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Pediatric Infectious Disease Precision Medicine Using Sequencing Evaluation of CSF (PIPSEC)

The safety and scientific validity of this study is the responsibility of the study sponsor and investigators. Listing a study does not mean it has been evaluated by the U.S. Federal Government. Read our disclaimer for details.
ClinicalTrials.gov Identifier: NCT03796546
Recruitment Status : Completed
First Posted : January 8, 2019
Last Update Posted : November 10, 2020
Rady Children's Hospital, San Diego
Information provided by (Responsible Party):
IDbyDNA, Inc.

Brief Summary:
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.

Condition or disease
Infection Meningitis

Detailed Description:

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.

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Study Type : Observational
Actual Enrollment : 71 participants
Observational Model: Other
Time Perspective: Prospective
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
Actual Study Start Date : January 22, 2019
Actual Primary Completion Date : October 7, 2020
Actual Study Completion Date : October 7, 2020

Primary Outcome Measures :
  1. Diagnostic Rate [ Time Frame: 24 months ]
    Comparison of the sensitivity, specificity, positive and negative predictive values of IDbyDNA NGS results with the Explify diagnostic platform compared with standard care.

Secondary Outcome Measures :
  1. Clinical Utilization [ Time Frame: 24 months ]

    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.

Other Outcome Measures:
  1. Post-Hoc Analysis - Economic Evaluation (1) [ Time Frame: 24 months ]

    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.

  2. Post-Hoc Analysis - Economic Evaluation (2) [ Time Frame: 24 months ]
    Cost analysis of what best available testing would have cost.

  3. Post-Hoc Analysis - Host Response [ Time Frame: 24 months ]
    RNA sequencing to determine if there is a specific host response to either specific infectious or noninfectious etiologies.

Biospecimen Retention:   Samples With DNA
Residual cerebrospinal fluid collected for standard of care clinical diagnostic purposes

Information from the National Library of Medicine

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Ages Eligible for Study:   0 Years to 17 Years   (Child)
Sexes Eligible for Study:   All
Accepts Healthy Volunteers:   No
Sampling Method:   Probability Sample
Study Population

This project will enroll children who are having an evaluation for central nervous system (CNS) infection and have already had a lumbar puncture to obtain cerebrospinal fluid (CSF) to evaluate for infection and host immune response. As such enrolled patients will be undergoing an evaluation for suspected meningitis, encephalitis, ventriculitis and VP shunt infection.

Patients in whom there is CSF remaining after standard testing has been obtained and who meet the other inclusion criteria will be approached for enrollment in the study.


Inclusion Criteria:

  • Age 0-17 years of age (not yet 18)
  • Clinical evaluation for CNS infection
  • CSF white blood cell count (WBC) > 15 cells/µL when there are less than 5000 RBCs on same
  • Admitted to a participating study site
  • CSF obtained per standard protocol
  • 1 mL of appropriately stored CSF is available following completion of all standard of care testing

Exclusion Criteria:

  • CSF Red blood cell (RBC) count > 5000 cells/µL on same CSF sample as with pleocytosis
  • Unable to obtain consent

Information from the National Library of Medicine

To learn more about this study, you or your doctor may contact the study research staff using the contact information provided by the sponsor.

Please refer to this study by its ClinicalTrials.gov identifier (NCT number): NCT03796546

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United States, California
CHOC Children's Hospital Orange County
Orange, California, United States, 92868
Rady Children's Hospital
San Diego, California, United States, 92123
United States, Florida
Nicklaus Children's Hospital
Miami, Florida, United States, 33155
Sponsors and Collaborators
IDbyDNA, Inc.
Rady Children's Hospital, San Diego
Additional Information:
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Responsible Party: IDbyDNA, Inc.
ClinicalTrials.gov Identifier: NCT03796546    
Other Study ID Numbers: PIPSEC - 01
First Posted: January 8, 2019    Key Record Dates
Last Update Posted: November 10, 2020
Last Verified: November 2020
Individual Participant Data (IPD) Sharing Statement:
Plan to Share IPD: Undecided

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Studies a U.S. FDA-regulated Drug Product: No
Studies a U.S. FDA-regulated Device Product: No
Keywords provided by IDbyDNA, Inc.:
Additional relevant MeSH terms:
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Central Nervous System Diseases
Nervous System Diseases