SEP 03, 2015 03:00 PM PDT

Next-Generation Sequencing for Diagnosis and Surveillance of Emerging Infections

Presented At Microbiology
  • Associate Professor, Laboratory Medicine and Medicine / Infectious Diseases Director, UCSF-Abbott Viral Diagnostics and Discovery Center Associate Director, UCSF Clinical Microbiology Laborat
      Dr. Charles Chiu, M.D./Ph.D., is an Assistant Professor in Laboratory Medicine and Medicine, Infectious Diseases at the University of California, San Francisco. He is also the Director of UCSF-Abbott Viral Diagnostics and Discovery Center (VDDC) at China Basin and Associate Director of the UCSF Clinical Microbiology Laboratory. Charles is an expert in the emerging field of viral metagenomics, and his research is focused on the development of microarray and deep sequencing technologies for viral pathogen discovery and clinical diagnostics. He is also the principal investigator on an R01 grant from the NIH on blood bank pathogen screening, California Discovery, UC-MEXUS, and National Research Fund for Tickborne Diseases (NRFTD) grants on the microbial epidemiology of encephalitis, diarrhea, and Lyme disease, a QB3 Rogers Family Foundation Award in translational diagnostics, and a UCSF-Abbott Viral Discovery Award. Charles has more than 30 patents and peer-reviewed publications in scientific journals and ongoing collaborations with research groups and public health agencies worldwide, including Abbott Diagnostics, Inc., Global Viral Forecasting, the United States CDC, the American Red Cross, and the Texas Biomedical Research Institute.


    Next-generation sequencing (NGS) technologies are powerful approaches for diagnosis and surveillance of emerging infections. Unbiased metagenomic NGS can detect the full spectrum of pathogens - viral, bacterial, fungal, or parasite - in clinical samples without the use of targeted primers or probes. Gene expression (transcriptome) profiling using NGS can facilitate the identification for host response biomarkers that may have diagnostic and prognostic utility. New technologies such as nanopore sequencing on a USB-sized platform can enable real-time sequencing analysis in field settings for management and diagnosis of outbreaks, such as Ebola outbreaks in Africa. Here we will discuss development and implementation of NGS approaches to addressing emerging infections in the United States and globally, including Lyme disease, enterovirus D68, chikungunya virus, and Ebola virus. Learning Objectives • To understand the principles and approach of metagenomics next-generation sequencing for unbiased detection of emerging pathogens • To understand how gene expression profiling of infectious diseases can facilitate the identification of diagnostic biomarkers • To understand clinical and public applications of NGS for emerging infections, including Lyme disease, enterovirus D68, chikungunya virus, Ebola virus.

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