Genetic Database May Enable Precision Medicine for COVID-19
The genetic database includes nearly 12,000 pieces of information that researchers and providers can use to develop precision medicine therapies for COVID-19.
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By Jessica Kent
- Researchers from the University of Alabama at Birmingham have created a genetic database designed to help advance precision medicine treatments for COVID-19.
The database, called PAGER-CoV-2, includes 11,835 pathways, annotated gene lists, and gene signatures (PAGs). Pathways are the roadmap that describes how genes are turned on and off and how they establish connections with each other. Annotated gene lists are empirical information that researchers collect from experiments or literature, while gene lists help researchers understand how a certain cell type behaves under different conditions.
A gene signature is a unique pattern of gene expression within a cell from a single or group of genes, providing information about the activity of those genes in the cell.
“SARS-CoV-2 is a new virus, and we didn’t know much about its function back in the summer of 2020,” said Jake Chen, PhD, professor in the Department of Genetics at the University of Alabama at Birmingham and associate director of the Informatics Institute in the UAB School of Medicine.
“The goal here is to gather all this information together in a searchable database so that researchers can gain a better understanding of how the virus’s genes behave or perform under various biophysical conditions, such as severe COVID-19 or long-haul COVID-19 patients.”
SARS-CoV-2 has 15 genes, but researchers have little information on how these genes impact human cells.
“We need to understand the differences in people who die from COVID-19 versus the person who only has a mild case of the disease,” said Chen. “This is a precision medicine approach, employing the database to organize all that we’ve learned about the virus so that the information can be used in an effective way.”
Because the downstream effects of COVID-19 are not yet well understood, a better understanding could lead to tailored, targeted therapies based on gene behavior.
“We need to know how the virus proteins are interacting with human cells, and we need to know what we can do about it,” said Chen. “There is no shortage of possible therapeutics. There is a shortage of regimens that will pair the right therapeutic with the right person. Precision data-driven medicine is what this work will help COVID-19 physicians understand.”
In a study published in Nucleic Acids Research, the team searched the medical literature for all articles dealing with the SARS-CoV-2 virus. The team then used data science tools to conduct comprehensive data processing and data integration. The group used supercomputers to establish quality measures and PAG-to-PAG relationships.
People can search the database with any human gene or PAG of interest, drill down to their database entry, and navigate to other related PAGs through either shared PAG-to-PAG co-membership relationships or PAG-to-PAG regulatory relationships.
To date, there are 19,996,993 PAG-to-PAG relationships stored in the database.
“Our intent is to provide a resource that researchers doing functional genomic studies of COVID-19 will use,” Chen said. “There is a lot of information here, organized in a way that we hope will spur new insights and lead to meaningful results.”
As new information is available and added to the database, PAGER-CoV-2 will grow. The research team is encouraging scientists around the world to make use of the portal and contribute to this community-based knowledge curation effort.
PAGER-CoV-2 is now freely available to the public without any login requirements or registration.
