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Whole Genome Sequencing (ChromoSeq) as an Adjunct to Conventional Genomic Profiling in MDS

Primary Purpose

Whole Genome Sequencing, Myelodysplastic Syndromes

Status
Recruiting
Phase
Not Applicable
Locations
United States
Study Type
Interventional
Intervention
ChromoSeq
Sponsored by
Washington University School of Medicine
About
Eligibility
Locations
Arms
Outcomes
Full info

About this trial

This is an interventional diagnostic trial for Whole Genome Sequencing

Eligibility Criteria

18 Years - undefined (Adult, Older Adult)All SexesAccepts Healthy Volunteers

Inclusion Criteria Patient:

  • Diagnosis of MDS, or a clinical suspicion for a new diagnosis of MDS, for whom routine diagnostic testing is requested or planned to be requested.
  • Seen in the outpatient setting.
  • Not been previously treated with disease-modifying therapy (such as lenalidomide or hypomethylating agents).

Note: Patients who have received transfusional support, erythropoietin-stimulating agents, growth factor support, or luspatercept are eligible.

At least 18 years of age.

-Able to understand and willing 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 stakeholder perceptions of ChromoSeq during the ChromoSeq implementation process. (Written documentation of informed consent is not required.)

Exclusion Criteria Patient:

-Younger than 18 years of age

Exclusion Criteria Physician

-Does not treat patients at Washington University School of Medicine

Sites / Locations

  • Washington University School of MedicineRecruiting

Arms of the Study

Arm 1

Arm 2

Arm Type

Experimental

No Intervention

Arm Label

Patients: ChromSeq

Stakeholders (Treating Physicians)

Arm Description

ChromoSeq will be performed on bone marrow or peripheral blood 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) will complete surveys/questionnaires

Outcomes

Primary Outcome Measures

Rate of assay success on first attempt between ChromoSeq and conventional cytogenetics as measured by total number of recurrent structural variants identified
-The number of recurrent structural variants detected by ChromoSeq will be compared to those detected by conventional cytogenetics using two non-inferiority tests for dependent samples using non-inferiority margin of 1%.
Rate of assay success on first attempt between ChromoSeq and conventional cytogenetics as measured by total number of copy number alterations identified
The number of copy number alterations detected by ChromoSeq will be compared to those detected by conventional cytogenetics using two non-inferiority tests for dependent samples using non-inferiority margin of 1%.
Proportion of failed ChromoSeq assays
As compared to failed standard of care genomic profiling assays The proportion of first-run failures for ChromoSeq assays will be compared to the proportion of failed standard of care genomic profiling assays using a directional Fisher's exact test.

Secondary Outcome Measures

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.

Full Information

First Posted
June 21, 2022
Last Updated
September 2, 2023
Sponsor
Washington University School of Medicine
Collaborators
American Society of Hematology
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1. Study Identification

Unique Protocol Identification Number
NCT05434598
Brief Title
Whole Genome Sequencing (ChromoSeq) as an Adjunct to Conventional Genomic Profiling in MDS
Official Title
A Prospective Study of Whole Genome Sequencing (ChromoSeq) as an Adjunct to Conventional Genomic Profiling in MDS
Study Type
Interventional

2. Study Status

Record Verification Date
September 2023
Overall Recruitment Status
Recruiting
Study Start Date
July 27, 2022 (Actual)
Primary Completion Date
July 31, 2024 (Anticipated)
Study Completion Date
August 31, 2024 (Anticipated)

3. Sponsor/Collaborators

Responsible Party, by Official Title
Sponsor
Name of the Sponsor
Washington University School of Medicine
Collaborators
American Society of Hematology

4. Oversight

Studies a U.S. FDA-regulated Drug Product
No
Studies a U.S. FDA-regulated Device Product
Yes
Device Product Not Approved or Cleared by U.S. FDA
Yes
Product Manufactured in and Exported from the U.S.
No
Data Monitoring Committee
Yes

5. Study Description

Brief 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 diagnosis of myelodysplastic syndrome (MDS).

6. Conditions and Keywords

Primary Disease or Condition Being Studied in the Trial, or the Focus of the Study
Whole Genome Sequencing, Myelodysplastic Syndromes

7. Study Design

Primary Purpose
Diagnostic
Study Phase
Not Applicable
Interventional Study Model
Parallel Assignment
Masking
None (Open Label)
Allocation
Non-Randomized
Enrollment
60 (Anticipated)

8. Arms, Groups, and Interventions

Arm Title
Patients: ChromSeq
Arm Type
Experimental
Arm Description
ChromoSeq will be performed on bone marrow or peripheral blood 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.
Arm Title
Stakeholders (Treating Physicians)
Arm Type
No Intervention
Arm Description
Stakeholders (treating physicians) will complete surveys/questionnaires
Intervention Type
Device
Intervention Name(s)
ChromoSeq
Intervention Description
Novel, streamlined whole genome sequencing approach
Primary Outcome Measure Information:
Title
Rate of assay success on first attempt between ChromoSeq and conventional cytogenetics as measured by total number of recurrent structural variants identified
Description
-The number of recurrent structural variants detected by ChromoSeq will be compared to those detected by conventional cytogenetics using two non-inferiority tests for dependent samples using non-inferiority margin of 1%.
Time Frame
Through completion of all ChromoSeq tests (estimated to be 24 months)
Title
Rate of assay success on first attempt between ChromoSeq and conventional cytogenetics as measured by total number of copy number alterations identified
Description
The number of copy number alterations detected by ChromoSeq will be compared to those detected by conventional cytogenetics using two non-inferiority tests for dependent samples using non-inferiority margin of 1%.
Time Frame
Through completion of all ChromoSeq tests (estimated to be 24 months)
Title
Proportion of failed ChromoSeq assays
Description
As compared to failed standard of care genomic profiling assays The proportion of first-run failures for ChromoSeq assays will be compared to the proportion of failed standard of care genomic profiling assays using a directional Fisher's exact test.
Time Frame
Through completion of all ChromoSeq tests (estimated to be 24 months)
Secondary Outcome Measure Information:
Title
Stakeholder perceptions of ChromoSeq
Description
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.
Time Frame
Through 1 month after generation of ChromoSeq for all patients enrolled (estimated to be 25 months)

10. Eligibility

Sex
All
Minimum Age & Unit of Time
18 Years
Accepts Healthy Volunteers
Accepts Healthy Volunteers
Eligibility Criteria
Inclusion Criteria Patient: Diagnosis of MDS, or a clinical suspicion for a new diagnosis of MDS, for whom routine diagnostic testing is requested or planned to be requested. Seen in the outpatient setting. Not been previously treated with disease-modifying therapy (such as lenalidomide or hypomethylating agents). Note: Patients who have received transfusional support, erythropoietin-stimulating agents, growth factor support, or luspatercept are eligible. At least 18 years of age. -Able to understand and willing 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 stakeholder perceptions of ChromoSeq during the ChromoSeq implementation process. (Written documentation of informed consent is not required.) Exclusion Criteria Patient: -Younger than 18 years of age Exclusion Criteria Physician -Does not treat patients at Washington University School of Medicine
Central Contact Person:
First Name & Middle Initial & Last Name or Official Title & Degree
Meagan A Jacoby, M.D., Ph.D.
Phone
314-362-9405
Email
mjacoby@wustl.edu
Overall Study Officials:
First Name & Middle Initial & Last Name & Degree
Meagan A Jacoby, M.D., Ph.D.
Organizational Affiliation
Washington University School of Medicine
Official's Role
Principal Investigator
Facility Information:
Facility Name
Washington University School of Medicine
City
Saint Louis
State/Province
Missouri
ZIP/Postal Code
63110
Country
United States
Individual Site Status
Recruiting
Facility Contact:
First Name & Middle Initial & Last Name & Degree
Meagan A Jacoby, M.D., Ph.D.
Phone
314-362-9405
Email
mjacoby@wustl.edu
First Name & Middle Initial & Last Name & Degree
Meagan A Jacoby, M.D., Ph.D.
First Name & Middle Initial & Last Name & Degree
Matthew J Walter, M.D.
First Name & Middle Initial & Last Name & Degree
David H Spencer, M.D., Ph.D.
First Name & Middle Initial & Last Name & Degree
Mary C Politi, Ph.D.
First Name & Middle Initial & Last Name & Degree
Matthew Schuelke

12. IPD Sharing Statement

Plan to Share IPD
Yes
IPD Sharing Plan Description
Individual participant data that underlie the results reported in the article, after deidentification (text, tables, figures, and appendices).
IPD Sharing Time Frame
Beginning 3 months and ending 5 years following article publication.
IPD Sharing Access Criteria
Researchers who provide a methodologically sound proposal may submit proposals to mjacoby@wustl.edu. To gain access, data requestors will need to sign a data access agreement.
Links:
URL
http://www.siteman.wustl.edu
Description
Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine

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Whole Genome Sequencing (ChromoSeq) as an Adjunct to Conventional Genomic Profiling in MDS

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