Genomic Profiling in Cancer Patients

July 3, 2023 updated by: Memorial Sloan Kettering Cancer Center

The purpose of this study is to determine whether certain genes in cancer may be abnormal. When a gene is abnormal this is called a mutation. Most mutations in cancer cells are not inherited (passed down from parents) but happen after birth in the cancer itself. Most cancers have many mutations. Some of these mutations are important for the cancer cells to survive while others are not. The goal of this study is test cancer for certain mutations using leftover tumor tissue from a previous surgery or biopsy. Participants will also be asked to provide a tube of blood cheek (also known as a buccal) swab, or a saliva sample that contains normal genes for comparison.

The purpose of Part B of this study is to:

Understand how genetic changes in tumor effect the chance of responding to experimental cancer treatment. Understand how the genes in the tumor change overtime in response to targeted cancer treatment.

Study Overview

Status

Recruiting

Conditions

Intervention / Treatment

Study Type

Observational

Enrollment (Estimated)

200

Contacts and Locations

This section provides the contact details for those conducting the study, and information on where this study is being conducted.

Study Contact

  • Name: David Solit, MD
  • Phone Number: 646-888-2641

Study Contact Backup

  • Name: Zsofia Stadler, MD
  • Phone Number: 646-888-4039

Study Locations

  • United States
    • Connecticut
      • Bridgeport, Connecticut, United States, 06606
        • Not yet recruiting
        • St. Vincent (Data Collection Only)
        • Contact:
          • Christopher Iannuzzi, MD
          • Phone Number: 203-576-6000
      • Hartford, Connecticut, United States, 06102
        • Not yet recruiting
        • Hartford Healthcare Cancer Institute @ Hartford Hospital
        • Contact:
          • Andrew Salner, MD
          • Phone Number: 860-972-2803
      • Norwalk, Connecticut, United States, 06850
        • Recruiting
        • Norwalk Hospital
        • Contact:
          • Linda Vahdat, MD
          • Phone Number: 203-845-4811
    • Florida
      • Miami, Florida, United States, 33143
        • Recruiting
        • Baptist Alliance MCI
        • Contact:
          • John Diaz, MD
          • Phone Number: 786-596-2000
    • New Jersey
      • Basking Ridge, New Jersey, United States, 07920
        • Recruiting
        • Memorial Sloan Kettering Basking Ridge
        • Contact:
          • David Solit, MD
          • Phone Number: 646-888-2641
      • Middletown, New Jersey, United States, 07748
        • Recruiting
        • Memorial Sloan Kettering Monmouth
        • Contact:
          • David Solit, MD
          • Phone Number: 646-888-2641
      • Montvale, New Jersey, United States, 07645
        • Recruiting
        • Memorial Sloan Kettering Bergen
        • Contact:
          • David Solit, MD
          • Phone Number: 646-888-2641
    • New York
      • Bronx, New York, United States, 10451
        • Recruiting
        • NYC Health & Hospitals /Lincoln Medical Center
        • Contact:
          • Monica Reddy Muppidi, MD
          • Phone Number: 718-579-4977
        • Principal Investigator:
          • Monica Reddy Muppidi, MD
      • Bronx, New York, United States, 10469
        • Recruiting
        • New York Cancer & Blood Specialists (Data collection only)
        • Contact:
          • Richard Zuniga, MD
          • Phone Number: 631-751-3000
      • Brooklyn, New York, United States, 11203
        • Recruiting
        • Kings County Hopsital Center
        • Contact:
          • Jason Gonsky, MD
          • Phone Number: 718-245-2847
      • Commack, New York, United States, 11725
        • Recruiting
        • Memorial Sloan Kettering Cancer Commack
        • Contact:
          • David Solit, MD
          • Phone Number: 646-888-2641
      • Harrison, New York, United States, 10604
        • Recruiting
        • Memorial Sloan Kettering Westchester
        • Contact:
          • David Solit, MD
          • Phone Number: 646-888-2641
      • Jamaica, New York, United States, 11432
        • Recruiting
        • Queens Cancer Center of Queens Hospital
        • Contact:
          • Margaret Kemeny, MD
          • Phone Number: 718-883-4031
      • New York, New York, United States, 10065
        • Recruiting
        • Memorial Sloan Kettering Cancer Center
        • Contact:
          • David Solit, MD
          • Phone Number: 646-888-2641
        • Contact:
          • Zsofia Stadler, MD
          • Phone Number: 646-888-4039
        • Principal Investigator:
          • David Solit, MD
      • New York, New York, United States, 10029
        • Recruiting
        • Metropolitan Hospital Center
        • Contact:
          • Anitha Srinivasan, MD
          • Phone Number: 212-423-6262
      • New York, New York, United States, 10035
        • Recruiting
        • Ralph Lauren Center for Cancer Care and Prevention
        • Contact:
          • Lewis P. Kampel, MD
          • Phone Number: 646-422-4474
      • Uniondale, New York, United States, 11553
        • Recruiting
        • Memorial Sloan Kettering Nassau
        • Contact:
          • David Solit, MD
          • Phone Number: 646-888-2641
    • Pennsylvania
      • Allentown, Pennsylvania, United States, 18103
        • Recruiting
        • Lehigh Valley Health Network
        • Contact:
          • Suresh Nair, MD
          • Phone Number: 610-402-7880

Participation Criteria

Researchers look for people who fit a certain description, called eligibility criteria. Some examples of these criteria are a person's general health condition or prior treatments.

Eligibility Criteria

Ages Eligible for Study

  • Child
  • Adult
  • Older Adult

Accepts Healthy Volunteers

No

Sampling Method

Non-Probability Sample

Study Population

Patients with solid or hematologic cancers who may be and considered potential candidates for a therapeutic protocol will be recruited to Part A of this study. Enrollment to therapeutic clinical trials will not be contingent on enrollment in this protocol.

Part B: Research Collection Cohort Patients potentially appropriate will be identified by their treating physician in each participating Disease Management Team.

Description

Inclusion Criteria:

Part A:

  • Patients with a history of cancer or patients without a documented cancer history undergoing a surgical procedure, endoscopy, biopsy, or liquid biopsy (for example cell free DNA testing) to confirm or exclude a cancer diagnosis, or
  • Any participant having a test or procedure that has the potential to provide a specimen that can be banked for future research purposes, or
  • Any participant who has already had a diagnostic or therapeutic procedure that has yielded tissue, blood or other bodily fluids presently in the archive but who has not yet been approached to participate is also eligible.

Part B:

  • Patients must be successfully registered to Part A of MSKCC IRB# 12-245
  • Prior written approval for patient consent obtained from the Principal/Co-Principal Investigator of MSKCC IRB # 12-245.

Part C:

  • Patient must be receiving ongoing care at MSK or a CHERPn/ Alliance/Affiliate site or have previously consulted with an MSK physician.
  • Patient must have successfully consented to Part A of this study.

Part D:

  • Patients with no personal cancer history at increased risk for cancer development due to family history, molecular cancer marker, know carrier status of a gene associated with increased cancer risk or prior/ongoing environmental exposures or lifestyle factors.

Exclusion Criteria:

All Parts:

  • Unwilling or unable to provide informed consent.

Part C:

  • All patients consenting to Part A are eligible to consent to 12-245, Part C. Most patients will be eligible to receive clinical germline testing with return of results to the patient/health care providers. However, several exclusion criteria apply and are outlined below

    1. Solid tumor patients: Secondary germline analysis using BAM files generated for MSK-IMPACT testing is not an option for patients with solid tumors and an acute or chronic hematologic neoplasm that would preclude the use of blood or saliva as a source of germline DNA. Such patient may be eligible for primary germline testing using a non-blood source of germline DNA as per standard clinical guidelines. Solid tumor patients who have had an allogenic bone marrow/stem cell transplant will only be considered eligible for germline testing under Part C if a sample adequate for germline testing had previously been collected prior to allogenic bone marrow/stem cell transplant.
    2. Hematologic cancer patients: For patients with a hematopoietic neoplasm, germline testing may be an option under Part C using nail clippings or another non-blood source of DNA as per standard clinical practice. For patients who have had an allogenic bone marrow/stem cell transplant, clinical germline testing will only be considered under Part C if a sample adequate for germline testing had previously been collected prior to Allogenic bone marrow/stem cell transplant.

Part D

  • Exclusion criteria are same as those for Part C outlined above.

Study Plan

This section provides details of the study plan, including how the study is designed and what the study is measuring.

How is the study designed?

Design Details

  • Observational Models: Cohort
  • Time Perspectives: Prospective

Cohorts and Interventions

Group / Cohort
Intervention / Treatment
Pts with solid tumors
Patients must have solid or hematologic cancer. for treatment on a . Patients must have undergone pathologic confirmation of their tumor at MSKCC and have either: 1) archival tissue available for analysis, 2) have fresh tissue collection planned as routine standard of care biopsy or part of a research biopsy under another clinical trial(or peripheral blood / bone marrow collection in the case of hematologic cancers) outside of the context of this protocol, or 3)archival tissue .available at an outside facility. For prospective genotyping tissue specimens from the primary site, a metastasis or recurrence will be used based upon the availability and quality of tissue.
Genetic: molecular profiling of tumors
Part A is the molecular profiling of tumors. No new tumor biopsies will be performed in the context of Part A. If a pt does have a surgery or tumor biopsy , leftover tissue (or an additional core) from this procedure may be used for molecular profiling. Clinical Assay(s): This testing will be performed in the CLIA-certified Molecular Diagnostics Service laboratory. Research Assay(s): This protocol will also be used as a platform to pilot the use of investigational "next-generation" profiling technologies .including whole exome sequencing, whole genome sequencing RNA sequencing cell-free tumor DNA/RNA sequencing, proteomics, & others. To confirm the findings obtained on these assays using an orthogonal assay, additional sequencing such as Sanger,Sequenom, MiSeq or IMPACT testing may be utilized in either the CLIA or non-CLIA setting Part B: DTC Cohort Pts successfully registered to Part B of this study will be eligible for minimal risk collection & research biopsies.
Genetic: Clinical Germline Analysis

Part C: Clinical Germline Analysis Participants who have donated a matched normal peripheral blood sample for comparison to somatic sequence will be offered the opportunity to have that germline DNA sample analyzed for the presence of deleterious or likely deleterious mutations in genes on the MSK-IMPACT panel that are known to be linked to inherited susceptibility or that are included on consensus lists of genes that should undergo secondary analysis (e.g. the "ACMG list").

Part D: Germline Profiling for Individuals at Elevated Cancer Risk

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Measure Description
Time Frame
frequency of "actionable" oncogenic mutations
Time Frame: 1 year
"Actionable" mutations will be defined as either 1) a mutation shown to predict for sensitivity or resistance to a drug FDA approved for use in another cancer indication or 2) a mutation which predicts for sensitivity or resistance in preclinical models to an investigational class of drugs.
1 year

Secondary Outcome Measures

Outcome Measure
Measure Description
Time Frame
To determine the impact of molecular profiling results performed in the CLIA-setting on the treatment of patients.
Time Frame: 1 year
The Bioinformatics Core will assist in interpreting data generated by next-generation sequencing techniques such as WES and WGS.
1 year
interrogate the mechanisms
Time Frame: 1 year
underlying response and resistance (de-novo and acquired) to targeted therapy. The research assay(s) used to accomplish this will vary based on the clinical setting and tissue available and may include Sanger, Sequenom, MiSeq, exon-capture (ie: IMPACT), whole exome, and whole genome sequencing.
1 year
To explore the genetic mechanisms of tumorigenesis
Time Frame: 2
in a subset of specimens with no identifiable culpritic genomic alterations on highly-multiplexed next-generation sequencing (i.e.: IMPACT testing) by using even more comprehensive investigational profiling techniques such as whole exome sequencing, whole genome sequencing or RNA sequencing
2

Collaborators and Investigators

This is where you will find people and organizations involved with this study.

Sponsor

Memorial Sloan Kettering Cancer Center

Investigators

  • Principal Investigator: David Solit, MD, Memorial Sloan Kettering Cancer Center

Publications and helpful links

The person responsible for entering information about the study voluntarily provides these publications. These may be about anything related to the study.

General Publications

Helpful Links

Study record dates

These dates track the progress of study record and summary results submissions to ClinicalTrials.gov. Study records and reported results are reviewed by the National Library of Medicine (NLM) to make sure they meet specific quality control standards before being posted on the public website.

Study Major Dates

Study Start

January 1, 2013

Primary Completion (Estimated)

January 1, 2025

Study Completion (Estimated)

January 1, 2025

Study Registration Dates

First Submitted

January 21, 2013

First Submitted That Met QC Criteria

January 21, 2013

First Posted (Estimated)

January 24, 2013

Study Record Updates

Last Update Posted (Actual)

July 5, 2023

Last Update Submitted That Met QC Criteria

July 3, 2023

Last Verified

July 1, 2023

More Information

Terms related to this study

Keywords

Additional Relevant MeSH Terms

Other Study ID Numbers

  • 12-245

This information was retrieved directly from the website clinicaltrials.gov without any changes. If you have any requests to change, remove or update your study details, please contact register@clinicaltrials.gov. As soon as a change is implemented on clinicaltrials.gov, this will be updated automatically on our website as well.

Clinical Trials on Solid Tumors

Clinical Trials on molecular profiling of tumors

Search Similar Trials

Sponsors and Collaborators

Medical Conditions

Drug Interventions

CROs by country

CROs in Sweden

Conditions

Rare Diseases

Drug Interventions

Dietary Supplements

Sponsor/Collaborators

Locations

3
Subscribe