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The Isolated Tissue Bank

The Isolated Tissue Bank. Tissue banks exist outside the core informatics (and operational, financial & legal) infrastructure of the medical center. The Isolated Tissue Bank. Manual Re-entry of clinical information into non-standard data elements in stand-alone databases and spread-sheets

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The Isolated Tissue Bank

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  1. The Isolated Tissue Bank • Tissue banks exist outside the core informatics (and operational, financial & legal) infrastructure of the medical center. UPMC Pathology and Oncology Informatics

  2. The Isolated Tissue Bank • Manual Re-entry of clinical information into non-standard data elements in stand-alone databases and spread-sheets • Variable IT architecture and support • Existence depends of research grants and powerful Principle Investigators • Local IRB, Consent and Permission Procedures, HIPAA and security issues, TUC, etc. • Limited access from the general research community • Extreme inefficiencies and costs UPMC Pathology and Oncology Informatics

  3. … Adenocarcinoma of the prostate from patients less than 60 years old at diagnosis…High Grade, organ confined, Five year follow up with no chemical or anatomic recurrences, No hormonal Rx prior to resection… UPMC Pathology and Oncology Informatics

  4. The Other Problem • Medical Centers support multiple tissue banks • Samples from a single patient (or a single operation) are stored in multiple tissue banks • Each bank operates and annotates differently • And there is chaos… Patient Accession Accession Collection Collection Collection Collection Collection UPMC Pathology and Oncology Informatics

  5. Visions and Goals • Bring tissue management into the mainstream operations of medical center • Not a single central tissue bank, but central operations for core annotation, consent, security, query, display, etc. • Place existing, funded, mandated hospital systems (AP LIS, Registry, etc) at the pleasure of the tissue bankers • Take advantage of ongoing initiatives such as CAP, LOINC, Cancer Registries, etc UPMC Pathology and Oncology Informatics

  6. caTISSUE, SPIN and TIES • The caTISSUE accepted SPIN/TIES as our first major initiative because it represents these concepts on a grand scale • TIES takes two major (and despised) components of every medical center’s infrastructure – the Paraffin Archive and the Free Text Pathology Report - and allows them to serve tissue banking UPMC Pathology and Oncology Informatics

  7. The Archive and the Bank Interact • The Banked and Archived Tissue are related through the tissue donor • The Archive contains • Diagnostic & Pre Diagnostic Biopsies • Diagnostic Tissue Samples • The Bank tends to have frozen tissue - protocol samples and clinical discards • One needs both the Archive and the Bank to get a complete view Pre Diagnostic Biopsy Diagnostic Biopsy Resection – Clinical Discards Progression Bx Protocol Bx Time UPMC Pathology and Oncology Informatics

  8. caTISSUEA Tissue Bank Centric Model caTISSUE Lite Annotation Services Lab Data Tissue Processing and Storage Standards Based Tissue Bank Database Pathology Data Clients and Projects Outcomes and Rx Tissue Bank Viewer On the caBIG Core Bank Activities Washington University Enterprise Activities University of Pittsburgh UPMC Pathology and Oncology Informatics

  9. Annotation Services Model Enterprise Activities Tissue Processing and Storage Clients and Projects Lab Data Pathology Data Outcomes and Rx Tissue Bank Data Aggregation Data Mapping Standard Data For Annotation Request for Information Tissue Bank Activities UPMC Pathology and Oncology Informatics

  10. Tissue Bank Tissue Bank Tissue Bank Tissue Bank Tissue Processing, Inventory and Availability Tissue Processing, Inventory and Availability Tissue Processing, Inventory and Availability Tissue Processing, Inventory and Availability Aggregator Enterprise View of Tissue Lab Data Pathology Data Outcomes and Rx Standard Tissue Processing Data Enterprise Annotation Services Enterprise Tissue Dataset Extend Local Dataset Enterprise wide Patient/Specimen centric view of tissue UPMC Pathology and Oncology Informatics

  11. UPMC System Identified “Clinical” Data in Silos Clinical LIS Anatomic LIS TissueBanks Clinical Trials Cancer Registry Outcomes Progression & Rx Permission Procession Status in trials Tumor Markers Synoptic Reports Datawarehouse Merging Data Mapping to Canonical Elements Mapping to disease De-identification Error Correction Mapping to Client Elements Data Mart Data Mart Data Mart Data Mart Integrated, Standard De-identified Data for Researchers UPMC Pathology and Oncology Informatics

  12. Enterprise Tissue Management • Standard Clinical Annotation provided centrally • A small number of processing data elements are provided from each bank • One can provide a standard, enterprise view of all tissue samples • The enterprise view can be mapped to standard national data elements and published to the caBIG • Any local bank can extend the central annotation UPMC Pathology and Oncology Informatics

  13. Enterprise Tissue Management • Standard Clinical Annotation provided centrally • A small number of processing data elements are provided from each bank • One can provide a standard, enterprise view of all tissue samples • The enterprise view can be mapped to standard national data elements and published to the caBIG • Any local bank can extend the central annotation UPMC Pathology and Oncology Informatics

  14. UPMC Pathology and Oncology Informatics

  15. Merged Annotation in “Containers” Patient Accession Sample Data Dictionaries AP LIS Registry CP LIS TIES CTMA Source Applications Application Adapters API or Reports Tissue Bank Applications Consent Data Tissue Bank Aggregator [identify patients/samples data across sources] Mapping Tissue Bank Tissue Bank Containers in Canonical Object Model Metadata Dictionary Download Canonical DE API/XLM Mapping Consent Data Download Data Mapped to “caBIG CDE” caDRS Published Data De-identification Institutional Firewall API/XLM API Tissue Bank Presentation Q/A Data Presentation SPORE Presentation Enterprise Presentation Tissue Res. CaBIG Presentation caBIG GRID UPMC Pathology and Oncology Informatics

  16. Data Dictionaries AP LIS Registry CP LIS TIES CTMA Source Applications Identification Metadata Data Containers Donor ID Rx History Tumor Marker Hx Pathology Hx Progression Disease Local Systems Metadata Business Rules Mapping Mapping and Transformations Canonical Metadata Clean Canonical Patient Model Mapping and Transformation CaBIG Metadata Tissue Bank Presentations Enterprise Presentation CaBIG Presentation UPMC Pathology and Oncology Informatics

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