Whole Genome SequencingNCT04986657
Whole Genome Sequencing (ChromoSeq) as an Adjunct to Conventional Genomic Profiling in AML and MDS
A study testing ChromoSeq in people with Whole Genome Sequencing and Acute Myeloid Leukemia, run by Washington University School of Medicine at 1 site in United States.
Trial summary
This is a single institution, prospective study of the whole genome sequencing assay, ChromoSeq. Using prospectively collected patient data, coupled with physician surveys, the investigators seek to determine the feasibility of implementing ChromoSeq in addition to standard genomic testing, for patients with the… Read more about this study
- Who is it for?
- Ages 18 years and olderHealthy volunteers can take part
- Conditions the study is for
- Whole Genome Sequencing, Acute Myeloid Leukemia, Myelodysplastic Syndromes
- What is being tested?
- ChromoSeq
- Type of treatment
- Medical device
- Could I receive a placebo?
- No, everyone receives an active treatment
- How many people
- 325 participants
- Where
- 1 siteUnited States
- Study dates
- 17 Sep 2021to 31 Dec 2027
- 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 18 years and older
- All sexes
- Healthy volunteers accepted
- Adult, Older adult
Who may be able to join
- Patient with a clinical suspicion for a new diagnosis of AML or MDS for whom the diagnostic molecular testing via the hematologic molecular algorithm (HMA) at BJH is requested or planned to be requested.
- Adult patients 18 years or older.
- Ability to understand and willingness to sign an IRB approved written informed consent document.
- Treating physician at Washington University School of Medicine who directs therapy for individuals with hematologic malignancies.
- Able and willing to complete standardized questionnaires about usability, and stakeholder perceptions of ChromoSeq during the ChromoSeq implementation process.
Who cannot join
- Younger than 18 years of age
- Does not treat patients at Washington University School of Medicine
Trial locations and contacts
1 site in 1 country. Contact the study team or a site near you to ask about taking part.
United States1 site, 1 recruiting
- Recruiting
Washington University School of Medicine
St Louis, Missouri, 63110
Meagan Jacoby, M.D., Ph.D., 314-747-8439, mjacoby@wustl.edu
Meagan Jacoby, M.D., Ph.D.
About this study
Official title: A Prospective Study of Whole Genome Sequencing (ChromoSeq) as an Adjunct to Conventional Genomic Profiling in AML and MDS
This is a single institution, prospective study of the whole genome sequencing assay, ChromoSeq. Using prospectively collected patient data, coupled with physician surveys, the investigators seek to determine the feasibility of implementing ChromoSeq in addition to standard genomic testing, for patients with the diagnoses of acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS).
- Being tested
- ChromoSeq
- Medical subject headings
- Leukemia, Myeloid, Acute, Myelodysplastic Syndromes
What participants receive
What participants receive. In a randomised study each person is assigned to one group by chance.
ChromoSeqDevice
Novel, streamlined whole genome sequencing approach
| Study group | Role | What they receive |
|---|---|---|
| Patients: ChromoSeq | Experimental | ChromoSeq will be performed on bone marrow DNA from consented patients in parallel with the standard of care cytogenetics, FISH, and the MyeloSeq gene panel obtained from that sample, in a CLIA licensed environment using CLIA-compliant ChromoSeq procedures. Receives: Device: ChromoSeq |
| Stakeholders (Treating Physicians) | No intervention | -Stakeholders (treating physicians) will complete surveys/questionnaires. As of protocol amendment 10/31/2023, the stakeholders (treating physicians) will no longer be completing surveys/questionnaires. |
What is being measured
The primary outcome is the main question the study is designed to answer.
Sensitivity of ChromoSeq as measured by total number of recurrent structural variants identified
- As compared to conventional cytogenetics in a real-time clinical setting
- The total number of recurrent structural variants will be measured in each sample by ChromoSeq and metaphase cytogenetics yielding a pair of measurements. Each measurement will also be dichotomized into the presence or absence of at least one recurrent structural variant. The hypothesis of no difference in the number of variants detected by each method will be analyzed by a paired-sample t-test. However, if it is determined that the assumptions of a t-test are not tenable then a paired-sample sign test will be used instead. McNemar's test will be used to compare whether or not at least one recurrent structural variant identified is by each method.
Measured: Through completion of all ChromoSeq tests (estimated to be 15 months)
Sensitivity of ChromoSeq as measured by total number of copy number alterations identified
- As compared to conventional cytogenetics in a real-time clinical setting
- The total number of copy number alterations will be measured in each sample by ChromoSeq and metaphase cytogenetics yielding a pair of measurements. Each measurement will also be dichotomized into the presence or absence of at least one copy number alteration. The hypothesis of no difference in the number of copy number alterations detected by each method will be analyzed by a paired-sample t-test. However, if it is determined that the assumptions of a t-test are not tenable then a paired-sample sign test will be used instead. McNemar's test will be used to compare whether or not at least one copy number alterations is identified is by each method.
Measured: Through completion of all ChromoSeq tests (estimated to be 15 months)
Sensitivity of ChromoSeq as measured by number of single nucleotide variants identified
- As compared to high coverage gene panels in a real-time clinical setting
- The number of single nucleotide variants will be counted for each sample. Additionally, the data will be dichotomized into the presence or absence of at least one single nucleotide variant. Data will be analyzed by paired-sample t-tests and McNemar's test.
Measured: Through completion of all ChromoSeq tests (estimated to be 15 months)
Sensitivity of ChromoSeq as measured by number of insertion-deletions identified
- As compared to high coverage gene panels in a real-time clinical setting
- The number of insertion-deletions will be counted for each sample. Additionally, the data will be dichotomized into the presence or absence of at least one insertion-deletion. Data will be analyzed by paired-sample t-tests and McNemar's test.
Measured: Through completion of all ChromoSeq tests (estimated to be 15 months)
Determine if risk-stratification using ChromoSeq correlates with overall-survival
- As compared to metaphase cytogenetics
- The relationship of risk-stratification defined by either ChromoSeq or conventional cytogenetics to clinical outcome will be illustrated with Kaplan-Meier survival analyses on overall survival for both ChromoSeq and metaphase cytogenetics. The predictive accuracy of the two methods will be tested by comparing the area under the ROC curves using the method of DeLong et al.
Measured: Through completion of follow-up for all patients (estimated to be 63 months)
Determine if risk-stratification using ChromoSeq correlates with event-free survival
- As compared to metaphase cytogenetics
- The relationship of risk-stratification defined by either ChromoSeq or conventional cytogenetics to clinical outcome will be illustrated with Kaplan-Meier survival analyses on event-free survival for both ChromoSeq and metaphase cytogenetics. The predictive accuracy of the two methods will be tested by comparing the area under the ROC curves using the method of DeLong et al.
Measured: Through completion of follow-up for all patients (estimated to be 63 months)
Proportion of cases in which ChromoSeq provides new genetic information to the clinician
- As compared to conventional genomic profiling (cytogenetics, FISH, and next-generation sequencing) that is used for clinical management (such as risk-stratification or institution of targeted gene therapy)
- Items in the ChromoSeq Implementation Physician Survey will be used to describe physician evaluation of ChromoSeq with conventional genomic profiling with regard to clinical management. Responses to these items will be presented in frequency tables. For statistical analysis, the values of each item will be recoded from 1-5 to -2 to +2 and one-sample t-tests used to test the null hypothesis that the mean value is 0 (neither agree nor disagree.) In addition, case-reports will be reviewed for qualitative evaluations of physician experience with the two methods.
Measured: Through completion of all ChromoSeq tests (estimated to be 15 months)
ChromoSeq turnaround time
-Measured from time of order requisition (hematologic molecular algorithm from Barnes Jewish Hospital) to return of report to the medical record
Measured: Through completion of all ChromoSeq tests (estimated to be 15 months)
Proportion of failed ChromoSeq assays
- As compared to failed standard of care genomic profiling assays
- Each assay will be categorized as successful or failed and a two-way table constructed displaying ChromoSeq assay status by standard assay status. A Pearson chi-square test will be calculated to test the null hypothesis that assay success is independent of type of assay.
Measured: Through completion of all ChromoSeq tests (estimated to be 15 months)
Secondary outcomes (5)
Stakeholder perceptions of ChromoSeq
- Using survey responses from treating physicians obtained from per case standardized questionnaires designed using Consolidated Framework for Implementation Research constructs
- For each case, the corresponding treating physician will be asked to answer a case-based ChromoSeq Implementation Physician Survey. In order to prospectively investigate how the ChromoSeq data was used or could be used by the treating physician for each case, and to evaluate perceptions in real time, the physician will be asked to complete the survey within 1 month of the ChromoSeq and completed conventional genomic profiling results being returned to the chart, whichever is later.
Measured: Within 1 month after generation of ChromoSeq (estimated to be 2 months)
Stakeholder perceptions of ChromoSeq as measured by the Acceptability of Intervention Measure
- Will complete survey at the time when 100 genomes have been sequenced
- 4 statements with answers ranging from 1=completely disagree to 5=completely agree.
Measured: When 100 genomes have been sequenced (estimated to be 12 months)
Stakeholder perceptions of ChromoSeq as measured by the Intervention Appropriateness Measure
- Will complete survey at the time when 100 genomes have been sequenced.
- 4 statements with answers ranging from 1=completely disagree to 5=completely agree.
Measured: When 100 genomes have been sequenced (estimated to be 12 months)
Stakeholder perceptions of ChromoSeq as measured by the Feasibility of Implementation Measure
-Will complete survey at the time when 100 genomes have been sequenced.
--4 statements with answers ranging from 1=completely disagree to 5=completely agree.
Measured: When 100 genomes have been sequenced (estimated to be 12 months)
Stakeholder perceptions of ChromoSeq as measured by the System Usability Scale
- Will complete survey at the time when 100 genomes have been sequenced.
- 10 statements about usability of ChromoSeq with answers ranging from 1=strongly disagree to 5=strongly agree
Measured: When 100 genomes have been sequenced (estimated to be 12 months)
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted3 Aug 2021
- Study start17 Sep 2021
- Primary completion31 Dec 2027 (estimated)
- Study completion31 Dec 2027 (estimated)
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Other trials for Whole Genome SequencingStudies of the same condition, open and under way.
- More trials run by Washington University School of MedicineThe sponsor's other registered studies.
- 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
- 325 participants (estimated)
Sponsor and investigators
- Lead sponsor
- Washington University School of Medicine
- Sponsor type
- University, hospital or other
- Responsible party
- Sponsor
- Investigators
- Meagan Jacoby, M.D., Ph.D., Principal investigator, Washington University School of Medicine
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT04986657
- Sponsor's protocol ID
- 202105123
- Status last verified
- Oct 2026
- First submitted
- 22 Jul 2021
- Last updated
- 21 Oct 2026
- Results posted
- No
- Data monitoring committee
- No
- FDA-regulated drug
- No
- FDA-regulated device
- Yes
- Individual data sharing
- Yes: Individual participant data that underlie the results reported in the article, after deidentification (text, tables, figures, and appendices).
Study at a glance
From the registry record, last updated by the sponsor on 21 Oct 2026. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- A Prospective Study of Whole Genome Sequencing (ChromoSeq) as an Adjunct to Conventional Genomic Profiling in AML and MDS
- ClinicalTrials.gov ID
- NCT04986657
- Acronym / sponsor ID
- 202105123
- Study type
- Interventional
- Recruitment status
- Recruiting
- Enrolment
- 325 participants (estimated)
- Lead sponsor
- Washington University School of MedicineUniversity, hospital or other
- Study start
- 17 Sep 2021 (actual)
- Primary completion
- 31 Dec 2027 (estimated)
- Study completion
- 31 Dec 2027 (estimated)
- First posted
- 3 Aug 2021 (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.
This is a single institution, prospective study of the whole genome sequencing assay, ChromoSeq. Using prospectively collected patient data, coupled with physician surveys, the investigators seek to determine the feasibility of implementing ChromoSeq in addition to standard genomic testing, for patients with the diagnoses of acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS).
Study design
- Primary purpose
- Diagnosis
- Allocation
- Non-randomised
- Intervention model
- Parallel groups
- Masking
- None (open label)
- Number of arms
- 2
| Arm | Type | Receives |
|---|---|---|
| Patients: ChromoSeq | Experimental | Device: ChromoSeqChromoSeq will be performed on bone marrow DNA from consented patients in parallel with the standard of care cytogenetics, FISH, and the MyeloSeq gene panel obtained from that sample, in a CLIA licensed environment using CLIA-compliant ChromoSeq procedures. |
| Stakeholders (Treating Physicians) | No intervention | –-Stakeholders (treating physicians) will complete surveys/questionnaires. As of protocol amendment 10/31/2023, the stakeholders (treating physicians) will no longer be completing surveys/questionnaires. |
Who may qualify
- Ages
- 18 years and older
- Sex
- All
- Healthy volunteers
- Accepted
- Age groups
- Adult, Older adult
Key inclusion criteria (5 listed)
- Patient with a clinical suspicion for a new diagnosis of AML or MDS for whom the diagnostic molecular testing via the hematologic molecular algorithm (HMA) at BJH is requested or planned to be requested.
- Adult patients 18 years or older.
- Ability to understand and willingness to sign an IRB approved written informed consent document.
- Treating physician at Washington University School of Medicine who directs therapy for individuals with hematologic malignancies.
- Able and willing to complete standardized questionnaires about usability, and stakeholder perceptions of ChromoSeq during the ChromoSeq implementation process.
Key exclusion criteria (2 listed)
- Younger than 18 years of age
- Does not treat patients at Washington University School of Medicine
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 |
|---|---|---|
| ChromoSeqNovel, streamlined whole genome sequencing approach | Device | Patients: ChromoSeq |
Primary outcome
Sensitivity of ChromoSeq as measured by total number of recurrent structural variants identified
Time frame: Through completion of all ChromoSeq tests (estimated to be 15 months)
* As compared to conventional cytogenetics in a real-time clinical setting * The total number of recurrent structural variants will be measured in each sample by ChromoSeq and metaphase cytogenetics yielding a pair of measurements. Each measurement will also be dichotomized into the presence or absence of at least one recurrent structural variant. The hypothesis of no difference in the number of variants detected by each method will be analyzed by a paired-sample t-test. However, if it is determined that the assumptions of a t-test are not tenable then a paired-sample sign test will be used instead. McNemar's test will be used to compare whether or not at least one recurrent structural variant identified is by each method.
Sensitivity of ChromoSeq as measured by total number of copy number alterations identified
Time frame: Through completion of all ChromoSeq tests (estimated to be 15 months)
* As compared to conventional cytogenetics in a real-time clinical setting * The total number of copy number alterations will be measured in each sample by ChromoSeq and metaphase cytogenetics yielding a pair of measurements. Each measurement will also be dichotomized into the presence or absence of at least one copy number alteration. The hypothesis of no difference in the number of copy number alterations detected by each method will be analyzed by a paired-sample t-test. However, if it is determined that the assumptions of a t-test are not tenable then a paired-sample sign test will be used instead. McNemar's test will be used to compare whether or not at least one copy number alterations is identified is by each method.
Sensitivity of ChromoSeq as measured by number of single nucleotide variants identified
Time frame: Through completion of all ChromoSeq tests (estimated to be 15 months)
* As compared to high coverage gene panels in a real-time clinical setting * The number of single nucleotide variants will be counted for each sample. Additionally, the data will be dichotomized into the presence or absence of at least one single nucleotide variant. Data will be analyzed by paired-sample t-tests and McNemar's test.
Sensitivity of ChromoSeq as measured by number of insertion-deletions identified
Time frame: Through completion of all ChromoSeq tests (estimated to be 15 months)
* As compared to high coverage gene panels in a real-time clinical setting * The number of insertion-deletions will be counted for each sample. Additionally, the data will be dichotomized into the presence or absence of at least one insertion-deletion. Data will be analyzed by paired-sample t-tests and McNemar's test.
Determine if risk-stratification using ChromoSeq correlates with overall-survival
Time frame: Through completion of follow-up for all patients (estimated to be 63 months)
* As compared to metaphase cytogenetics * The relationship of risk-stratification defined by either ChromoSeq or conventional cytogenetics to clinical outcome will be illustrated with Kaplan-Meier survival analyses on overall survival for both ChromoSeq and metaphase cytogenetics. The predictive accuracy of the two methods will be tested by comparing the area under the ROC curves using the method of DeLong et al.
Determine if risk-stratification using ChromoSeq correlates with event-free survival
Time frame: Through completion of follow-up for all patients (estimated to be 63 months)
* As compared to metaphase cytogenetics * The relationship of risk-stratification defined by either ChromoSeq or conventional cytogenetics to clinical outcome will be illustrated with Kaplan-Meier survival analyses on event-free survival for both ChromoSeq and metaphase cytogenetics. The predictive accuracy of the two methods will be tested by comparing the area under the ROC curves using the method of DeLong et al.
Proportion of cases in which ChromoSeq provides new genetic information to the clinician
Time frame: Through completion of all ChromoSeq tests (estimated to be 15 months)
* As compared to conventional genomic profiling (cytogenetics, FISH, and next-generation sequencing) that is used for clinical management (such as risk-stratification or institution of targeted gene therapy) * Items in the ChromoSeq Implementation Physician Survey will be used to describe physician evaluation of ChromoSeq with conventional genomic profiling with regard to clinical management. Responses to these items will be presented in frequency tables. For statistical analysis, the values of each item will be recoded from 1-5 to -2 to +2 and one-sample t-tests used to test the null hypothesis that the mean value is 0 (neither agree nor disagree.) In addition, case-reports will be reviewed for qualitative evaluations of physician experience with the two methods.
ChromoSeq turnaround time
Time frame: Through completion of all ChromoSeq tests (estimated to be 15 months)
-Measured from time of order requisition (hematologic molecular algorithm from Barnes Jewish Hospital) to return of report to the medical record
Proportion of failed ChromoSeq assays
Time frame: Through completion of all ChromoSeq tests (estimated to be 15 months)
* As compared to failed standard of care genomic profiling assays * Each assay will be categorized as successful or failed and a two-way table constructed displaying ChromoSeq assay status by standard assay status. A Pearson chi-square test will be calculated to test the null hypothesis that assay success is independent of type of assay.
5 secondary outcomes
Stakeholder perceptions of ChromoSeq
Time frame: Within 1 month after generation of ChromoSeq (estimated to be 2 months)
Stakeholder perceptions of ChromoSeq as measured by the Acceptability of Intervention Measure
Time frame: When 100 genomes have been sequenced (estimated to be 12 months)
Stakeholder perceptions of ChromoSeq as measured by the Intervention Appropriateness Measure
Time frame: When 100 genomes have been sequenced (estimated to be 12 months)
Stakeholder perceptions of ChromoSeq as measured by the Feasibility of Implementation Measure
Time frame: When 100 genomes have been sequenced (estimated to be 12 months)
Stakeholder perceptions of ChromoSeq as measured by the System Usability Scale
Time frame: When 100 genomes have been sequenced (estimated to be 12 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 21 Oct 2026.
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of MedicineLink provided by the sponsor.
- Individual participant dataSharing planned: Yes. Individual participant data that underlie the results reported in the article, after deidentification (text, tables, figures, and appendices).
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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.
Meagan Jacoby, M.D., Ph.D. principal investigator
Washington University School of Medicine
1 site in 1 country: see every site and its status.
Questions about this trial
What is this clinical trial studying?
A study testing ChromoSeq in people with Whole Genome Sequencing and Acute Myeloid Leukemia, run by Washington University School of Medicine at 1 site in United States.
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 5 inclusion and 2 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 21 Oct 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 United States. 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 Meagan Jacoby, M.D., Ph.D. (314-747-8439, mjacoby@wustl.edu), or a site near the patient. AzTrials does not enrol participants or take referrals.
What does the primary outcome measure?
Sensitivity of ChromoSeq as measured by total number of recurrent structural variants identified (time frame: Through completion of all ChromoSeq tests (estimated to be 15 months)). The study lists 9 primary outcomes in all. 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 21 Oct 2026.