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Charles Chiu

Nanopore sequencing for metagenomic diagnosis of infectious deseases

About Charles Chiu

Charles Chiu, M.D./Ph.D. is Associate Professor of Laboratory Medicine and Medicine, Division of Infectious Diseases at University of California, San Francisco, Director of the UCSF-Abbott Viral Diagnostics and Discovery Center (VDDC), and Associate Director of the UCSF Clinical Microbiology Laboratory. Dr. Chiu received an MD and PhD in biophysics from UCLA, and trained at UCSF as a resident and clinical fellow in infectious diseases. He currently heads a translational research laboratory focused on clinical diagnostic next-generation sequencing assay development for infectious diseases and investigation of emerging pathogens, including Borrelia burgdorferi, Ebola virus, enterovirus D68, and Zika virus. His work is supported by research grants from the NIH, Bay Area Lyme Disease Foundation, UC Center for Accelerated Innovation, and the California Initiative to Advance Precision Medicine. Dr. Chiu has authored more than 50 peer-reviewed publications, holds over 15 patents and patent applications, and serves on the scientific advisory board for Karius Diagnostics and Rubicon Genomics.

Abstract

Unbiased diagnosis of all pathogens in a single test by metagenomic next-generation sequencing is now feasible, but has been limited to date by concerns regarding sensitivity and sample-to-answer turnaround times. Here we will describe the development, validation, and implementation of a rapid, field-ready assay for differential diagnosis of acute febrile illness on an Oxford Nanopore MinION sequencer that can be performed in under 6 hours. Nanopore sequencing data will be analyzed in real-time on a laptop computer using SURPIrt, a portable version of the SURPI computational pipeline that is currently being implemented for precision medicine diagnosis in hospitals. The eventual goal of these studies is clinical performance validation and deployment at field sites for use in clinical diagnosis and public health surveillance in patients with any unknown febrile illness — including but not limited to infections by Zika virus, Ebola virus, Lassa virus, chikungunya virus, dengue virus, and the malarial parasite Plasmodium falciparum.

Charles Chiu

Charles Chiu

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