Chan Zuckerberg Initiative supports Human Cell Atlas data platform

The Data Coordination Platform will check, share and analyse the vast amounts of diverse information generated

The Chan Zuckerberg Initiative (CZI) has announced financial and engineering support for the Human Cell Atlas, an ambitious international collaboration led by the Wellcome Trust Sanger Institute and the Broad Institute, which is using sequencing technology to redefine every cell in the body. Support from CZI will enable the European Bioinformatics Institute (EMBL-EBI), the Broad Institute and the University of California Santa Cruz (UCSC) to set up an open, cloud-based Data Coordination Platform to check, share and analyse the vast amounts of diverse information generated in the initiative.

The field of human genetics has advanced so far and so fast in the past two decades that scientists believe it’s time to rethink human anatomy, starting with DNA. The Human Cell Atlas aims to do just that by creating a new, open, accessible reference map of the healthy human body.

“Anatomy textbooks as they are now were designed about 100 years ago by people assigning meaning according to how things look and function. Now, we’re using molecular tools to characterise what’s going on in organs and tissues and to get a deeper view of anatomy. That’s the Human Cell Atlas.”

Dr John Marioni Research Group Leader at EMBL-EBI and a key member of the Data Coordination Platform

This international collaboration is using RNA sequencing technology to define cells in a whole new way. Such a highly specific, sequencing-based reference of healthy human function will be transformative for biomedical research, in any number of ways. This will mean a lot of data.

“The scale of the Atlas will be in the tens of millions of datasets. Interoperability and transparency are essential for keeping so many moving parts working – we know this from our long experience collaborating with one another. We’ve designed the data architecture as open-source and modular from the get-go. That will make it easier for others to use and add to the Atlas in the future.”

Dr Sarah Teichmann Head of Cellular Genetics at the Wellcome Trust Sanger Institute and joint leader of the Human Cell Atlas

Moving away from ftp-based file sharing, the new cloud-based pipeline will allow Human Cell Atlas partners to upload their datasets, analyse them jointly, and compare healthy and diseased tissues in meaningful ways. This will involve cloud technologies including Open Stack, Google and Amazon Web Services.

“The size and scope of this new data platform will require large-scale collaborations between informatics and genomics experts across academia and industry. That is why we are thrilled to bring together three of the world’s leading institutions in genomics, informatics, and data sharing to build this important new resource – and our own software engineers will help develop the tools and facilitate the collaboration. It is a great example of how we can help accelerate science by supporting collaborations across institutions and by bringing scientists and engineers together in new ways.”

Cori Bargmann President of science at the Chan Zuckerberg Initiative

The raw data produced by Human Cell Atlas researchers will be stored and accessed at EMBL-EBI, flowed to platform partners in the US for cloud-based analysis and annotation, then sent back to EMBL-EBI to be stored and shared in the public archives, making it available to the wider world.

“Science is truly international, and that is clear in the way the Human Cell Atlas partners work across continents. Each partner brings substantial experience building essential data services for the life sciences. CZI is not just funding the project – they’re a hands-on partner. So we know the Atlas will be built with the best engineering possible.”

Ewan Birney Director of EMBL-EBI and Chair of the Global Alliance for Genomics and Health

“This contribution is for all the world’s biomedical scientists, because the Human Cell Atlas will be shared with everyone. CZI’s support will help us start to build a data platform for scientists around the world to see and analyse each other’s data, and to share the results of their work widely and openly. This will inspire others to ask new questions, and empower them to find the answers.”

Dr Aviv Regev Chair of the Faculty at the Broad Institute and joint leader of the Human Cell Atlas

Building the platform is just the start of a colossal undertaking that will take many years to complete, during which technologies will inevitably change. The next step for the Data Coordination Platform is to plan for emerging technologies such as bioimaging, and for sustaining the public resource over the long term.

More information

The Human Cell Atlas initiative was launched in October 2016.

Selected websites

  • Human Cell Atlas initiative

    The Human Cell Atlas, as ambitious in scope as the Human Genome Project, aims to chart the types and properties of all human cells, across all tissues and organs, to build a new reference map of the healthy human body. The Human Cell Atlas will be freely available to scientists all over the world, transforming the fundamental understanding of human development and the progression of diseases.

  • The EMBL-EBI–Sanger Single-Cell Genomics Centre

    The EMBL-EBI–Wellcome Trust Sanger Institute Single Cell Genomics Centre (SCGC) seeks to answer key biological questions by exploring cellular genetics at the highest resolution possible. It enables researchers to identify differences between individual cells within developing tissues, which is crucial to discovering how cancer spreads or how specialised cells can be grown for use in regenerative medicine.

  • About EMBL-EBI

    The European Bioinformatics Institute (EMBL-EBI) is a global leader in the storage, analysis and dissemination of large biological datasets. We help scientists realise the potential of ‘big data’ by enhancing their ability to exploit complex information to make discoveries that benefit humankind. We are at the forefront of computational biology research, with work spanning sequence analysis methods, multi-dimensional statistical analysis and data-driven biological discovery, from plant biology to mammalian development and disease. We are part of EMBL, and are located on the Wellcome Genome Campus, one of the world’s largest concentrations of scientific and technical expertise in genomics.

  • About EMBL

    EMBL is Europe’s flagship laboratory for the life sciences. We are an intergovernmental organisation established in 1974 and are supported by over 20 member states. EMBL performs fundamental research in molecular biology, studying the story of life. We offer services to the scientific community; train the next generation of scientists and strive to integrate the life sciences across Europe. We are international, innovative and interdisciplinary. We are more than 1600 people, from over 80 countries, operating across six sites in Barcelona (Spain), Grenoble (France), Hamburg (Germany), Heidelberg (Germany), Hinxton (UK) and Monterotondo (Italy). Our scientists work in independent groups and conduct research and offer services in all areas of molecular biology. Our research drives the development of new technology and methods in the life sciences. We work to transfer this knowledge for the benefit of society.

  • About the Chan-Zuckerberg Initiative

    The Chan Zuckerberg Initiative was launched in December 2015 by Mark Zuckerberg, founder and CEO of Facebook, and his wife, Dr. Priscilla Chan, a pediatrician and founder of The Primary School in East Palo Alto. The Chan Zuckerberg Initiative is dedicated to advancing human potential and promoting equal opportunity through grant making, impact investing, engineering, policy, and advocacy work. Initial areas of focus include science and education.

  • About the Broad Institute of MIT and Harvard

    Broad Institute of MIT and Harvard was launched in 2004 to empower this generation of creative scientists to transform medicine. The Broad Institute seeks to describe all the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods, and data openly to the entire scientific community. Founded by MIT, Harvard, Harvard-affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff, and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide.

  • About the Wellcome Trust Sanger Institute

    The Wellcome Trust Sanger Institute is one of the world’s leading genome centres. Through its ability to conduct research at scale, it is able to engage in bold and long-term exploratory projects that are designed to influence and empower medical science globally. Institute research findings, generated through its own research programmes and through its leading role in international consortia, are being used to develop new diagnostics and treatments for human disease.