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Center for Clinical and Translational Science

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Jennifer Croker, PhD
Sr. Administrative Director, CCTS 
jcroker@uab.edu

COVID-19 Enterprise Research Initiative

COVID-19 Enterprise Research Initiative

  • Working with the Division of Infectious Diseases, Departments of Microbiology and Pathology, as well as other UAB divisions and departments and coordinated by the CCTS, the IRB has endorsed an Enterprise Research Platform for COVID-19 to shepherd the safe and efficient consent process and collection of specimens and clinical data, which is ongoing. CCTS Informatics, with the Center for Outcomes & Effectiveness Research, Informatics Institute and multiple schools, is coordinating clinical data and longitudinal follow-up for rigorous secondary analysis that ensures efficient and respectful engagement of research participants. This new Enterprise Platform will serve to anchor and enable all COVID-19-related human subjects research across the campus.

    Enterprise Advantages:

    • Recruitment process that protects the safety and health of research teams and patients
    • Coordinated strategy for specimen and data collection that respects the good will of the participant
    • Consent of affected individuals and healthy controls for longitudinal follow-up, recall and invitation to participate in future studies
    • Inclusion of broad spectrum of infection (healthy, asymptomatic, ambulatory, inpatient, ICU, autopsy) and vaccination statuses (null, partial, full, boosted)

  • Biospecimen

    The COVID-19 Enterprise Biorepository is approved to collect a wide-variety of specimens, including research-specific samples as well as remnant clinical and autopsy specimens. Due to the constraints restricting non-essential personnel in the hospital and limiting specimen volumes/quantity, it is essential that we work together in a coordinated fashion to maximize this resource.

    COVID Enterprise Biorepository at a Glance (PDF) – a brief description of the specimen sources, types and quantities as well as the demography of the participant enrollment.

    For more information or to discuss specimen needs, please contact Dr. Jennifer Croker.

    Teams: Biospecimen Governance Committee (Goepfert), Host Genomics Work Group (Korf), Immune Response Work Group (Lund)

    INVESTIGATOR GUIDANCE

    • There are special handling and processing considerations required when working with infectious materials. Please consult with the UAB COVID-19 Containment Guidance for Researchers to make sure that your research plans meet required biocontainment standards.

    • IRB Proposals: The COVID-19 Enterprise protocol addresses the consent process and specimen/data collection on behalf of the entire research community. Investigators will be able to leverage these specimens and data through independent IRB submissions describing specific research goals that can “bolt on” to the coordinated frame.

      IRB-300005127: COVID-19 Enterprise Biorepository
      Paul Goepfert, MD, Principal Investigator
      Paul Benson, MD, Jeffrey Edberg, PhD, Nathan Erdmann, MD, Co-Principal Investigators     

      How to decide which protocol type:

      • NHSR – the COVID-19 Biospecimen Governance Committee provides a letter that indicates the investigator will only receive completely de-identified data or biospecimens (no dates, no PHI). These data can be coded, but must be stripped of everything else. 

      • Exempt – this is only for identifiable, private data for secondary use (can’t use exempt for use of biospecimens). They could also use this if they wanted to contact the participant for a survey (however, they could not link the survey with the clinical data obtained.)

      • Expedited – this would be for identifiable, private biospecimens. This would also be the case if an investigator wanted to contact the participant for surveys and link those responses to the clinical data collected and organized by the Enterprise protocol.  

      For more information and language for IRB protocols, please contact Dr. This email address is being protected from spambots. You need JavaScript enabled to view it..

    • As part of the COVID-19 Enterprise Research Initiative, efforts are underway to collect the following:

      Blood, Plasma, Serum
      PBMCs
      Genomic DNA
      Tracheal Aspirates
      Oral Saline Rinse
      Nasal Swabs
      Urine
      Autopsy Tissues

      At this time, fecal swabs and bronchoalveolar lavage (BAL) are not possible in the current emergency state due to limitations of PPE, reliance on clinical staff, elevated risk for patients & staff and increased time, effort and reagents. The committee is willing to revisit this possibility at a later date as the constraints in the health system ease.

    • Outline for Provision of FFPE Material from COVID-19 Positive Autopsy Cases for Research Investigations

      For those interested in accessing autopsy samples, please see the FAQs below and the guidance at the link above and fill out the Biospecimen Request Form (below).  These requests are reviewed on a rolling basis by the Governance Committee.  When endorsed by the committee, investigators will be referred to the UAB Tissue Biorepository (TBR; Pathology), who will follow-up to obtain additional details to fulfill the request.  The TBR may require the investigator to complete an additional form to make sure PIs understand additional terms and conditions of use.

      • What is included in the repository?

        In the event of autopsy, the COVID-19 Enterprise Biorepository may have access to a variety of tissues available for study, including lung, heart, brain, liver, kidney and some intestine tissue.

      • How do I obtain unstained slides?

        The request for the unstained slides, will need to be submitted through the COVID-19 Enterprise Protocol Biospecimen Request Form (see Biospecimen tab).  

      • What approvals are needed in advance?

        The Enterprise protocol captures consent for research use and access to clinical data that accompanies the biomaterials.

        Investigators must still seek an independent, IRB-approved NHSR protocol (or in rare cases, an expedited HSP).  Please consult with the IRB for details.

      • Are digital slides available?

        The Pathology department has made de-identified H&E digitally available at the UAB Heersink School of Medicine PEIR website.  Google chrome is recommended for use.  There are currently 45 COVID-19 cases and one H1N1 case available for viewing.  Just click on the H&E slide to pull up the virtual viewer. These slides are de-identified. Digital slides are also available for download once IRB approval is received (and/or any MTA is approved).



    * This form is to be completed in one sitting. Review the form here to ensure you have all necessary information prepared when you begin. Note: If you have already entered the form once before and encounter an issue starting a new submission, clear your browser's cache.

    Biospecimen Request Form

  • Clinical Data

    The COVID-19 Collaborative Outcomes Research Enterprise (CORE) is leading the initial and longitudinal data collection and information curation to support a broad set of research goals. Through the CORE, investigators benefit from the permissions established by the COVID-19 Enterprise Research Platform to use clinical data (HIPAA Limited and Detailed Data Sets), to access protected health information and to allow longitudinal follow up.

    For more information or to discuss data needs, please contact This email address is being protected from spambots. You need JavaScript enabled to view it..

    Teams:

    • Health System Data Team (Willig, Wyatt)                              

    • Questionnaires & PRO Data (Hall, Fletcher)

    • Community & Public Health Data (Asif, Aswani)

    • Research Coordination (Mugavero, Levitan)                                                            

    Resources:

     

  • The COVID-19 Biomedical Data Science website contains an array of useful resources. Connect with an expert, request data sets, explore analysis tools, and engage in educational offerings.

    The purpose behind this effort is threefold: 
    1. Integrate COVID-19 epidemiology, viral genomics, clinical informatics, imaging, mulit-omics, and other data for basic scientists, data scientists, translational researchers, and clinicians.
    2. Provide online training for next-generation biomedical data scientists to practice data-driven COVID-19 research in knowledge curation, data management, open science, and machine learning.
    3. Foster fast, data-driven, high-quality knowledge discoveries and precision medicine in COVID-19 with multi-disciplinary team-based scientific research and development.

  • Organization & Governance


    This enterprise platform is an effort that has and continues to involve a multitude of departments and schools across the UAB campus.

    COVID-19 Biospecimen Leadership Team:

    COVID-19 Data Leadership Team:

    Paul Goepfert, MD (PI)
    Paul Benson, MD (Co-PI)
    Jeffrey Edberg, PhD (Co-PI)
    Nathan Erdmann (Co-PI)

    Michael Mugavero, MD, MHSc (PI)
    Emily Levitan, PhD (Co-PI)

    Working Groups:

    • Biospecimen Governance Committee

      Membership

      Paul Goepfert (PI)
      Nathan Erdmann (Co-PI)
      Paul Benson (Co-PI)
      Jeffrey Edberg (Co-PI)
      Robert Kimberly (CCTS)
      Fran Lund (Micro)
      Olaf Kutsch (ID)
      Sadeep Shrestha (SOPH)
      Kevin Harrod (SEBLAB)
      Suresh Boppana (Peds)
      Cindy Joiner (ex officio - DOM)
      Jennifer Croker (ex officio - CCTS)
      Justin Roth (ex officio – EH&S)
      Jason Nichols (ex officio – VPR’s office and SOO)

    • Collaborative Outcomes Research Enterprise (CORE)

      Purpose: To engage a collaborative working group to coordinate, collate, and facilitate the rigorous and expeditious completion of COVID-19 health services, outcomes and population health studies conducted by interdisciplinary research teams addressing prescient questions germane to the individuals, communities and populations we serve in our city, county, state, and Deep South region.

      TEAMS:


      Health System Data Team (Willig, Wyatt)

      • Define case definitions for cohorts (e.g., testing, PUI, confirmed cases)

      • Determine harmonized catalog of health systems data elements

      - Determine structured data elements amenable to query

      - Determine unstructured data elements requiring abstraction

      • Develop data management / data coordination procedures

      Questionnaires & PRO Data (Hall, Fletcher)

      • Identify potential questionnaires / validated instruments and Patient Reported Outcomes (PROs) for adjunctive data capture

      • Determine prioritization for questionnaire and PRO administration

      • Define timing, frequency and preferred modality of questionnaire and PRO administration

      Community & Public Health Data (Asif, Aswani)

      • Identify and collate sources of COVID-19 community data capture

      • Liaise with Jefferson County Health Department and Alabama Department of Public Health re: COVID-19 surveillance data capture

      • Liaise with the City of Birmingham #BHMstrong team re: non-health related data capture germane to COVID-19 (e.g., economic, employment)

      Research Coordination (Mugavero, Levitan)

      • Determine humans subjects and regulatory considerations with IRB

      • Develop COVID-19 CORE Concept Proposal

      • Develop procedures for project coordination following concept proposal submission in collaboration with data management / data coordination and BERD (Biostatistics, Epidemiology, Research Design)

      Advisory Committee:

      Robert Kimberly (CCTS Director)

      Kenneth Saag (COERE Director)

      Jeanne Marrazzo (Med/ID, SOM)

      Paul Muntner (Epidemiology, SOPH)

      Jim Cimino (Informatics Institute)

    • Biomedical Data Science Working Group

      GOALS:

      Integrate COVID-19 epidemiology, viral genomics, clinical informatics, imaging, mulit-omics, and other data for basic scientists, data scientists, translational researchers, and clinicians.

      Provide online training for next-generation biomedical data scientists to practice data-driven COVID-19 research in knowledge curation, data management, open science, and machine learning.

      Foster fast, data-driven, high-quality knowledge discoveries and precision medicine in COVID-19 with multi-disciplinary team-based scientific research and development.


      http://ubrite.informatics.uab.edu/covid19/
    • Host Genomics Working Group

      Membership

      Bruce Korf
      Nita Limdi
      Hemant Tiwari
      Sadeep Shrestha
      Jim Cimino
      Greg Cooper (HAIB)
      Greg Barsh (HAIB)
      Devin Absher (HAIB)
      Jake Chen
      Jeff Edberg
      Noha Sharafeldin
      Robert Kimberly
      Jennifer Croker
      Renie Moss

    • Immune Response Working Group

      In Development

    • Therapeutic Discovery Working Group

      In Development

  • Activities:


    Forms:


    Additional Information:

  • The following content is meant to assist in a thorough literature review when studying COVID-19. To add literature of relevance or special interest, simply share it with This email address is being protected from spambots. You need JavaScript enabled to view it..

    Literature containing information on the disproportionate burden of COVID-19 on minorities:


    COVID-19 News Feeds:

  • Contact

    For questions or more information:

    Jennifer Croker, PhD
    Assistant Professor of Medicine
    This email address is being protected from spambots. You need JavaScript enabled to view it.

    Paul Goepfert, MD
    Professor of Medicine
    UAB Department of Medicine, Division of Infectious Diseases
    This email address is being protected from spambots. You need JavaScript enabled to view it.

    Michael Mugavero, MD, MHSc
    Professor of Medicine
    UAB Department of Medicine, Division of Infectious Diseases
    This email address is being protected from spambots. You need JavaScript enabled to view it.

    Robert Kimberly, MD
    Director
    Center for Clinical and Translational Science
    This email address is being protected from spambots. You need JavaScript enabled to view it.




Contact

Jennifer Croker, PhD
Sr. Administrative Director, CCTS 
jcroker@uab.edu