<clinical_study>
  <!-- This xml conforms to an XML Schema at:
    https://clinicaltrials.gov/ct2/html/images/info/public.xsd -->
  <required_header>
    <download_date>ClinicalTrials.gov processed this data on September 20, 2023</download_date>
    <link_text>Link to the current ClinicalTrials.gov record.</link_text>
    <url>https://clinicaltrials.gov/ct2/show/NCT02213822</url>
  </required_header>
  <id_info>
    <org_study_id>2055-13</org_study_id>
    <nct_id>NCT02213822</nct_id>
  </id_info>
  <brief_title>Molecular Testing of Cancer by Integrated Genomic, Transcriptomic, and Proteomic Analysis</brief_title>
  <official_title>MOLECULAR TESTING OF CANCER BY INTEGRATED GENOMIC, TRANSCRIPTOMIC, AND PROTEOMIC ANALYSIS</official_title>
  <sponsors>
    <lead_sponsor>
      <agency>Rhode Island Hospital</agency>
      <agency_class>Other</agency_class>
    </lead_sponsor>
  </sponsors>
  <source>Rhode Island Hospital</source>
  <oversight_info>
    <has_dmc>No</has_dmc>
  </oversight_info>
  <brief_summary>
    <textblock>
      The purpose of this study is to discover genetic changes associated with different cancers.&#xD;
      With the information from this study the investigators hope to provide better ways to&#xD;
      prevent, detect and treat many cancers.&#xD;
&#xD;
      Many diseases can result from changes in a person's genetic material that causes cells to not&#xD;
      work properly. Currently, researchers and doctors know some of the genetic changes that can&#xD;
      cause disease, but they do not know all of the genetic changes that can cause disease.&#xD;
&#xD;
      This project is designed to identify genetic changes that can cause cancer in humans.&#xD;
      Specimens will be collected from a scheduled diagnostic or routine (i.e. blood draw for&#xD;
      counts) procedure and may include samples from the tissue itself (surgery), bone marrow,&#xD;
      blood, saliva, urine, spinal fluid, sputum, joint fluid, seminal fluid, ascites (a fluid that&#xD;
      fills up in the abdomen), and/or pleural fluid (fluid in the lung cavity), to either confirm&#xD;
      the diagnosis of cancer or to help to decide how best to treat cancer or other illness.&#xD;
      Additionally archived tissue may be analyzed. Samples may be stored for future use in later&#xD;
      experiments. The Department of Pathology at Rhode Island Hospital will store the samples.&#xD;
&#xD;
      Information from the medical record, such as responses to treatments or family history of&#xD;
      cancer, will be collected.&#xD;
    </textblock>
  </brief_summary>
  <detailed_description>
    <textblock>
      Complex, progressive, multigenic, somatic mutations of the genome are now widely accepted as&#xD;
      the primary driving force in the evolution of cancer initiation, growth, metastasis and&#xD;
      pharmacoresistance. Different types of tumors are associated with mutations in distinct sets&#xD;
      of genes, and there is a pressing need for a sequencing-based method of analyzing panels of&#xD;
      candidate genes that differ for each tumor type.&#xD;
&#xD;
      Traditional approaches to sequence analysis employing capillary electrophoresis-based Sanger&#xD;
      sequencing are widely used to guide therapy for patients with lung and colorectal cancer and&#xD;
      for melanoma, sarcomas, leukemias and lymphomas. This technology is limited in throughput,&#xD;
      scalability, speed, and resolution. The emerging technology such as next-generation&#xD;
      sequencing (NGS) - holds a number of advantages over traditional methods, including the&#xD;
      ability to fully sequence large numbers of genes in a single test and simultaneously detect&#xD;
      deletions, insertions, copy number alterations, translocations, and exome-wide base&#xD;
      substitutions in all known cancer-related genes.&#xD;
&#xD;
      Sequencing the whole genome is financially prohibitive for many potentially valuable&#xD;
      applications. One alternative to whole genome methods is target enrichment, such as exome&#xD;
      sequencing, which captures and sequences only protein coding regions. The exome represents&#xD;
      1-2% of the human genome; however contains the vast majority of disease causing alterations.&#xD;
      In addition to exome sequencing, full-length transcriptome (mRNA) sequencing offers a fast&#xD;
      and inexpensive alternative. It is an easier method to identify coding sequences and capture&#xD;
      variants in genes that are expressed, as well as to generate additional information, such as&#xD;
      gene expression level and splicing patterns.&#xD;
&#xD;
      The goal of this study is to investigate genomic, transcriptomic and proteomic alterations in&#xD;
      human solid cancers and hematologic malignancies.&#xD;
&#xD;
      Patients &gt;18 y.o. diagnosed with cancer (including any solid tumor or hematologic malignancy)&#xD;
      or patients who are undergoing a procedure for the diagnosis of a presumed cancer are&#xD;
      eligible.&#xD;
&#xD;
      The research analysis will be performed by the department of pathology or the division of&#xD;
      hematology oncology. The body/blood tissue analyzed will be from extra tissue/blood that is&#xD;
      not needed for diagnosis or evaluation of the patient's cancer. All samples will be&#xD;
      de-identified. Samples will be stored for an indefinite period of time or until all samples&#xD;
      are utilized.&#xD;
    </textblock>
  </detailed_description>
  <overall_status>Unknown status</overall_status>
  <last_known_status>Recruiting</last_known_status>
  <start_date>May 2013</start_date>
  <completion_date type="Anticipated">August 2015</completion_date>
  <primary_completion_date type="Anticipated">August 2015</primary_completion_date>
  <study_type>Observational [Patient Registry]</study_type>
  <has_expanded_access>No</has_expanded_access>
  <study_design_info>
    <observational_model>Case-Only</observational_model>
    <time_perspective>Prospective</time_perspective>
  </study_design_info>
  <target_duration>5 Years</target_duration>
  <primary_outcome>
    <measure>The Frequency of &quot;Actionable&quot; Oncogenic Mutations</measure>
    <time_frame>1 year</time_frame>
  </primary_outcome>
  <primary_outcome>
    <measure>The Prevalence of Genomic, Transcriptomic, and Proteomic Abnormalities in Human Cancer</measure>
    <time_frame>1 year</time_frame>
  </primary_outcome>
  <number_of_groups>1</number_of_groups>
  <enrollment type="Anticipated">500</enrollment>
  <condition>Solid Tumors</condition>
  <condition>Hematological Malignancies</condition>
  <arm_group>
    <arm_group_label>Pts with Solid Tumors/ Hematological Cancer</arm_group_label>
    <description>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.</description>
  </arm_group>
  <intervention>
    <intervention_type>Other</intervention_type>
    <intervention_name>Molecular Analysis of Cancer</intervention_name>
    <description>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.</description>
    <arm_group_label>Pts with Solid Tumors/ Hematological Cancer</arm_group_label>
  </intervention>
  <biospec_retention>Samples With DNA</biospec_retention>
  <biospec_descr>
    <textblock>
      Tissue, blood, saliva, body fluid&#xD;
    </textblock>
  </biospec_descr>
  <eligibility>
    <study_pop>
      <textblock>
        Patients in this study will have either a suspected or confirmed solid tumor or&#xD;
        hematological malignancy&#xD;
      </textblock>
    </study_pop>
    <sampling_method>Probability Sample</sampling_method>
    <criteria>
      <textblock>
        Inclusion Criteria:&#xD;
&#xD;
          -  Documented informed consent&#xD;
&#xD;
          -  Patient has either a suspected or confirmed solid tumor or hematological malignancy&#xD;
&#xD;
          -  There is enough tissue or body fluid to allow for experimental study&#xD;
&#xD;
          -  The patient is over the age of 18&#xD;
&#xD;
        Exclusion Criteria:&#xD;
&#xD;
          -  The patient is unwilling or unable to provide informed consent&#xD;
      </textblock>
    </criteria>
    <gender>All</gender>
    <minimum_age>18 Years</minimum_age>
    <maximum_age>N/A</maximum_age>
    <healthy_volunteers>No</healthy_volunteers>
  </eligibility>
  <overall_official>
    <last_name>Kimberly Perez, M.D.</last_name>
    <role>Principal Investigator</role>
    <affiliation>Lifespan Corporation</affiliation>
  </overall_official>
  <overall_contact>
    <last_name>Andrew Schumacher, M.S.</last_name>
    <phone>(401) 444-3234</phone>
  </overall_contact>
  <overall_contact_backup>
    <last_name>Allison Jean, B.A.</last_name>
    <phone>(401) 444- 8856</phone>
  </overall_contact_backup>
  <location>
    <facility>
      <name>Rhode Island Comprehensive Cancer Center at East Greenwich</name>
      <address>
        <city>East Greenwich</city>
        <state>Rhode Island</state>
        <zip>02818</zip>
        <country>United States</country>
      </address>
    </facility>
    <status>Recruiting</status>
    <contact>
      <last_name>Andrew Schumacher, M.S.</last_name>
      <phone>401-444-3234</phone>
    </contact>
    <contact_backup>
      <last_name>Allison Jean, B.A.</last_name>
      <phone>(401) 444- 8856</phone>
    </contact_backup>
    <investigator>
      <last_name>Priscilla Merriam, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Howard Safran, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Maria Constantinou, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Anthony Mega, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Kimberly Perez, M.D.</last_name>
      <role>Principal Investigator</role>
    </investigator>
    <investigator>
      <last_name>Amy Pilotte, N. P.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
  </location>
  <location>
    <facility>
      <name>Rhode Island Hospital</name>
      <address>
        <city>Providence</city>
        <state>Rhode Island</state>
        <zip>02903</zip>
        <country>United States</country>
      </address>
    </facility>
    <status>Recruiting</status>
    <contact>
      <last_name>Andrew Schumacher, M.S.</last_name>
      <phone>401-444-3234</phone>
    </contact>
    <contact_backup>
      <last_name>Allison Jean, B.A.</last_name>
      <phone>(401) 444- 8856</phone>
    </contact_backup>
    <investigator>
      <last_name>Kimberly Perez, M.D.</last_name>
      <role>Principal Investigator</role>
    </investigator>
    <investigator>
      <last_name>Howard Safran, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Humera Khurshid, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Maria Constantinou, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Evgeny Yakirevich, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Murray Resnick, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>James Butera, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Mary Anne Fenton, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Lucia Fontes-Bortes, N.P.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Peter Quesenberry, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Matthew Quesenberry, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>John Reagan, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Eric Winer, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Thomas DiPetrillo, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Jaroslaw Hepel, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Kara Lynne Leonard, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>David Tracey, P.A.</last_name>
      <role>Principal Investigator</role>
    </investigator>
    <investigator>
      <last_name>Inna Yakirevich, N.P.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Sharon Benson, N.P.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Heinrich Elinzano, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Timothy Kinsella, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Thomas Ng, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
  </location>
  <location>
    <facility>
      <name>The Miriam Hospital</name>
      <address>
        <city>Providence</city>
        <state>Rhode Island</state>
        <zip>02906</zip>
        <country>United States</country>
      </address>
    </facility>
    <status>Recruiting</status>
    <contact>
      <last_name>Maureen Jean, R.N.</last_name>
      <phone>401-793-4283</phone>
    </contact>
    <contact_backup>
      <last_name>Diane Martel, R.N.</last_name>
      <phone>(401) 793- 4282</phone>
    </contact_backup>
    <investigator>
      <last_name>Howard Safran, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Kimberly Perez, M.D.</last_name>
      <role>Principal Investigator</role>
    </investigator>
    <investigator>
      <last_name>Eric Winer, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Jennifer Collins, N.P.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Irene Kolberg, N.P.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Jodi Layton, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Anthony Mega, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Priscilla Merriam, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Fred Schiffman, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>John Reagan, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Edward Wittles, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Angela Taber, M.D.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Camille Higel-McGovern, N.P.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Amy Pilotte, N.P.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
    <investigator>
      <last_name>Xristin Maestri, N.P.</last_name>
      <role>Sub-Investigator</role>
    </investigator>
  </location>
  <location_countries>
    <country>United States</country>
  </location_countries>
  <verification_date>July 2014</verification_date>
  <study_first_submitted>July 31, 2014</study_first_submitted>
  <study_first_submitted_qc>August 7, 2014</study_first_submitted_qc>
  <study_first_posted type="Estimate">August 12, 2014</study_first_posted>
  <last_update_submitted>August 26, 2014</last_update_submitted>
  <last_update_submitted_qc>August 26, 2014</last_update_submitted_qc>
  <last_update_posted type="Estimate">August 27, 2014</last_update_posted>
  <responsible_party>
    <responsible_party_type>Sponsor</responsible_party_type>
  </responsible_party>
  <keyword>genome</keyword>
  <keyword>transcriptome</keyword>
  <keyword>molecular</keyword>
  <keyword>proteome</keyword>
  <keyword>oncogenic mutations</keyword>
  <keyword>sequencing</keyword>
  <keyword>solid tumor</keyword>
  <keyword>hematological malignancy</keyword>
  <keyword>cancer</keyword>
  <keyword>analysis</keyword>
  <keyword>genetic</keyword>
  <keyword>mutation</keyword>
  <condition_browse>
    <!-- CAUTION:  The following MeSH terms are assigned with an imperfect algorithm            -->
    <mesh_term>Neoplasms</mesh_term>
    <mesh_term>Hematologic Neoplasms</mesh_term>
  </condition_browse>
  <!-- Results have not yet been posted for this study                                          -->
</clinical_study>


download date: ClinicalTrials.gov processed this data on September 20, 2023
link text: Link to the current ClinicalTrials.gov record.
url: https://clinicaltrials.gov/ct2/show/NCT02213822
org study id: 2055-13
nct id: NCT02213822
lead sponsor: 
has dmc: No
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.
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.
observational model: Case-Only
time perspective: Prospective
measure: The Frequency of "Actionable" Oncogenic Mutations
time frame: 1 year
measure: The Prevalence of Genomic, Transcriptomic, and Proteomic Abnormalities in Human Cancer
time frame: 1 year
arm group label: Pts with Solid Tumors/ Hematological Cancer
description: 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.
intervention type: Other
intervention name: Molecular Analysis of Cancer
description: 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.
arm group label: Pts with Solid Tumors/ Hematological Cancer
Tissue, blood, saliva, body fluid
study pop: 
sampling method: Probability Sample
criteria: 
gender: All
minimum age: 18 Years
maximum age: N/A
healthy volunteers: No
last name: Kimberly Perez, M.D.
role: Principal Investigator
affiliation: Lifespan Corporation
last name: Andrew Schumacher, M.S.
phone: (401) 444-3234
last name: Allison Jean, B.A.
phone: (401) 444- 8856
facility: 
status: Recruiting
contact: 
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status: Recruiting
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status: Recruiting
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country: United States
responsible party type: Sponsor
mesh term: Neoplasms
mesh term: Hematologic Neoplasms