Abstract
Rapid and precise diagnosis is critical to combat infectious disease globally. When diagnosis and treatment is
delayed, infectious disease, which can be caused by bacteria, fungi, viruses or parasites, can lead to
debilitating or life-threatening illness. Therefore, rapid and accurate identification of etiology of infectious
disease at the point-of-service is of paramount importance for clinicians planning treatment. Rapid DNA and
RNA sequencing has been demonstrated in multiple diseases as a way to identify pathogen with broad
coverage and exquisite sensitivity. Such systems are capable of identifying any nucleic acid-based lifeform
with high throughput. However, challenges in meeting the need for field deployable rapid diagnosis has
detrimentally impacted adoption of sequencing technology in global medicine. In order to address this need,
ChromoLogic LLC (CL), in partnership with the University of Washington (UW), propose to develop the Eye-
Path™. The Eye-Path system contains 2 distinct modules; (1) an automated DNA and RNA preparation
sample kit subsystem and (2) a cloud-based genomic sequencing analysis software, currently in clinical trials
at UW for characterizing ocular infections. The pathogen identification subsystem consists of a metagenomic
detection that contains real-time sequencing reads uploaded to a cloud-based computing platform for real-time
sequence matching. The system uses scalable metagenomics alignment research tool (SMART), a novel tool
developed and licensed from our collaborator, Dr. Russell Van Gelder from University of Washington, and his
team [5] to detect DNA and RNA-based life forms—including bacteria, fungi, parasites, and viruses with
unprecedented detail. Furthermore, this technology can be applicable to many other infectious disease and
microbial sampling operations. During Phase I, ChromoLogic will establish the analytical validation and provide
preliminary clinical validation data of Eye-Path™. To assess for the clinical validity of using Eye-Path, we will
process vitreous humor sample from patients with suspected endophthalmitis and perform real-time pathogen
identification. The extracted samples will be partitioned for sequencing with a next generation sequencer
(Illumina) and an Oxford Nanopore technology equipped with the EYE-Path bioinformatic software and sample
processing. With the data obtained from this study, we will expect (1) assess Eye-Path™'s analytical validity
for CMS CLIA review as a Laboratory Developed Test (LDT).