PHILADELPHIA— To provide greater clinical insight for the fight against COVID-19, a consortium of research scientists that included faculty from the Perelman School of Medicine at the University of Pennsylvania pooled their efforts to create a common data model and a shared analytics framework that will aggregate information from disparate electronic health records (EHR) internationally. With the creation of this model – the Consortium for Clinical Characterization of COVID-19 by EHR (4CE) –clinical teams and researchers will now have a powerful tool available to them to quickly discover trends and provide answers to questions about the virus. A paper on the effort was published this month in NPJ Digital Medicine.
Like the other sites in the study, clinical data from Penn Medicine was analyzed and provided for the effort. And for future studies with 4CE, PennAI, a free self-service machine learning tool developed at the Institute for Biomedical Informatics, will be available to each member site to power the project.
“We are excited to use our PennAI software for this project,” said paper co-author Jason Moore, PhD, the director of the Institute for Biomedical Informatics and a professor of Informatics. “It can be installed locally at each site and used to generate machine learning models for predicting COVID-19 outcomes such as death or disease severity. This is a critical need that we will contribute to the project.”
The consortium consists of 96 hospitals from around the world and so far, has gathered data on more than 27,000 COVID-19 cases with 187,000 laboratory tests. Previously, because of differences in electronic health records, all of this data would not have been able to “talk” to each other in a way necessary for analysis. But with so many sites putting their data into a common data model and making it available to be processed and analyzed, consortium scientists were able to detect trends and patterns of this new virus that were previously invisible.
“For example, laboratory data were standardized from Penn Medicine's electronic health record to Logical Observation Identifiers, Names, and Codes (LOINC) and shared units of measure before analyzing their change over time. These steps were critical to uncovering initial clinical insights,” said Danielle Lee Mowery, PhD, Penn Medicine’s chief research information officer and an assistant professor of Informatics. “Notable insights include abnormal trends in D-dimer protein, which is a measure of blood clotting, and C-reactive protein, a measure of inflammation, among COVID-19 patients.”
Among other immediate insights were that liver functions initially presented as typical, but worsened over time as patients were hospitalized. White blood cell counts were also typically normal among patients but only elevated among those with the most serious forms of COVID-19.
“The COVID-19 data warehouse established at Penn Medicine will enable our researchers to access standardized data and generate results which can be replicated at sites around the world,” said John H. Holmes, PhD, IBI’s associate director for Medical Informatics and a professor of Informatics in Epidemiology. “This opens the door to local insights about COVID-19 patients from the Philadelphia area while at the same time contributing to the global battle against this infectious disease.”
While the consortium itself is new and addressing a new threat, it is actually the culmination of years of work in health analytics.
“Our ability to rapidly respond to a global pandemic was made possible by years of institutional investments in health information technology and biomedical informatics expertise and infrastructure.”, said Moore. “We are seeing the value of electronic health records and artificial intelligence in real-time.”
Penn Medicine is one of the world’s leading academic medical centers, dedicated to the related missions of medical education, biomedical research, and excellence in patient care. Penn Medicine consists of the Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania (founded in 1765 as the nation’s first medical school) and the University of Pennsylvania Health System, which together form a $8.6 billion enterprise.
The Perelman School of Medicine has been ranked among the top medical schools in the United States for more than 20 years, according to U.S. News & World Report's survey of research-oriented medical schools. The School is consistently among the nation's top recipients of funding from the National Institutes of Health, with $494 million awarded in the 2019 fiscal year.
The University of Pennsylvania Health System’s patient care facilities include: the Hospital of the University of Pennsylvania and Penn Presbyterian Medical Center—which are recognized as one of the nation’s top “Honor Roll” hospitals by U.S. News & World Report—Chester County Hospital; Lancaster General Health; Penn Medicine Princeton Health; and Pennsylvania Hospital, the nation’s first hospital, founded in 1751. Additional facilities and enterprises include Good Shepherd Penn Partners, Penn Medicine at Home, Lancaster Behavioral Health Hospital, and Princeton House Behavioral Health, among others.
Penn Medicine is powered by a talented and dedicated workforce of more than 43,900 people. The organization also has alliances with top community health systems across both Southeastern Pennsylvania and Southern New Jersey, creating more options for patients no matter where they live.
Penn Medicine is committed to improving lives and health through a variety of community-based programs and activities. In fiscal year 2019, Penn Medicine provided more than $583 million to benefit our community.