Gigapixel Next-Generation-Sequencing: An Ultra-Sensitive Diagnostic for Infections of the CNS

ABSTRACT
Infectious diseases remain a significant cause of morbidity worldwide, highlighting the critical need for accurate
diagnosis. However, shared symptoms among different infections and the emergence of drug resistance make
diagnosis and treatment selection challenging. In this competing renewal, we propose to develop Gigapixel NGS
(gNGS) to enable rapid, sensitive, and information-rich infectious disease diagnosis. gNGS builds upon our
Gigapixel PCR (gPCR) technology by incorporating powerful next-generation sequencing capabilities. By
utilizing double emulsion vesicles for single cell assays, gNGS eliminates the need for specialized droplet
analyzers and allows common flow cytometers to be used for genome isolation.
Our goal in this renewal is to leverage the capabilities of Gigapixel NGS to detect, isolate, and sequence
infectious pathogen genomes from patient samples, which will improve the efficiency and sensitivity of pathogen
sequencing. We will collaborate with Dr. Charles Chiu, a renowned expert in infectious disease diagnostics who
leads the CLIA-certified pathogen lab at UCSF, to develop clinical workflows and bioinformatic tools for
interrogating the recovered genomes for relevant biomarker sequences, including virulence factors and drug
resistance genes. Dr. Chiu's expertise in infectious disease diagnostics and practical experience in clinical
sample sequencing for pathogen detection will ensure that the new diagnostic is effective and practical in a
clinical setting.

Grant Number: 5R01AI178795-11
NIH Institute/Center: NIH
Principal Investigator: Adam Abate