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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 LDMS and LabVantage.

After using drill-down functionality to select a cohort of interest, the user can:
    • Download de-identified data
    • Submit a request for identified information using an honest broker (IRB approval required)
    • Contact investigators with samples to inquire about sharing process
THE DATA

PI: Loretta Que
Contact: loretta.que@duke.edu

The primary objective of this project is to develop a comprehensive and extensive repository of biological samples and relevant clinical data from critically ill patients admitted to Duke Hospital with the intent to develop collaboration across Duke and other external institutions. The repository collects biological samples and clinical data from COVID-19 positive patients who have been evaluated at Duke for COVID-19. Collaborators may utilize the biorepository to ascertain relevant clinical data and crucial biological samples, such as, but not limited to, plasma and serum (blood draw), oral/nasopharyngeal swabs, questionnaire data (SF-12, PHQ-9, CAT, CV Resp, modified BORG) and relevant clinical data (via electronic medical record) from COVID-19 positive patients who were seen at Duke Hospital, Duke Regional Hospital or Duke Raleigh Hospital and clinics. The biological samples are collected at 6 weeks, 3 months, 6 months and 12 months post-discharge when patients are seen in pulmonary clinic.

PI: Christina Barkauskas
Contact: christina.barkauskas@duke.edu

This protocol seeks to establish a data and biological sample repository to specifically collect biological samples and relevant clinical data from critically ill patients in an ICU setting. All biological samples will be collected prospectively; however, relevant clinical data on enrolled patients may be collected retrospectively and prospectively from their electronic health record to obtain adequate data so as to better understand critically illnesses, diseases and medical conditions of interest. Biological samples are collected on Study Days 1, 3, 7, 14, and 21 and consist of respiratory samples, blood samples, urine samples, and nasopharyngeal swabs.

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. 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 informed consent forms for all other participating COVID-19 studies enrolling Duke patients. Each participating study will have its own separate IRB approved protocol. Specimens consist of residual (left-over) clinical samples from the testing and treatment of patients with COVID-19 at Duke. All specimens were processed in the clinical laboratory and retained for future use. Identifiable data will only be available for consented participants or patients meeting waiver of informed consent; any data for patients who were not approached for consent or do not fall under a waiver will only be shared in a deidentified manner.

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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: 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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This page updated 31 March 2022