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NCT Number: NCT04986657

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).

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Key information

Conditions

Whole Genome Sequencing Acute Myeloid Leukemia Bone Marrow Diseases Hematologic Diseases Hemic and Lymphatic Diseases Leukemia Leukemia, Myeloid Leukemia, Myeloid, Acute Myelodysplastic Syndromes Neoplasms Neoplasms by Histologic Type

Age range

18 year and older

Sex eligibility

All sexes

Study type

Interventional

Phase

Not applicable

Primary location

Washington University School of Medicine

St Louis, Missouri, 63110, United States

Location status: Recruiting

Location contact

David Spencer, M.D., Ph.D.

SUB_INVESTIGATOR

Feng Gao, Ph.D.

SUB_INVESTIGATOR

Mary Politi, Ph.D.

SUB_INVESTIGATOR

Meagan Jacoby, M.D., Ph.D.

CONTACT

[email protected]

314-747-8439

Meagan Jacoby, M.D., Ph.D.

PRINCIPAL_INVESTIGATOR

Timothy Ley, M.D.

SUB_INVESTIGATOR

Who can participate

Healthy volunteers accepted: Yes

Only the study team can determine whether someone qualifies for participation.

Inclusion criteria

Patient

  • 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.

Inclusion criteria

Physician

  • 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.

Exclusion criteria

Patient

  • Younger than 18 years of age

Exclusion criteria

Physician

  • Does not treat patients at Washington University School of Medicine

Treatment and study plan

ChromoSeq

Device

Novel, streamlined whole genome sequencing approach

Primary outcomes

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

Secondary outcomes

  1. Stakeholder perceptions of ChromoSeq

    Time frame: Within 1 month after generation of ChromoSeq (estimated to be 2 months)

    • 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.

  2. 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)

    • 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.

  3. Stakeholder perceptions of ChromoSeq as measured by the Intervention Appropriateness Measure

    Time frame: When 100 genomes have been sequenced (estimated to be 12 months)

    • 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.

  4. 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)

    -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.

  5. Stakeholder perceptions of ChromoSeq as measured by the System Usability Scale

    Time frame: When 100 genomes have been sequenced (estimated to be 12 months)

    • 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

Study contacts

Contact information is provided by the study sponsor or research team.

Meagan Jacoby, M.D., Ph.D.

CONTACT

[email protected]

314-747-8439

Sponsors and collaborators

Lead sponsor

Washington University School of Medicine

Other

Registry information

Official study title

A Prospective Study of Whole Genome Sequencing (ChromoSeq) as an Adjunct to Conventional Genomic Profiling in AML and MDS

Important dates

Study start
2021
Primary completion
2027
Study completion
2027
First posted
Aug 3, 2021
Registry last updated
Oct 16, 2025

OpenTrials presents study information sourced from ClinicalTrials.gov. The official registry record should be consulted for the latest information.

View the official ClinicalTrials.gov record (opens in a new tab)

This listing is for discovery and informational purposes only. It is not medical advice, does not guarantee that a study is recruiting, and does not determine eligibility. Contact the study team and a qualified healthcare professional when considering participation.

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