Finding Genomic Profiles of COVID-19 Phenotypes from the EHR

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Abstract: As the world searches for effective treatments and potential cures for the COVID-19 pandemic, the ability to consolidate data, insights, and expertise from many disparate sources will be key to fully understanding the patient outcomes of the infection. Key to facilitating this type of research is a cohesive and secure research environment that enables clinicians, researchers, data scientists, and technologists from multiple organizations to work together with a common goal of better understanding COVID-19 symptoms, associated risk factors, and successful therapies. Building upon faculty, staff and infrastructure already in place through the eMERGE IV Clinical Center at Mass General Brigham, we are proposing the creation of a COVID- 19 Biobank Portal to provide a foundation for building a truly collaborative environment that is compliant with patient privacy and offers a common set of bioinformatic tools and a standardized IT approach for the staging of data and analyses. We will do this by accomplishing the following three Specific Aims which supplement the parent grant’s Aim I which is: “Polygenic risks scores will allow us to stratify eMERGE participants based on genetic risk for common complex traits” which will focus in this supplement on risk factors for severity of COVID-19 illness in our biobank participants. We propose to build on our expertise to accomplish the specific aims: Aim 1: We will create a COVID-19 Centric Biobank Portal that allows general institutional use with proper research agreements in place where patient cohorts can be studied using easily assessable and transformed data and through which genomic samples can be obtained. Aim 2: Supplement the COVID-19 Biobank Portal with test results, phenotype risk factors, symptoms, and outcomes for COVID-19 which are derived from data in the electronic health record (EHR) by using natural language processing and computational phenotypes and by performing chart reviews to validate severity indices and clinical outcomes found in COVID-19 infected patients. Aim 3: Genetic data (array and sequence data) will be contributed to the eMERGE IV network and to the International l COVID-19 Host Genetics Initiative (https://covid19hg.org) such that data can be used to calculate polygenic risk scores (PRS) for genome-wide association studies of risk phenotypes and patient outcomes and polygenic risk scores (PRS) for COVID-19 outcomes in our dataset and in collaborations with others.