Molecular Testing of Cancer by Integrated Genomic, Transcriptomic, and Proteomic Analysis

August 26, 2014 updated by: Rhode Island Hospital

MOLECULAR TESTING OF CANCER BY INTEGRATED GENOMIC, TRANSCRIPTOMIC, AND PROTEOMIC ANALYSIS

The purpose of this study is to discover genetic changes associated with different cancers. With the information from this study the investigators hope to provide better ways to prevent, detect and treat many cancers.

Many diseases can result from changes in a person's genetic material that causes cells to not work properly. Currently, researchers and doctors know some of the genetic changes that can cause disease, but they do not know all of the genetic changes that can cause disease.

This project is designed to identify genetic changes that can cause cancer in humans. Specimens will be collected from a scheduled diagnostic or routine (i.e. blood draw for counts) procedure and may include samples from the tissue itself (surgery), bone marrow, blood, saliva, urine, spinal fluid, sputum, joint fluid, seminal fluid, ascites (a fluid that fills up in the abdomen), and/or pleural fluid (fluid in the lung cavity), to either confirm the diagnosis of cancer or to help to decide how best to treat cancer or other illness. Additionally archived tissue may be analyzed. Samples may be stored for future use in later experiments. The Department of Pathology at Rhode Island Hospital will store the samples.

Information from the medical record, such as responses to treatments or family history of cancer, will be collected.

Study Overview

Status

Unknown

Conditions

Intervention / Treatment

Detailed Description

Complex, progressive, multigenic, somatic mutations of the genome are now widely accepted as the primary driving force in the evolution of cancer initiation, growth, metastasis and pharmacoresistance. Different types of tumors are associated with mutations in distinct sets of genes, and there is a pressing need for a sequencing-based method of analyzing panels of candidate genes that differ for each tumor type.

Traditional approaches to sequence analysis employing capillary electrophoresis-based Sanger sequencing are widely used to guide therapy for patients with lung and colorectal cancer and for melanoma, sarcomas, leukemias and lymphomas. This technology is limited in throughput, scalability, speed, and resolution. The emerging technology such as next-generation sequencing (NGS) - holds a number of advantages over traditional methods, including the ability to fully sequence large numbers of genes in a single test and simultaneously detect deletions, insertions, copy number alterations, translocations, and exome-wide base substitutions in all known cancer-related genes.

Sequencing the whole genome is financially prohibitive for many potentially valuable applications. One alternative to whole genome methods is target enrichment, such as exome sequencing, which captures and sequences only protein coding regions. The exome represents 1-2% of the human genome; however contains the vast majority of disease causing alterations. In addition to exome sequencing, full-length transcriptome (mRNA) sequencing offers a fast and inexpensive alternative. It is an easier method to identify coding sequences and capture variants in genes that are expressed, as well as to generate additional information, such as gene expression level and splicing patterns.

The goal of this study is to investigate genomic, transcriptomic and proteomic alterations in human solid cancers and hematologic malignancies.

Patients >18 y.o. diagnosed with cancer (including any solid tumor or hematologic malignancy) or patients who are undergoing a procedure for the diagnosis of a presumed cancer are eligible.

The research analysis will be performed by the department of pathology or the division of hematology oncology. The body/blood tissue analyzed will be from extra tissue/blood that is not needed for diagnosis or evaluation of the patient's cancer. All samples will be de-identified. Samples will be stored for an indefinite period of time or until all samples are utilized.

Study Type

Observational

Enrollment (Anticipated)

500

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: Andrew Schumacher, M.S.
  • Phone Number: (401) 444-3234

Study Contact Backup

  • Name: Allison Jean, B.A.
  • Phone Number: (401) 444- 8856

Study Locations

  • United States
    • Rhode Island
      • East Greenwich, Rhode Island, United States, 02818
        • Recruiting
        • Rhode Island Comprehensive Cancer Center at East Greenwich
        • Contact:
          • Allison Jean, B.A.
          • Phone Number: (401) 444- 8856
        • Contact:
          • Andrew Schumacher, M.S.
          • Phone Number: 401-444-3234
        • Sub-Investigator:
          • Priscilla Merriam, M.D.
        • Sub-Investigator:
          • Howard Safran, M.D.
        • Sub-Investigator:
          • Maria Constantinou, M.D.
        • Sub-Investigator:
          • Anthony Mega, M.D.
        • Principal Investigator:
          • Kimberly Perez, M.D.
        • Sub-Investigator:
          • Amy Pilotte, N. P.
      • Providence, Rhode Island, United States, 02903
        • Recruiting
        • Rhode Island Hospital
        • Contact:
          • Allison Jean, B.A.
          • Phone Number: (401) 444- 8856
        • Contact:
          • Andrew Schumacher, M.S.
          • Phone Number: 401-444-3234
        • Sub-Investigator:
          • Howard Safran, M.D.
        • Sub-Investigator:
          • Maria Constantinou, M.D.
        • Principal Investigator:
          • Kimberly Perez, M.D.
        • Sub-Investigator:
          • Humera Khurshid, M.D.
        • Sub-Investigator:
          • Evgeny Yakirevich, M.D.
        • Sub-Investigator:
          • Murray Resnick, M.D.
        • Sub-Investigator:
          • James Butera, M.D.
        • Sub-Investigator:
          • Mary Anne Fenton, M.D.
        • Sub-Investigator:
          • Lucia Fontes-Bortes, N.P.
        • Sub-Investigator:
          • Peter Quesenberry, M.D.
        • Sub-Investigator:
          • Matthew Quesenberry, M.D.
        • Sub-Investigator:
          • John Reagan, M.D.
        • Sub-Investigator:
          • Eric Winer, M.D.
        • Sub-Investigator:
          • Thomas DiPetrillo, M.D.
        • Sub-Investigator:
          • Jaroslaw Hepel, M.D.
        • Sub-Investigator:
          • Kara Lynne Leonard, M.D.
        • Principal Investigator:
          • David Tracey, P.A.
        • Sub-Investigator:
          • Inna Yakirevich, N.P.
        • Sub-Investigator:
          • Sharon Benson, N.P.
        • Sub-Investigator:
          • Heinrich Elinzano, M.D.
        • Sub-Investigator:
          • Timothy Kinsella, M.D.
        • Sub-Investigator:
          • Thomas Ng, M.D.
      • Providence, Rhode Island, United States, 02906
        • Recruiting
        • The Miriam Hospital
        • Sub-Investigator:
          • Priscilla Merriam, M.D.
        • Sub-Investigator:
          • Howard Safran, M.D.
        • Sub-Investigator:
          • Anthony Mega, M.D.
        • Principal Investigator:
          • Kimberly Perez, M.D.
        • Sub-Investigator:
          • John Reagan, M.D.
        • Sub-Investigator:
          • Eric Winer, M.D.
        • Contact:
          • Maureen Jean, R.N.
          • Phone Number: 401-793-4283
        • Contact:
          • Diane Martel, R.N.
          • Phone Number: (401) 793- 4282
        • Sub-Investigator:
          • Jennifer Collins, N.P.
        • Sub-Investigator:
          • Irene Kolberg, N.P.
        • Sub-Investigator:
          • Fred Schiffman, M.D.
        • Sub-Investigator:
          • Edward Wittles, M.D.
        • Sub-Investigator:
          • Angela Taber, M.D.
        • Sub-Investigator:
          • Camille Higel-McGovern, N.P.
        • Sub-Investigator:
          • Amy Pilotte, N.P.
        • Sub-Investigator:
          • Xristin Maestri, N.P.

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

18 years and older (Adult, Older Adult)

Accepts Healthy Volunteers

No

Genders Eligible for Study

All

Sampling Method

Probability Sample

Study Population

Patients in this study will have either a suspected or confirmed solid tumor or hematological malignancy

Description

Inclusion Criteria:

  • Documented informed consent
  • Patient has either a suspected or confirmed solid tumor or hematological malignancy
  • There is enough tissue or body fluid to allow for experimental study
  • The patient is over the age of 18

Exclusion Criteria:

  • The patient is unwilling or unable to provide informed consent

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: Case-Only
  • Time Perspectives: Prospective

Cohorts and Interventions

Group / Cohort
Intervention / Treatment
Pts with Solid Tumors/ Hematological Cancer
Patients on this study must have either a suspected or confirmed solid tumor or hematological cancer. The intervention performed in this study is the molecular analysis of cancer. The samples will be taken at the time of the patient's planned diagnostic or staging procedure. If the patient is scheduled for surgery a sample of tissue not required for their diagnosis will be obtained and used for this research study. If the patient has undergone a previous diagnostic procedure, some of the stored tissue from that procedure will be submitted for molecular analysis as well.
Other: Molecular Analysis of Cancer
The intervention performed in this study is the molecular analysis of cancer. Samples to be tested for genetic alterations will be collected during the course of a routine diagnostic procedure such as a surgery or tumor biopsy. Samples that have been stored from previous diagnostic procedures will be analyzed as well. This testing will be performed by the Department of Pathology at Rhode Island Hospital or an outside laboratory designated by Rhode Island Hospital. The extent of molecular testing will be different in each individual case. For example, in some cases, study of genetic alterations will start with whole genome or exome sequencing and will be confirmed by targeted Sanger resequencing, single nucleotide polymorphism, and transcriptome analysis. In other cases targeted multigene panel sequencing or targeted amplicon Sanger sequencing will be the initial and only step.

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Time Frame
The Frequency of "Actionable" Oncogenic Mutations
Time Frame: 1 year
1 year
The Prevalence of Genomic, Transcriptomic, and Proteomic Abnormalities in Human Cancer
Time Frame: 1 year
1 year

Collaborators and Investigators

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

Sponsor

Rhode Island Hospital

Investigators

  • Principal Investigator: Kimberly Perez, M.D., Lifespan Corporation

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

May 1, 2013

Primary Completion (Anticipated)

August 1, 2015

Study Completion (Anticipated)

August 1, 2015

Study Registration Dates

First Submitted

July 31, 2014

First Submitted That Met QC Criteria

August 7, 2014

First Posted (Estimate)

August 12, 2014

Study Record Updates

Last Update Posted (Estimate)

August 27, 2014

Last Update Submitted That Met QC Criteria

August 26, 2014

Last Verified

July 1, 2014

More Information

Terms related to this study

Keywords

Additional Relevant MeSH Terms

Other Study ID Numbers

  • 2055-13

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.

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