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Completed

NCT Number: NCT03796546

Pediatric Infectious Disease Precision Medicine Using Sequencing Evaluation of CSF

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.

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Key information

Conditions

Infection Infections Meningitis Nervous System Diseases Neuroinflammatory Diseases

Age range

0 year–17 year

Sex eligibility

All sexes

Study type

Observational

Primary location

CHOC Children's Hospital Orange County, Orange, California, United States

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About this study

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.

Who can participate

Healthy volunteers accepted: No

Only the study team can determine whether someone qualifies for participation.

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

Treatment and study plan

Primary outcomes

  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 outcomes

  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 outcomes

  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.

Sponsors and collaborators

Lead sponsor

IDbyDNA, Inc.

Industry

Collaborators

  • Rady Children's Hospital, San Diego

Registry information

Official study 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

Acronym: PIPSEC

Important dates

Study start
2019
Primary completion
2020
Study completion
2020
First posted
Jan 8, 2019
Registry last updated
Nov 10, 2020

OpenTrials presents study information sourced from ClinicalTrials.gov. The official registry record should be consulted for the latest information.

View the official ClinicalTrials.gov record (opens in a new tab)

This listing is for discovery and informational purposes only. It is not medical advice, does not guarantee that a study is recruiting, and does not determine eligibility. Contact the study team and a qualified healthcare professional when considering participation.

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