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Genomic Profiling in Cancer Patients

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ClinicalTrials.gov Identifier: NCT01775072
Recruitment Status : Recruiting
First Posted : January 24, 2013
Last Update Posted : September 10, 2022
Information provided by (Responsible Party):
Memorial Sloan Kettering Cancer Center

Tracking Information
First Submitted Date January 21, 2013
First Posted Date January 24, 2013
Last Update Posted Date September 10, 2022
Study Start Date January 2013
Estimated Primary Completion Date January 2024   (Final data collection date for primary outcome measure)
Current Primary Outcome Measures
 (submitted: January 21, 2013)
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.
Original Primary Outcome Measures Same as current
Change History
Current Secondary Outcome Measures
 (submitted: March 20, 2014)
  • 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.
  • 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.
  • 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
Original Secondary Outcome Measures
 (submitted: January 21, 2013)
  • proportion of patients with an actionable mutation identified [ Time Frame: 1 year ]
    by the research assay (IMPACT) in a gene or hotspot that is not part of the clinical panel performed by the Molecular Diagnostics Service (Sequenom)
  • associate the results of retrospective/prospective tumor sequencing data [ Time Frame: 1 year ]
    assembled by the protocol with treatment response in the subset of patients that enroll on a therapeutic DTC protocol. Both response rate and time on study will be evaluated for patients treated on "matched" and "unmatched" DTC protocols. A patient will be considered "matched" if the investigational agent(s) used in the therapeutic protocol or known or believed to target an actionable mutation present in the patient's tumor.
Current Other Pre-specified Outcome Measures Not Provided
Original Other Pre-specified Outcome Measures Not Provided
Descriptive Information
Brief Title Genomic Profiling in Cancer Patients
Official Title Genomic Profiling in Cancer Patients
Brief Summary

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.

Detailed Description Not Provided
Study Type Observational
Study Design Observational Model: Cohort
Time Perspective: Prospective
Target Follow-Up Duration Not Provided
Biospecimen Retention:   Samples With DNA
tissue, blood, saliva or nail clippings
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.

  • Solid Tumors
  • Hematologic Cancers
  • 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

Study Groups/Cohorts 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
  • Genetic: Clinical Germline Analysis
Publications *

*   Includes publications given by the data provider as well as publications identified by ClinicalTrials.gov Identifier (NCT Number) in Medline.
Recruitment Information
Recruitment Status Recruiting
Estimated Enrollment
 (submitted: January 21, 2013)
Original Estimated Enrollment Same as current
Estimated Study Completion Date January 2024
Estimated Primary Completion Date January 2024   (Final data collection date for primary outcome measure)
Eligibility Criteria

Inclusion Criteria:

Part A:

  • Patients with a history of cancer or patients w ithout a documented cancer history undergoing a surgical procedure, biopsy, or liquid biopsy (for example cell free DNA testing) to confirm or exclude a cancer diagnosis.

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 and D:

  • Patients who have had an Allogenic bone marrow/stem cell transplant.
  • Patients with an acute or chronic myeloid neoplasm, histiocytic neoplasm, or other myeloproliferative disease (e.g. MDS, MPN, MDS/MPN) that would preclude the use of blood or saliva as a source of germline DNA. For example, patients with a hematologic malignancy with a high circulating disease burden (defined as >10% of WBCs from flow cytometry or CBC differential).
Sexes Eligible for Study: All
Ages Child, Adult, Older Adult
Accepts Healthy Volunteers No
Contact: David Solit, MD 646-888-2641
Contact: Zsofia Stadler, MD 646-888-4039
Listed Location Countries United States
Removed Location Countries  
Administrative Information
NCT Number NCT01775072
Other Study ID Numbers 12-245
Has Data Monitoring Committee Not Provided
U.S. FDA-regulated Product Not Provided
IPD Sharing Statement Not Provided
Current Responsible Party Memorial Sloan Kettering Cancer Center
Original Responsible Party Same as current
Current Study Sponsor Memorial Sloan Kettering Cancer Center
Original Study Sponsor Same as current
Collaborators Not Provided
Principal Investigator: David Solit, MD Memorial Sloan Kettering Cancer Center
PRS Account Memorial Sloan Kettering Cancer Center
Verification Date September 2022