The urgency of scientific data sharing is never more apparent than during a global disease outbreak. Rapid sharing of high quality data is critical for the effective and timely response to any pandemic. In late January, Wellcome called on researchers, journals, and funders to rapidly and openly share research findings and data relevant to COVID-19; GA4GH has signed the statement and our community is actively supporting its guidance through the development of a variety of research and data sharing platforms and initiatives.
Continuing to strengthen international genomics standards and approaches over time will help prepare us to more rapidly respond to future outbreaks; ensuring translation into the infectious disease community will allow us to respond more effectively. GA4GH has aligned with the Public Health Alliance for Genomic Epidemiology (PHA4GE) to guide efforts to share pathogen genomic data.
PHA4GE models itself on GA4GH in its goals and structure and aims to develop an open source, community-supported ecosystem for bioinformatic software development, implementation, and validation. PHA4GE is working with the US CDC’s Advanced Molecular Detection Program to coordinate “SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES)”, a US national effort to help accelerate the use of near-real time pathogen genomic data for the pandemic response, through data standards and sharing. Through PHA4GE, these standards will then be disseminated into the broader international community.
Many in the GA4GH human genetics community are appropriately being pulled directly into viral genomics research as well as analyzing host response studies, leveraging their expertise at both the genetics and functional genomics levels. Activities being coordinated by the GA4GH community include:
COVID-19 Beacon: a platform for the scientific and medical communities to share and discover knowledge about the genetics of the virus in real time (read more).
COVID-19 Host Genetics Initiative: a collaborative effort among members of the International Common Disease Alliance and the broader human genetics community working together to generate, share, and analyze COVID-19 data. Studies can register with the initiative here to contribute to this global effort.
COVID-19 Portal: a platform that uses federated components from the European Nucleotide Archive (ENA) and the European Genome-phenome Archive (EGA) to provide access to relevant datasets submitted to the European Bioinformatics Institute (EMBL-EBI) and other major centers for biomedical data.
Covidaware.me: a platform that leverages the GA4GH Phenopackets standard to allow participants and families to share descriptions of their condition and its progression over time (read more).
Pan-European Privacy-Preserving Proximity Tracing: a core technology created by members of the GA4GH Data Security Work Stream that provides an internationally applicable mechanism upon which any country can develop a secure app for local proximity tracing.
Secure Collective COVID-19 Research (SCOR): Members of the GA4GH Data Security Work Stream have helped establish the Secure Collective COVID-19 Research (SCOR) consortium, which aims to support international collaboration on COVID-19 research while respecting patient privacy.
Testing and Sequencing: Our Host Institutions—Broad Institute, Wellcome Sanger Institute, and Ontario Institute for Cancer Research—have all repurposed existing laboratory space to provide rapid, large-scale diagnostic testing and whole genome sequencing and analysis of both virus and host.
This list is not exhaustive. The GA4GH network is expansive and diverse. We will maintain a list of activities on our website to facilitate collaboration and awareness. Please email us if you would like your COVID-19 project to be listed.
We are fortunate to live in an age when technology enables many of us to collaborate and maintain the research endeavor despite world-wide social distancing mandates. But in order to ensure truly equitable access to and participation in both the scientific process and its benefits, we must rigorously maintain technical and ethical standards that support the open sharing of data and knowledge—now and always.