzTrials does not enrol participants or take referrals.
What does the primary outcome measure?
Sensitivity of targeted NGS assay for ctDNA mutation detection (time frame: Through study completion, an average of 24 months.). It is what the study was designed to measure, not a finding.
Where can I read the original study information?
Does a listing mean the treatment is approved or proven to work?
No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.
How often is this information updated?
AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 24 Jun 2026.