COVID Integrated Data Repository

Self-service access to COVID-related datasets

COVID-related research studies initiated at Duke number in the hundreds and continue to be added apace. Many of the studies are collecting and storing similar types of patient-reported data that can be harmonized, merged with clinical and biospecimen data, and made available for further research.

The Duke Crucible team has developed a highly scalable, cloud-based software platform that allows self-service access to these datasets and biospecimen samples, incorporating HL7’s FHIR standard and a suite of custom APIs. With its robust quality and security controls, the Integrated Data Repository (IDR) reduces the need for labor intensive data management while positioning Duke to expand interoperability and democratization of valuable research data beyond the COVID research domain.

The COVID-IDR dashboard provides access to de-identified patient demographic data from the EHR, registration, and consent information from REDCap and available biospecimens from LMDS, Excel, and LabVantage.

After using drill-down functionality to select a cohort of interest, the user can request identified information and samples using an honest broker. 

Duke NetID required 

THE DATA

PI: Chris Woods
Contact: chris.woods@duke.edu, susanna.naggie@duke.edu

The aim of this data and specimen repository is to provide a secure and centralized storage location and resource for the collection of core variables of interest, as well as the retaining of relevant patient samples, across COVID-19 related protocols at Duke. The core data variables were in-part selected to specifically match those agreed upon by Academic Medical Centers across the U.S., with the intention of aiding the efficiency and effectiveness of de-identified data reuse for population-level research. An additional benefit is that centralized, shared data storage of demographic and longitudinal variables will reduce subject burden, as many questions will now only need to be asked once, rather than each time a given subject joins another COVID-19 related study at Duke.

This shared data and bio-repository project will house all the core data for all patients with COVID-19 (or suspected cases), as well as individual participants ICFs for all other participating COVID-19 studies enrolling Duke patients. Each participating study will have its own separate IRB approved protocol. Samples may be either collected specifically by the protocol, or include left-over clinical samples from the testing and treatment of patients with COVID-19 at Duke.

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PI: Chris Woods
Contact: chris.woods@duke.edu

This observational multi-visit study will enroll up to 4,000 patients presenting to an outpatient clinic, emergency department, hospitalized patients, as well as patients in the community with suspected symptoms of infection, including bacterial, viral, parasitic or tick-borne infection, or with symptoms that mimic infectious illness. Patients may also self-refer to the study. We may also recruit subjects who are exposed to infectious disease from a close contact.

We will collect samples and data from the patient, including blood, nasal swabs, throat swabs, urine and stool. The primary objective is to identify biomarkers for early diagnosis of, or for prognosis of poor outcome in patients with infections. We will collect samples and data from the subject, including blood, nasal swabs, throat swabs, urine and stool. The primary objective is to identify biomarkers for early diagnosis of, or for prognosis of poor outcome in patients with infections.

PI: Matthew Kelly
Contact: matthew.kelly@duke.edu

The purpose of this study is to collect longitudinal biospecimens and clinical information from children, adolescents, and young adults at Duke University Health System (DUHS) practices and/or in the local surrounding community who have been diagnosed with coronavirus disease 2019 (i.e., COVID-19), the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We will primarily recruit patients enrolled in Pro00105249 to this study protocol, but other eligible participants will also be included. This repository will support the development of basic science, translational, and clinical research projects to define mechanisms underlying SARS-CoV-2 disease severity and to examine long-term immune responses to SARS-CoV-2 in a pediatric population.

Study participants will include children, adolescents, and young adults with confirmed or suspected SARS-CoV-2 infection and/or who are known to have had close contact with an individual suspected or confirmed to have SARS-CoV-2 infection. It is anticipated that we will enroll up to 1000 children, adolescents, and young adults in this study. The participants and/or their parent/legal guardian or legal authorized representative will be asked to consent to: 1) a brief caregiver or patient questionnaire assessing the child or adolescent’s past medical history and details of his/her COVID-19 infection/illness course and/or SARS-CoV-2 exposure risk; 2) review of electronic health record data; 3) prospective access to electronic health data for 5 years; and 4) collection of biospecimens, i.e., whole blood, nasal swabs, and saliva at study visits.

PI: Matthew Kelly
Contact: matthew.kelly@duke.edu

The purpose of this study is to collect clinical data and biospecimens from children, adolescents, and young adults, and their family/household members at Duke University Health System (DUHS) practices or in the surrounding community who have symptoms suggestive of coronavirus disease 19 (COVID-19), or who have had close contact with someone infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19. The collection of data and samples from these patients will support the development of basic science, translational, and clinical research projects that will identify mechanisms underlying SARS-CoV-2 infection susceptibility and disease severity. Participants will include children, adolescents, and young adults, and their family/household members who present with symptoms suggestive of COVID-19 and/or are known to have had close contact with an individual suspected or confirmed to have SARS-CoV-2 infection.

PI: Dana Pasquale
Contact: dana.pasquale@duke.edu

The purpose of this study is to use community sampling to detect active, undiagnosed COVID-19 cases and/or determine the spread or distribution of active infection. The objective is to use a network targeted sampling design to direct testing to yield a higher proportion of results which indicate active infection and possibly differentiating between venues or communities where transmission is active and undiagnosed.

PI: Shannon J. McCall
Contact: shannon.mccall@duke.edu

Acquisition of high quality tissue specimens and blood is a crucial prerequisite for present and future translational research programs within DUHS. A centralized and coordinated biorepository that can perform the functions of patient identification, consent, specimen collection, specimen banking, with processing to commonly derived products (nucleic acids), and annotation of banked specimens with equitable release for ongoing research projects represents an unmet need within DUHS. In addition, with the increasing complexity of regulatory compliance and the need for close attention to patient safety, the consolidation of biobanking into a single infrastructure represents an opportunity to ensure 1) high quality biospecimens, 2) global institutional compliance with CAP and FDA regulations around biobanking and associated research, 3) maximization of biospecimen utility, and 4) global and equitable access to investigators. Here we propose a single protocol that will allow DUHS patients to give broad consent to donation of biospecimens annotated paired with their identifying information.

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