What is the difference between the Chiu laboratory and the UCSF-Abbott VDDC?

The Chiu laboratory at UCSF is supported in part by a joint multi-year initiative between UCSF and Abbott Laboratories to establish a center for viral diagnostics and discovery in 2008 (UCSF-Abbott VDDC). The VDDC thus is part of the Chiu laboratory, and there are many mutually collaborative projects ongoing between both facilities.

I heard about the metagenomic next-generation sequencing (mNGS) clinical test. What is it and how can I get tested?

The mNGS test is a comprehensive approach to diagnose infections by detecting nucleic acid (DNA and/or DNA) corresponding to any pathogen – virus, bacterium, fungus, or parasite – in clinical samples. This test can be run on any body fluid (cerebrospinal fluid, blood, respiratory swabs, bronchoalveolar lavage fluid, urine, stool, abscess fluid, etc.) or tissue. Currently, the only clinical testing available at UCSF is for diagnosis of meningoencephalitis from cerebrospinal fluid (CSF). This service is provided by the UCSF Clinical Microbiology Laboratory and is part of the UCSF Center for Next-Gen Precision Diagnostics (NGDx). See the Diagnostic Lab at NGDx.

Why is only mNGS testing from cerebrospinal fluid (CSF)? What about from other sample types, such as blood, or for other kinds of infections, such as pneumonia?

All clinical diagnostic tests require rigorous validation in CLIA (Clinical Laboratory Improvement Amendments)-licensed clinical laboratories, such as the UCSF Clinical Microbiology Laboratory, to ensure that the tests are accurate. We are actively working on validation of other sample types – especially blood and respiratory fluid for sepsis and pneumonia respectively – in addition to CSF.

I am a patient and I want to get mNGS testing done for myself or a loved one. How do I proceed?

Testing can only be done by establishing an institutional account between UCSF and your hospital/clinic. Please contact your clinical provider and have him or her obtain more information about testing. Note that only mNGS testing for meningoencephalitis from CSF is available from UCSF at this time. We will update this web site as soon as testing for other clinical indications becomes available.

I am a clinical provider and I want to get mNGS testing done for my patient. How do I proceed?

If you want to get mNGS testing done from CSF, please visit our instructions for providers. mNGS testing on other sample types or for clinical indications other than meningoencephalitis is not currently available.

I have questions about hantavirus exposure and diagnostic testing.

Dr. Chiu gave an interview explaining hantavirus and precautions to take to avoid potential exposure. If you have questions regarding diagnostic testing, please contact Dr. Chiu at charles.chiu@ucsf.edu.

I want to join the Chiu lab!

We are always interested in recruiting postdoctoral fellows, clinicians, and/or researchers with strong interests in pathogen discovery, next-generation sequencing, bioinformatics analysis, and/or clinical translational applications. Please contact Dr. Chiu at charles.chiu@ucsf.edu with questions and visit the Chiu Lab Facebook group to see what it’s like to work in the Chiu Lab.