NCI Data Jamboree (Project Abstract Submission): Submission #60

serial: '60'
sid: '189198'
uuid: 3cfa540d-c450-46d0-a89d-813a2cf1b8af
uri: /nci/datajamboree/abstractsubmission
created: '1785200345'
completed: '1785203906'
changed: '1785203906'
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data:
  list_of_additional_authors:
    - add_author_letters: PhD
      affiliation: 'Department of Veterans Afffairs'
      first_name: Alice
      last_name: Kwak
    - add_author_letters: MS
      affiliation: 'Department of Veterans Affairs'
      first_name: Nicholas
      last_name: Lemmer
    - add_author_letters: MS
      affiliation: 'Department of Veterans Affairs'
      first_name: Nithin
      last_name: Weerasinghe
    - add_author_letters: PhD
      affiliation: 'Department of Veterans Affairs'
      first_name: Stephan
      last_name: Foianini
  category: 'Enhancing data interoperability (e.g., data harmonization, data federation)'
  degree_s_: M.S.
  email: Trevor.Michelson@va.gov
  first_name: Trevor
  keywords_abstracts: 'Precision Oncology, Federated Data Integration, VA EHR, Multi-Modal Oncology Data'
  last_name: Michelson
  middle_initial: R
  organization: BVARI
  organization_address:
    address: ''
    address_2: ''
    city: Boston
    country: ''
    postal_code: ''
    state_province: ''
  summary: |-
    A crucial challenge facing oncological data analysis is the lack of available data sets that have large enough patient cohorts for gaining insights into specific cancer types.  To meet this particular challenge, we propose to leverage the US Department of Veterans Affairs (VA) large-scale electronic patient health record that contains millions of patients spanning over several decades.  We plan to develop solutions for integrating VA data with other public data sets available through the NCI, resulting in a large-scale longitudinal multi-modal oncology data set accessible to the larger research community.  The Precision Oncology Data Repository (PODR) is a VA data set that aggregates, curates, and shares clinical, imaging, and genomic data from various VA and external partner sources.  Specifically, the VA has aggregated a cohort of over 140k decedent oncology patients that includes various cancer types with regulatory approval to de-identify and share with trusted external partners.  Our goal is to develop various methods for utilizing PODR with other resources to demonstrate data analysis within a federated infrastructure.

    The following NCI public data sets are planned to be used, but not limited to:
    -	Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial Data
            - Lung
            - Colorectal
            - Questionnaires
    -	Cancer Epidemiology Descriptive Cohort Database (CEDCD)
            - Cancer Prevention Study II Nutrition Cohort (CPS-II Nutrition)
            - Millenium Cohort Study Panels 1 – 5
    -	SEER Research 
             - Prostate Cancer with Decipher Prostate Genomic Classifier Database
    -	All of Us Research (AoU) Program

    The project will require members with experience in ETL processes, healthcare data and analysis, and using version control systems to help facilitate collaborative development. Potential to explore NLP-derived concept code extraction through clinical notes and surveys.

    We will make use of VA internal workspaces (e.g., VINCI, ARCHES) as well as test out the Bridges Cancer Genomics Cloud.
  title: 'Data Scientisti'
  ttile: 'Integrating VA Precision Oncology Data with NCI Public Resources for Large-Scale Federated Cancer Research'