Hospitals

UCSF’s one-size-fits-all precision medicine test for infection

What pathogen is causing a patient's disease? A coalition of University of California researchers, doctors and Silicon Valley companies are working together to create a test that can diagnose whether a severely ill patient has a virus, bacteria, fungus or parasite.

Is it a superbug? A parasite? How about a fungus? Diagnosing an acute infection is a time-pressured guessing game – with doctors often flummoxed over what pathogen is causing a patient’s rapidly declining health.

The University of California health system, led by UC San Francisco, is using a precision medicine approach to quickly detect infectious disease among patients in its health system. It is using next-gen sequencing and a proprietary algorithm to figure out what virus, bacteria, fungus or parasite is causing a patient’s illness.

The health system is working with four Silicon Valley companies: Quest Diagnostics, Google Genomics, DNANexus and Syapse. After an 18-month rollout across several hospitals in the University of California health system, the ultimate goal is to commercialize a fast-acting test for hospital-acquired infection that could broadly be available around the globe.

The project uses the work led by UCSF researcher Dr. Charles Chiu, who has developed a DNA sequencing scheme that can detect any pathogen with a single test. It’s already been tested a fair amount, and notably helped save the life of a 14-year-old boy with bacterial encephalitis.

“The traditional diagnostic paradigm is to send off diagnostic test after diagnostic test – and still have no solid diagnosis, and treat patients empirically based on our best guess,” Chiu told MedCity News. “That’s why we have developed a test to detect a full spectrum of pathogens in a universal test – and will if this is cost effective and helps improve clinical outcomes.”

They’ll begin by studying patients presenting with encephalitis, meningitis, sepsis or pneumonia – sequencing their genes and integrating this data into their medical records.

The project will involve Chiu’s lab, the four Silicon Valley companies and the UC health systems to work in tandem. An around-the-clock precision medicine consult team will be on hand to interpret results and guide treatment, the health system says.

Once a patient’s genes are sequenced, technology from DNANexus integrates Chiu’s algorithm into the cloud, “ultimately allowing samples and sequencing from a range of sites to be analyzed and securely shared using a common platform,” David Shaywitz, the company’s chief medical officer, wrote in a blog post.

Google Genomics will help with the distribution of Chiu’s software. Syapse then integrates all of the molecular genomic data with the clinical data that comes from medical records. It’ll provide clinical decision support to doctors, pointing them toward appropriate treatment options.

“We could scale this very, very quickly,” Syapse founder and President Jonathon Hirsch told MedCity News. “Infectious disease is one of the most important areas we can address with precision medicine – and the way this project is structured, we could actually get this done in one year.”

Quest Diagnostics will help develop the test for UC-wide use, and ultimately serve as a main commercialization partner if the project goes as planned.

“We’re definitely thinking along the lines of commercializing this,” Chiu said. “There’s also potential in licensing the assay itself, as well as the software.”

In addition to grant funding, this project has received $1.2 million from the California Initiative to Advance Precision Medicine, a public/private partnership launched in April by Jerry Brown, the state’s governor, to help advance President Obama’s Precision Medicine Initiative.

 

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