<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/NCT02976090</url>
  </required_header>
  <id_info>
    <org_study_id>NI14026</org_study_id>
    <nct_id>NCT02976090</nct_id>
  </id_info>
  <brief_title>Phenotyping of Small Bowel Adenocarcinoma</brief_title>
  <acronym>BIONADEGE</acronym>
  <official_title>Phenotyping of Small Bowel Adenocarcinoma</official_title>
  <sponsors>
    <lead_sponsor>
      <agency>Assistance Publique - Hôpitaux de Paris</agency>
      <agency_class>Other</agency_class>
    </lead_sponsor>
    <collaborator>
      <agency>University of Paris 5 - Rene Descartes</agency>
      <agency_class>Other</agency_class>
    </collaborator>
    <collaborator>
      <agency>Centre Hospitalier Universitaire de Besancon</agency>
      <agency_class>Other</agency_class>
    </collaborator>
    <collaborator>
      <agency>GERCOR - Multidisciplinary Oncology Cooperative Group</agency>
      <agency_class>Other</agency_class>
    </collaborator>
  </sponsors>
  <source>Assistance Publique - Hôpitaux de Paris</source>
  <oversight_info>
    <has_dmc>No</has_dmc>
  </oversight_info>
  <brief_summary>
    <textblock>
      Despite the fact that small intestine makes up 75% of the length of the digestive tract and&#xD;
      90% of its mucosal surface area, small bowel adenocarcinoma (SBA) is rare. SBA is not equally&#xD;
      dispatched along the small bowel, a predisposing disease is frequently associated. All these&#xD;
      data suggest particular carcinogenesis pathway. SBA carries poor prognosis at all stages and&#xD;
      no standard treatment have proved efficacy. So far, no data are available for targeted&#xD;
      therapy. From the literature and a previous study of our group some biologic data showed that&#xD;
      SBA carcinogenesis is closer to colorectal than gastric carcinogenesis. Nevertheless, some&#xD;
      differences arise (ie: low Adenomatous Polyposis Coli mutation rate or frequent DNA mismatch&#xD;
      repair deficiency). Even if some trends are founded the prognostic value of molecular&#xD;
      alteration and phenotype variation according to small bowel segment, or predisposing disease&#xD;
      could not been demonstrate due to small sample size.&#xD;
&#xD;
      BIONADEGE study is a planned biologic ancillary study of the NADEGE cohort that enrolled 366&#xD;
      patients with SBA from 2009 to 2012 in France. The tumour blocks and clinical data of 187&#xD;
      patients have been collected. The main objective is to assess the prognostic value for&#xD;
      recurrence free survival (RFS) in non-metastatic patients and overall survival (OS) in&#xD;
      metastatic patients of molecular alteration in a set of 46 genes and abnormal protein&#xD;
      expression potentially implicated in carcinogenesis. The mains secondary objectives are: 1)&#xD;
      to identify potential mutation targetable in small intestine tumours and protein expression,&#xD;
      2) to state the frequency of molecular alteration according to the tumour location, stage or&#xD;
      predisposing disease and established clinico-biologic correlation. Tissue microarrays will be&#xD;
      performed and several potential prognostic markers will be assessed. Sequencing on tumour DNA&#xD;
      will investigate the presence of 740 hot spot somatic mutations in 46 genes involved.The&#xD;
      abnormal protein expression or the genetic alterations with an expected frequency superior to&#xD;
      10% will be assessed as potential prognostic factor to RFS and OS.&#xD;
&#xD;
      These evaluations on a large cohort could allow comparison between pathways and will offer&#xD;
      better knowledge of tumour molecular phenotype and prognosis will give rational for targeted&#xD;
      therapy trials The predisposing diseases for SBA involved several different carcinogenesis&#xD;
      pathways. Finally, a molecular classification of SBA will be attempt.&#xD;
    </textblock>
  </brief_summary>
  <detailed_description>
    <textblock>
      The NADEGE cohort involves 75 centres and had enrolled 365 patients. Among them 232 patients&#xD;
      had a resection of the primary tumour in 58 centres. This will is be the largest series in&#xD;
      the world of SBA for biological study. The patients enrolled in the NADEGE cohort were aware&#xD;
      of the biologic study and their authorisation to perform is already collected.&#xD;
&#xD;
      Baseline clinical data of patients enrolled in NADEGE cohort are already available and were&#xD;
      presented in a poster discussion session at the European Society for Medical Oncology&#xD;
      congress 2013. In all the cohort the primary location was duodenum in 51% of the patients,&#xD;
      and a predisposing disease was reported in 18.8% of the patient mainly Crohn disease in 8%&#xD;
      and Lynch syndrome in 6% of the patients. The follow-up is ongoing. The analyses of 3-years&#xD;
      recurrence-free survival is planned in 2015 and the analysis of 5-years overall survival in&#xD;
      2017.&#xD;
&#xD;
      Today 187 tumour sample are collected and archived in the pathology department of Saint&#xD;
      Antoine hospital (Paris). Among these 187 tumours the tumour stage are: stage 0: 4, stage I:&#xD;
      10, stage II: 34, stage III: 63, undetermined stage non-metastatic: 30 (thus 141&#xD;
      non-metastatic tumours) and stage IV: 48, and the primary are: duodenum: 128, jejunum: 31,&#xD;
      ileon: 27, undetermined: 3. The chemotherapy performed was FOLFOX in 80% of the cases.&#xD;
&#xD;
      Work Package 1: Database (team 1) The clinical data of NADEGE cohort are collected with an&#xD;
      e-crf. The initial descriptive data are already monitored by the GERCOR team. The results&#xD;
      have been already presented. BIONADEGE is a planned ancillary study of the NADEGE cohort. The&#xD;
      complementary queries for the purpose of BIONADEGE will be addressed by the team 1 to the&#xD;
      NADEGE investigator. The follow-up data for progression (metastatic patients), recurrence&#xD;
      (non-metastatic patient) and death (all patients) will be obtained every 6 months. Follow-up&#xD;
      data will be collected until 2019 in order to obtain 5-years follow-up for all the patients.&#xD;
&#xD;
      Work Package 2: Anatomopathology (team 2) All the tumour samples are already bank in the&#xD;
      pathology laboratory of Saint Antoine hospital. Slides from representative tumour area will&#xD;
      be selected and send to Paris Descartes university to allow DNA extraction. Tissue&#xD;
      microarrays (TMA) for immunohistochemistry validation studies will be performed. Several&#xD;
      potential prognostic markers will be assessed as MismatchRepair (MMR) protein, P53,&#xD;
      beta-catenin, c-myc protein. Other predictive markers for chemotherapy as hENT1,&#xD;
      O6-methylguanine DNA methyltransferase (MGMT) and for targeted therapy as Proto-oncogene&#xD;
      tyrosine-protein kinase (ROS1), hepatocyte growth factor receptor c-Met (HGFR), Alk, Human&#xD;
      Epidermal Growth Factor Receptor-2 (HER-2) and Programmed cell death 1 (PD-1) will also be&#xD;
      assessed. The cases overexpressing HER-2 and HGFR protein by immunohistochemistry will be&#xD;
      tested by Fluorescent In Situ Hybridisation (FISH).&#xD;
&#xD;
      Work Package 3: Biochemistry (team 3) DNA will be extracted from tumour block in the&#xD;
      university unit S1147 according to the following protocol. Using a 1.0-mm punch, paraffin&#xD;
      embedded tissues from all cases will be sampled from representative areas that will contain&#xD;
      more than 50% of tumour cells. DNA will be thereafter extracted from each sample following&#xD;
      the manufacturer's recommendation. The team3 will use a competitive allele specific taqman&#xD;
      probe designed on Kras wild type allele (Hs.00000174-rf - Life Technologies) on serial&#xD;
      dilution of each DNA sample in order to quantify amplifiable DNA. Only samples with more than&#xD;
      10 ng of amplifiable DNA will be retained for the sequencing. DNA from each sample will be&#xD;
      amplified. The presence of more than 740 hot spot somatic mutations in the 46 genes will be&#xD;
      investigate. Data analysis, including alignment to the hg19 human reference genome and&#xD;
      variant calling, will be done using the Software of Life Technologies. Alignments will be&#xD;
      visually verified and annotated with the software of Integrative Biosoftware. A sequence&#xD;
      variation will be considered as a potential mutation if (i) the coverage is superior to 200×,&#xD;
      (ii) the allelic frequency is superior to 10%, (iii) the strand bias is from 0.2 to 0.8, (iv)&#xD;
      the variation is not reported in the 1000 genomes database, (v) the variation is a missense&#xD;
      or a non-sense variation. All these selected variations will be controlled using the Sanger&#xD;
      sequencing technics using amplified fragments of less than 150 bp centred on the potential&#xD;
      mutation.&#xD;
    </textblock>
  </detailed_description>
  <overall_status>Completed</overall_status>
  <start_date type="Actual">January 2017</start_date>
  <completion_date type="Actual">December 24, 2020</completion_date>
  <primary_completion_date type="Actual">December 15, 2019</primary_completion_date>
  <study_type>Observational</study_type>
  <has_expanded_access>No</has_expanded_access>
  <study_design_info>
    <observational_model>Cohort</observational_model>
    <time_perspective>Retrospective</time_perspective>
  </study_design_info>
  <primary_outcome>
    <measure>RFS in non-metastatic patients according to 46 genes and abnormal protein expression potentially implicated in carcinogenesis.</measure>
    <time_frame>3 years</time_frame>
  </primary_outcome>
  <secondary_outcome>
    <measure>OS in metastatic patients according to 46 genes and abnormal protein expression potentially implicated in carcinogenesis</measure>
    <time_frame>3 years</time_frame>
  </secondary_outcome>
  <secondary_outcome>
    <measure>Rate of MMR status</measure>
    <time_frame>3 years</time_frame>
  </secondary_outcome>
  <enrollment type="Actual">187</enrollment>
  <condition>Small Bowel Adenocarcinoma</condition>
  <biospec_retention>Samples With DNA</biospec_retention>
  <biospec_descr>
    <textblock>
      Tumour block&#xD;
    </textblock>
  </biospec_descr>
  <eligibility>
    <study_pop>
      <textblock>
        patients included in NADEGE cohort&#xD;
      </textblock>
    </study_pop>
    <sampling_method>Probability Sample</sampling_method>
    <criteria>
      <textblock>
        Inclusion Criteria:&#xD;
&#xD;
          -  patients included in NADEGE cohort&#xD;
&#xD;
          -  patients with available and exploitable biological samples from NADEGE cohort&#xD;
&#xD;
        Exclusion Criteria:&#xD;
&#xD;
          -  none&#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>Sabine HELFEN</last_name>
    <role>Study Chair</role>
    <affiliation>Assistance Publique - Hôpitaux de Paris</affiliation>
  </overall_official>
  <verification_date>November 2018</verification_date>
  <study_first_submitted>October 25, 2016</study_first_submitted>
  <study_first_submitted_qc>November 24, 2016</study_first_submitted_qc>
  <study_first_posted type="Estimate">November 29, 2016</study_first_posted>
  <last_update_submitted>January 12, 2021</last_update_submitted>
  <last_update_submitted_qc>January 12, 2021</last_update_submitted_qc>
  <last_update_posted type="Actual">January 13, 2021</last_update_posted>
  <responsible_party>
    <responsible_party_type>Sponsor</responsible_party_type>
  </responsible_party>
  <condition_browse>
    <!-- CAUTION:  The following MeSH terms are assigned with an imperfect algorithm            -->
    <mesh_term>Adenocarcinoma</mesh_term>
  </condition_browse>
  <patient_data>
    <sharing_ipd>No</sharing_ipd>
  </patient_data>
  <!-- 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/NCT02976090
org study id: NI14026
nct id: NCT02976090
lead sponsor: 
collaborator: 
collaborator: 
collaborator: 
has dmc: No
Despite the fact that small intestine makes up 75% of the length of the digestive tract and
      90% of its mucosal surface area, small bowel adenocarcinoma (SBA) is rare. SBA is not equally
      dispatched along the small bowel, a predisposing disease is frequently associated. All these
      data suggest particular carcinogenesis pathway. SBA carries poor prognosis at all stages and
      no standard treatment have proved efficacy. So far, no data are available for targeted
      therapy. From the literature and a previous study of our group some biologic data showed that
      SBA carcinogenesis is closer to colorectal than gastric carcinogenesis. Nevertheless, some
      differences arise (ie: low Adenomatous Polyposis Coli mutation rate or frequent DNA mismatch
      repair deficiency). Even if some trends are founded the prognostic value of molecular
      alteration and phenotype variation according to small bowel segment, or predisposing disease
      could not been demonstrate due to small sample size.

      BIONADEGE study is a planned biologic ancillary study of the NADEGE cohort that enrolled 366
      patients with SBA from 2009 to 2012 in France. The tumour blocks and clinical data of 187
      patients have been collected. The main objective is to assess the prognostic value for
      recurrence free survival (RFS) in non-metastatic patients and overall survival (OS) in
      metastatic patients of molecular alteration in a set of 46 genes and abnormal protein
      expression potentially implicated in carcinogenesis. The mains secondary objectives are: 1)
      to identify potential mutation targetable in small intestine tumours and protein expression,
      2) to state the frequency of molecular alteration according to the tumour location, stage or
      predisposing disease and established clinico-biologic correlation. Tissue microarrays will be
      performed and several potential prognostic markers will be assessed. Sequencing on tumour DNA
      will investigate the presence of 740 hot spot somatic mutations in 46 genes involved.The
      abnormal protein expression or the genetic alterations with an expected frequency superior to
      10% will be assessed as potential prognostic factor to RFS and OS.

      These evaluations on a large cohort could allow comparison between pathways and will offer
      better knowledge of tumour molecular phenotype and prognosis will give rational for targeted
      therapy trials The predisposing diseases for SBA involved several different carcinogenesis
      pathways. Finally, a molecular classification of SBA will be attempt.
The NADEGE cohort involves 75 centres and had enrolled 365 patients. Among them 232 patients
      had a resection of the primary tumour in 58 centres. This will is be the largest series in
      the world of SBA for biological study. The patients enrolled in the NADEGE cohort were aware
      of the biologic study and their authorisation to perform is already collected.

      Baseline clinical data of patients enrolled in NADEGE cohort are already available and were
      presented in a poster discussion session at the European Society for Medical Oncology
      congress 2013. In all the cohort the primary location was duodenum in 51% of the patients,
      and a predisposing disease was reported in 18.8% of the patient mainly Crohn disease in 8%
      and Lynch syndrome in 6% of the patients. The follow-up is ongoing. The analyses of 3-years
      recurrence-free survival is planned in 2015 and the analysis of 5-years overall survival in
      2017.

      Today 187 tumour sample are collected and archived in the pathology department of Saint
      Antoine hospital (Paris). Among these 187 tumours the tumour stage are: stage 0: 4, stage I:
      10, stage II: 34, stage III: 63, undetermined stage non-metastatic: 30 (thus 141
      non-metastatic tumours) and stage IV: 48, and the primary are: duodenum: 128, jejunum: 31,
      ileon: 27, undetermined: 3. The chemotherapy performed was FOLFOX in 80% of the cases.

      Work Package 1: Database (team 1) The clinical data of NADEGE cohort are collected with an
      e-crf. The initial descriptive data are already monitored by the GERCOR team. The results
      have been already presented. BIONADEGE is a planned ancillary study of the NADEGE cohort. The
      complementary queries for the purpose of BIONADEGE will be addressed by the team 1 to the
      NADEGE investigator. The follow-up data for progression (metastatic patients), recurrence
      (non-metastatic patient) and death (all patients) will be obtained every 6 months. Follow-up
      data will be collected until 2019 in order to obtain 5-years follow-up for all the patients.

      Work Package 2: Anatomopathology (team 2) All the tumour samples are already bank in the
      pathology laboratory of Saint Antoine hospital. Slides from representative tumour area will
      be selected and send to Paris Descartes university to allow DNA extraction. Tissue
      microarrays (TMA) for immunohistochemistry validation studies will be performed. Several
      potential prognostic markers will be assessed as MismatchRepair (MMR) protein, P53,
      beta-catenin, c-myc protein. Other predictive markers for chemotherapy as hENT1,
      O6-methylguanine DNA methyltransferase (MGMT) and for targeted therapy as Proto-oncogene
      tyrosine-protein kinase (ROS1), hepatocyte growth factor receptor c-Met (HGFR), Alk, Human
      Epidermal Growth Factor Receptor-2 (HER-2) and Programmed cell death 1 (PD-1) will also be
      assessed. The cases overexpressing HER-2 and HGFR protein by immunohistochemistry will be
      tested by Fluorescent In Situ Hybridisation (FISH).

      Work Package 3: Biochemistry (team 3) DNA will be extracted from tumour block in the
      university unit S1147 according to the following protocol. Using a 1.0-mm punch, paraffin
      embedded tissues from all cases will be sampled from representative areas that will contain
      more than 50% of tumour cells. DNA will be thereafter extracted from each sample following
      the manufacturer's recommendation. The team3 will use a competitive allele specific taqman
      probe designed on Kras wild type allele (Hs.00000174-rf - Life Technologies) on serial
      dilution of each DNA sample in order to quantify amplifiable DNA. Only samples with more than
      10 ng of amplifiable DNA will be retained for the sequencing. DNA from each sample will be
      amplified. The presence of more than 740 hot spot somatic mutations in the 46 genes will be
      investigate. Data analysis, including alignment to the hg19 human reference genome and
      variant calling, will be done using the Software of Life Technologies. Alignments will be
      visually verified and annotated with the software of Integrative Biosoftware. A sequence
      variation will be considered as a potential mutation if (i) the coverage is superior to 200×,
      (ii) the allelic frequency is superior to 10%, (iii) the strand bias is from 0.2 to 0.8, (iv)
      the variation is not reported in the 1000 genomes database, (v) the variation is a missense
      or a non-sense variation. All these selected variations will be controlled using the Sanger
      sequencing technics using amplified fragments of less than 150 bp centred on the potential
      mutation.
observational model: Cohort
time perspective: Retrospective
measure: RFS in non-metastatic patients according to 46 genes and abnormal protein expression potentially implicated in carcinogenesis.
time frame: 3 years
measure: OS in metastatic patients according to 46 genes and abnormal protein expression potentially implicated in carcinogenesis
time frame: 3 years
measure: Rate of MMR status
time frame: 3 years
Tumour block
study pop: 
sampling method: Probability Sample
criteria: 
gender: All
minimum age: 18 Years
maximum age: N/A
healthy volunteers: No
last name: Sabine HELFEN
role: Study Chair
affiliation: Assistance Publique - Hôpitaux de Paris
responsible party type: Sponsor
mesh term: Adenocarcinoma
sharing ipd: No