Pediatric Infectious Disease Precision Medicine Using Sequencing Evaluation of CSF

Completed

• Conditions: Infection; Meningitis

• Registration Number: NCT03796546
• Lead Sponsor: 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.

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.

Study Timeline

• Study First Submitted: 2018-12-19
• Study First Submitted QC: 2019-01-03
• Study First Posted: 2019-01-08
• Study Start: 2019-01-22
• Primary Completion: 2020-10-07
• Study Completion: 2020-10-07
• Status Verified: 2020-11
• Last Update Submitted: 2020-11-06
• Last Update Posted: 2020-11-10

Recruitment & Eligibility

• Status: COMPLETED
• Sex: All
• Target Recruitment: 71

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

Study & Design

• Study Type: OBSERVATIONAL
• Study Design: Not specified

Primary Outcome Measures

Name	Time	Method
Diagnostic Rate	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

Name	Time	Method
Clinical Utilization	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.

Trial Locations

Locations (3)

CHOC Children's Hospital Orange County; 🇺🇸 Orange, California, United States

Rady Children's Hospital; 🇺🇸 San Diego, California, United States

Nicklaus Children's Hospital; 🇺🇸 Miami, Florida, United States