The corona pandemic has dominated the research world like no other topic in the last two years. Genome research plays a big part in SARS-CoV-2 and COVID-19 research. From sequencing the virus to understanding its biology and pathology, to vaccine development and variant tracking, analysing the viral genome was and remains a key technology in this pandemic. Additionally, multi-omics analysis of human samples provide important information around SARS-CoV-2 infections and the disease-related aspects of COVID-19. From defining individual genetic disposition, to detailed analysis of immune cell changes during SARS-CoV-2 infections, human omics data is crucial in trying to understand what happens in the different tissues during COVID-19 and finding explanations for differing disease courses and severity.
Assisting the German research community around SARS-CoV-2 and COVID-19, GHGA partners with the Deutsche COVID-19 OMICS Initiative (DeCOI). DeCOI is a national network based on the DFG-funded network of NGS competence centres and formed to support and develop the use of NGS-based omics data in COVID-19 research as well as help manage the produced data.
One project within DeCOI is CoGDat, an initiative committed to making sequence data from SARS-CoV-2 molecular surveillance available and usable. As part of CoGDat GHGA has developed DataMeta, a generic submission portal for data with associated metadata, to fulfil the technical requirements of CoGDat in the domain of data collection and management.
Another project GHGA supports is CoFGen, a data portal for research on functional genomics in COVID-19, which is currently being developed. CoFGen will enable researchers to answer questions about changed biological processes and mechanisms, after an infection with SARS-CoV-2 and further centralize and democratize data storage, as well as the storage of analysis workflows.
Here we collected relevant materials for the COVID-19 community, such as highlighting GHGA-associated projects and other news and events.
The initiative aims to conduct research on the sequence data that is being generated in the context of the SARS-CoV-2 viral genome sequencing efforts in Germany, but also to enable other scientists by making this data available to the public.
A particular focus lies on the sequencing raw data, which will be collected and made available in addition to the viral genome assembly data collection and sharing carried out by the Robert-Koch-Institut (RKI). The raw data enables reproduction of the assembly calculations run by the individual laboratories, benchmarking and evaluation of assembly pipelines and the identification of multiple variants in the same sample, i.e. identification of intra-host viral evolution events.
To achieve these goals the major milestones of CoGDat are:
GHGA has developed DataMeta, a generic submission portal for data with associated metadata, to fulfil the technical requirements of CoGDat in the domain of data collection and management. Furthermore, the CoGDat project has established a data privacy and legal concept as well as a data anonymization concept and is in exchange with the relevant authorities to ensure that patients interests are protected.
Over the last two years, SARS-CoV-2 and COVID-19 were and still are the dominating topics in research focusing on health and medicine in general and genomics and functional genomics in specific. In functional genomics, which studies the interplay of genes, signaling pathways and gene products, research is focused on answering questions about the immune response to an infection with SARS-CoV-2 and finding explanations for differing disease courses and severity. During the course of the pandemic, German researchers alone published nearly 25 000 papers on COVID-19 and were one of the most active contributors to research about various topics related to the pandemic.
However, research data and findings are not yet bundled or centralized, and the data sharing culture is still under development. This is why we develop CoFGen, a data portal for research on functional genomics in COVID-19. CoFGen will enable researchers to answer questions about changed biological processes and mechanisms, e.g. regulations of signaling pathways, after an infection with SARS-CoV-2 and further centralize and democratize data storage, as well as the storage of analysis workflows.
Our goal is to collect single-cell and bulk RNA-sequencing datasets and analyses from German research groups, execute basic metadata analyses, and make data more easily available to other researchers focusing on different parts of the immune response to COVID-19. To achieve this, we will work closely together with DeCOI and the Lung Biological Network of the Human Cell Atlas, who are our initial data providers. Storage of datasets, corresponding analysis workflows, as well as data access will be managed by FASTGenomics, a collaborative research effort of Comma Soft AG in Bonn and the LIMES Institute from Bonn University.
GHGA’s first whitepaper contains and explains different consent modules to be integrated into existing consent documents. These will enable data sharing for secondary research via GHGA.
GHGA reached an important milestone in signing a cooperation agreement to become a national node in the federated European Genome-Phenome Archive. This will make data in GHGA finadable and interoperable beyond German borders.
To further evaluate the needs of research groups generating human sequencing data with regards to storage, analysis and sharing of those data, GHGA launches a landscape survey.