<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/NCT03796546</url>
  </required_header>
  <id_info>
    <org_study_id>PIPSEC - 01</org_study_id>
    <nct_id>NCT03796546</nct_id>
  </id_info>
  <brief_title>Pediatric Infectious Disease Precision Medicine Using Sequencing Evaluation of CSF</brief_title>
  <acronym>PIPSEC</acronym>
  <official_title>A Prospective Trial to Investigate the Clinical Utility and Application of a Next Generation Sequencing Test for Pathogen Detection of Cerebral Spinal Fluid (CSF) Samples to Diagnose Pediatric Central Nervous System (CNS) Infections</official_title>
  <sponsors>
    <lead_sponsor>
      <agency>IDbyDNA, Inc.</agency>
      <agency_class>Industry</agency_class>
    </lead_sponsor>
    <collaborator>
      <agency>Rady Children's Hospital, San Diego</agency>
      <agency_class>Other</agency_class>
    </collaborator>
  </sponsors>
  <source>IDbyDNA, Inc.</source>
  <oversight_info>
    <has_dmc>No</has_dmc>
    <is_fda_regulated_drug>No</is_fda_regulated_drug>
    <is_fda_regulated_device>No</is_fda_regulated_device>
  </oversight_info>
  <brief_summary>
    <textblock>
      Prospective, multi-site, study to evaluate the diagnosis rate of DNA and RNA sequencing of&#xD;
      cerebrospinal fluid for identification of pathogens directly in patients who have already had&#xD;
      a spinal tap to evaluate for infection and were found to have a pleocytosis. Diagnostic rate&#xD;
      and clinical utility of concurrent standard testing will be compared to diagnostic rate and&#xD;
      clinical utility of DNA and RNA sequencing.&#xD;
    </textblock>
  </brief_summary>
  <detailed_description>
    <textblock>
      IDbyDNA, Inc. has developed a robust sequencing reference database for viruses, bacteria,&#xD;
      fungi and parasites and developed novel analysis methods to analyze next-generation (NGS)&#xD;
      sequencing data to rapidly identify infectious agents. This technology suite, known as the&#xD;
      Explify™ platform, holds the promise to improve patient care and efficiently guide provider&#xD;
      treatment planning for those suffering from infectious disease.&#xD;
&#xD;
      The PIPSEC trial, developed by pediatric physicians specializing in genomic medicine, is&#xD;
      intended to facilitate the acquisition of high quality and clinically annotated biospecimens&#xD;
      for the purpose of research discovery. This project intends to advance metagenomics,&#xD;
      microbial genetics, bioinformatics and data analytics, for pathogen detection utilizing&#xD;
      cerebral spinal fluid (CSF) specimens to contribute to the diagnosis of infectious agents&#xD;
      impacting the central nervous system among pediatric patients. Clinically annotated specimens&#xD;
      will facilitate continued development and validation of the Explify test and its clinical&#xD;
      utility for providers treating central nervous system (CNS) infections.&#xD;
&#xD;
      The primary objective is to assess clinical utility of the Explify test compared to&#xD;
      concurrent standard of care testing to identify pathogens from CSF fluid within a pediatric&#xD;
      patient population.&#xD;
    </textblock>
  </detailed_description>
  <overall_status>Completed</overall_status>
  <start_date type="Actual">January 22, 2019</start_date>
  <completion_date type="Actual">October 7, 2020</completion_date>
  <primary_completion_date type="Actual">October 7, 2020</primary_completion_date>
  <study_type>Observational</study_type>
  <has_expanded_access>No</has_expanded_access>
  <study_design_info>
    <observational_model>Other</observational_model>
    <time_perspective>Prospective</time_perspective>
  </study_design_info>
  <primary_outcome>
    <measure>Diagnostic Rate</measure>
    <time_frame>24 months</time_frame>
    <description>Comparison of the sensitivity, specificity, positive and negative predictive values of IDbyDNA NGS results with the Explify diagnostic platform compared with standard care.</description>
  </primary_outcome>
  <secondary_outcome>
    <measure>Clinical Utilization</measure>
    <time_frame>24 months</time_frame>
    <description>Change of Management resulting from NGS diagnosis versus diagnosis based on standard of care. Change of Management is a binary (yes or no) based on assignments made by the PI or designee at each site using the following domains:&#xD;
Diagnosis specific pharmacological treatment&#xD;
Diagnosis specific management&#xD;
Diagnosis specific supportive interventions A change in any of these domains will be considered a change of clinical management for utilization purposes.</description>
  </secondary_outcome>
  <other_outcome>
    <measure>Post-Hoc Analysis - Economic Evaluation (1)</measure>
    <time_frame>24 months</time_frame>
    <description>Economic evaluation of cost of standard of care testing compared to economic cost of NGS testing:&#xD;
Determination of what diagnosis made could have been made with best possible clinical tests currently available.</description>
  </other_outcome>
  <other_outcome>
    <measure>Post-Hoc Analysis - Economic Evaluation (2)</measure>
    <time_frame>24 months</time_frame>
    <description>Cost analysis of what best available testing would have cost.</description>
  </other_outcome>
  <other_outcome>
    <measure>Post-Hoc Analysis - Host Response</measure>
    <time_frame>24 months</time_frame>
    <description>RNA sequencing to determine if there is a specific host response to either specific infectious or noninfectious etiologies.</description>
  </other_outcome>
  <enrollment type="Actual">71</enrollment>
  <condition>Infection</condition>
  <condition>Meningitis</condition>
  <biospec_retention>Samples With DNA</biospec_retention>
  <biospec_descr>
    <textblock>
      Residual cerebrospinal fluid collected for standard of care clinical diagnostic purposes&#xD;
    </textblock>
  </biospec_descr>
  <eligibility>
    <study_pop>
      <textblock>
        This project will enroll children who are having an evaluation for central nervous system&#xD;
        (CNS) infection and have already had a lumbar puncture to obtain cerebrospinal fluid (CSF)&#xD;
        to evaluate for infection and host immune response. As such enrolled patients will be&#xD;
        undergoing an evaluation for suspected meningitis, encephalitis, ventriculitis and VP shunt&#xD;
        infection.&#xD;
&#xD;
        Patients in whom there is CSF remaining after standard testing has been obtained and who&#xD;
        meet the other inclusion criteria will be approached for enrollment in the study.&#xD;
      </textblock>
    </study_pop>
    <sampling_method>Probability Sample</sampling_method>
    <criteria>
      <textblock>
        Inclusion Criteria:&#xD;
&#xD;
          -  Age 0-17 years of age (not yet 18)&#xD;
&#xD;
          -  Clinical evaluation for CNS infection&#xD;
&#xD;
          -  CSF white blood cell count (WBC) &gt; 15 cells/µL when there are less than 5000 RBCs on&#xD;
             same&#xD;
&#xD;
          -  Admitted to a participating study site&#xD;
&#xD;
          -  CSF obtained per standard protocol&#xD;
&#xD;
          -  1 mL of appropriately stored CSF is available following completion of all standard of&#xD;
             care testing&#xD;
&#xD;
        Exclusion Criteria:&#xD;
&#xD;
          -  CSF Red blood cell (RBC) count &gt; 5000 cells/µL on same CSF sample as with pleocytosis&#xD;
&#xD;
          -  Unable to obtain consent&#xD;
      </textblock>
    </criteria>
    <gender>All</gender>
    <minimum_age>0 Years</minimum_age>
    <maximum_age>17 Years</maximum_age>
    <healthy_volunteers>No</healthy_volunteers>
  </eligibility>
  <location>
    <facility>
      <name>CHOC Children's Hospital Orange County</name>
      <address>
        <city>Orange</city>
        <state>California</state>
        <zip>92868</zip>
        <country>United States</country>
      </address>
    </facility>
  </location>
  <location>
    <facility>
      <name>Rady Children's Hospital</name>
      <address>
        <city>San Diego</city>
        <state>California</state>
        <zip>92123</zip>
        <country>United States</country>
      </address>
    </facility>
  </location>
  <location>
    <facility>
      <name>Nicklaus Children's Hospital</name>
      <address>
        <city>Miami</city>
        <state>Florida</state>
        <zip>33155</zip>
        <country>United States</country>
      </address>
    </facility>
  </location>
  <location_countries>
    <country>United States</country>
  </location_countries>
  <link>
    <url>http://idbydna.com</url>
    <description>Sponsor Website</description>
  </link>
  <verification_date>November 2020</verification_date>
  <study_first_submitted>December 19, 2018</study_first_submitted>
  <study_first_submitted_qc>January 3, 2019</study_first_submitted_qc>
  <study_first_posted type="Actual">January 8, 2019</study_first_posted>
  <last_update_submitted>November 6, 2020</last_update_submitted>
  <last_update_submitted_qc>November 6, 2020</last_update_submitted_qc>
  <last_update_posted type="Actual">November 10, 2020</last_update_posted>
  <responsible_party>
    <responsible_party_type>Sponsor</responsible_party_type>
  </responsible_party>
  <keyword>Pediatric</keyword>
  <condition_browse>
    <!-- CAUTION:  The following MeSH terms are assigned with an imperfect algorithm            -->
    <mesh_term>Infections</mesh_term>
    <mesh_term>Meningitis</mesh_term>
  </condition_browse>
  <patient_data>
    <sharing_ipd>Undecided</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/NCT03796546
org study id: PIPSEC - 01
nct id: NCT03796546
lead sponsor: 
collaborator: 
has dmc: No
is fda regulated drug: No
is fda regulated device: No
Prospective, multi-site, study to evaluate the diagnosis rate of DNA and RNA sequencing of
      cerebrospinal fluid for identification of pathogens directly in patients who have already had
      a spinal tap to evaluate for infection and were found to have a pleocytosis. Diagnostic rate
      and clinical utility of concurrent standard testing will be compared to diagnostic rate and
      clinical utility of DNA and RNA sequencing.
IDbyDNA, Inc. has developed a robust sequencing reference database for viruses, bacteria,
      fungi and parasites and developed novel analysis methods to analyze next-generation (NGS)
      sequencing data to rapidly identify infectious agents. This technology suite, known as the
      Explify™ platform, holds the promise to improve patient care and efficiently guide provider
      treatment planning for those suffering from infectious disease.

      The PIPSEC trial, developed by pediatric physicians specializing in genomic medicine, is
      intended to facilitate the acquisition of high quality and clinically annotated biospecimens
      for the purpose of research discovery. This project intends to advance metagenomics,
      microbial genetics, bioinformatics and data analytics, for pathogen detection utilizing
      cerebral spinal fluid (CSF) specimens to contribute to the diagnosis of infectious agents
      impacting the central nervous system among pediatric patients. Clinically annotated specimens
      will facilitate continued development and validation of the Explify test and its clinical
      utility for providers treating central nervous system (CNS) infections.

      The primary objective is to assess clinical utility of the Explify test compared to
      concurrent standard of care testing to identify pathogens from CSF fluid within a pediatric
      patient population.
observational model: Other
time perspective: Prospective
measure: Diagnostic Rate
time frame: 24 months
description: Comparison of the sensitivity, specificity, positive and negative predictive values of IDbyDNA NGS results with the Explify diagnostic platform compared with standard care.
measure: Clinical Utilization
time frame: 24 months
description: Change of Management resulting from NGS diagnosis versus diagnosis based on standard of care. Change of Management is a binary (yes or no) based on assignments made by the PI or designee at each site using the following domains:
Diagnosis specific pharmacological treatment
Diagnosis specific management
Diagnosis specific supportive interventions A change in any of these domains will be considered a change of clinical management for utilization purposes.
measure: Post-Hoc Analysis - Economic Evaluation (1)
time frame: 24 months
description: Economic evaluation of cost of standard of care testing compared to economic cost of NGS testing:
Determination of what diagnosis made could have been made with best possible clinical tests currently available.
measure: Post-Hoc Analysis - Economic Evaluation (2)
time frame: 24 months
description: Cost analysis of what best available testing would have cost.
measure: Post-Hoc Analysis - Host Response
time frame: 24 months
description: RNA sequencing to determine if there is a specific host response to either specific infectious or noninfectious etiologies.
Residual cerebrospinal fluid collected for standard of care clinical diagnostic purposes
study pop: 
sampling method: Probability Sample
criteria: 
gender: All
minimum age: 0 Years
maximum age: 17 Years
healthy volunteers: No
facility: 
facility: 
facility: 
country: United States
url: http://idbydna.com
description: Sponsor Website
responsible party type: Sponsor
mesh term: Infections
mesh term: Meningitis
sharing ipd: Undecided