- New open-source cloud-based tool rapidly interprets terabytes of data to detect disease-causing pathogens
- In an ongoing pilot project and partnership with the Bill & Melinda Gates Foundation, IDseq is helping to identify mystery infections at a hospital in Dhaka, Bangladesh
- New funding from the Bill & Melinda Gates Foundation to expand the pilot by providing next-generation genome sequencers and IDseq training for labs and clinics throughout the world
BERLIN — Oct. 16, 2018 Today the Chan Zuckerberg Biohub (Biohub) and the Chan Zuckerberg Initiative (CZI) unveiled the soft-launch of IDseq, an open source cloud-based analysis platform that has the potential to transform our ability to detect and respond to infectious disease outbreaks around the world. Dr. Joseph DeRisi, co-president of the Biohub and professor of biochemistry and biophysics at UC San Francisco, made the announcement at the Gates Grand Challenges meeting in Berlin, Germany.
The tool, which began as a research project at Dr. DeRisi’s UCSF lab, works by rapidly combing through terabytes of metagenomic data for pathogens in a given sample — be it bacteria, a virus, fungus, or even a parasite. By identifying disease-causing pathogens, IDseq can then provide an actionable report of what is happening on the ground in labs and clinics anywhere in the world.
“Pathogens don’t respect geographic borders,” said DeRisi. “An emerging infectious disease in one community can affect surrounding areas and countries. The global health community needs the ability to share data quickly to track outbreaks or emerging diseases. With IDseq, we hope to empower data-driven decisions about how to better manage antibiotics, where to prioritize immunization campaigns, how to shape vector control and surveillance efforts.”
“IDseq is a powerful weapon to advance global health,” said Dr. Cori Bargmann, head of science for CZI. “By revealing trends in global pathogen distribution, we can help inform disease management and policy decisions that can ultimately save thousands of lives.”
IDseq has already demonstrated its ability to detect disease in the field. In a recent pilot project, Dr. Senjuti Saha of the Child Health Research Foundation (Dhaka, Bangladesh) used IDseq to identify the presence of the mosquito-borne viral chikungunya disease in the spinal fluid of patients at the largest pediatric hospital in Bangladesh (Dhaka Shishu Hospital). Based on this information, follow-up testing identified additional cases of neuroinvasive chikungunya from the same time period that were previously labeled “mystery cases.”
“It was eye-opening”, said Dr. Saha. “Chikungunya was previously thought to be neuroinvasive only in very rare instances. But the data from IDseq suggested otherwise — it helped shed light on what were otherwise mysterious brain infections. This will help inform policy makers and initiate appropriate evidence-based case management.”
“The ultimate vision for IDseq is for it to be a dashboard of real-time pathogen detection around the world,” said Priscilla Chan, who together with her husband, Mark Zuckerberg, pledged $600 million in funding to launch the Biohub two years ago. “Nothing like this exists — but it could be a major step forward in our ability to cure, prevent, or manage all disease. These are exactly the types of advances we envisioned when we started the Biohub.”
To enable broader access to IDseq and valuable on-the-ground feedback, the Bill & Melinda Gates Foundation today announced a new funding opportunity for global health workers via the Bill & Melinda Gates Foundation Grand Challenges Explorations Initiative. Awardees will receive molecular biology and bioinformatics training from Dr. DeRisi and his infectious disease team at the Biohub, free access and compute on the IDseq platform supported by CZI, along with the necessary equipment and supplies immediately needed to begin work in their own countries. Results from these partnerships will provide valuable feedback to inform product development.The ultimate goal is to make the tool openly available to global health workers everywhere.
“Empowering labs and clinics around the world with pathogen genome sequencing capability and access to IDseq’s rapid, cloud-based analysis will boost the potential of the technology to deliver on its promise – identifying unknown causes of infectious disease in newborns and infants.” said Chris Karp, Director of Discovery & Translational Sciences at the Bill & Melinda Gates Foundation. “What we learn from putting the technology into the hands of front-line professionals will inform next generation preparedness, helping direct investments in upstream discovery platforms toward novel vaccines and other previously unanticipated interventions.
While the IDseq service is still a rapidly evolving research project, the Biohub and CZI plan to make it available within the next year to partner organizations, and then more broadly afterward. The software itself is open-source and freely available
About the Chan Zuckerberg Biohub
The CZ Biohub is an independent non-profit medical research organization collaborating with the University of California, Berkeley, Stanford University and the University of California, San Francisco. The organization’s goal is to harness the power of science, technology and human capacity to cure, prevent or manage all disease during our children’s lifetime. For more information about the CZ Biohub, visit https://czbiohub.org.
About the Chan Zuckerberg Initiative
The Chan Zuckerberg Initiative, founded by Mark Zuckerberg and Priscilla Chan in December 2015, is a new kind of philanthropic organization that brings together world-class engineering, grant-making, impact investing, policy, and advocacy work. Our initial areas of focus include supporting science through basic biomedical research and education through personalized learning. We are also exploring other issues tied to the promotion of equal opportunity including access to affordable housing and criminal justice reform.
About the Bill & Melinda Gates Foundation
Guided by the belief that every life has equal value, the Bill & Melinda Gates Foundation works to help all people lead healthy, productive lives. In developing countries, it focuses on improving people’s health and giving them the chance to lift themselves out of hunger and extreme poverty. In the United States, it seeks to ensure that all people—especially those with the fewest resources—have access to the opportunities they need to succeed in school and life. Based in Seattle, Washington, the foundation is led by CEO Sue Desmond-Hellmann and Co-chair William H. Gates Sr., under the direction of Bill and Melinda Gates and Warren Buffett.
About Gates Grand Challenges
Grand Challenges is a family of initiatives fostering innovation to solve key global health and development problems.
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