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Automated Annotation of a Novel Virtual Tumor Neuropathology Report Database:

Automated Annotation of a Novel Virtual Tumor Neuropathology Report Database: A Paradigm for Creating Patient-Friendly Reports.

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Automated Annotation of a Novel Virtual Tumor Neuropathology Report Database:

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  1. Automated Annotation of a Novel Virtual Tumor Neuropathology Report Database: A Paradigm for Creating Patient-Friendly Reports Bei Hu1, Tomer Schechori1, Steven S. Silver B.Sc.1,2, Alberto Marchevsky M.D.2, X. Fan M.D.2, William H. Yong M.D.1,2; Department of Pathology (Neuropathology), UCLA Medical Center1 and Department of Pathology, Cedars-Sinai Medical Center2; David Geffen School of Medicine at UCLA, Los Angeles, CA 90048

  2. Goals • Create a pathology report generator that writes simulated brain tumor reports (with fictional patients) suitable for informatics experimentation • Demonstrate that annotating these simulated reports in an automated fashion is feasible

  3. The Need for Annotated Pathology Reports • Pathology reports contain obscure terminology. For example… • Dysembryoplastic neuroepithelial tumor (WHO Grade I) • Atypical teratoid/rhabdoid tumor (WHO Grade IV) • Automated addition of explanations oriented to the reader, e.g. clinicians and patients, may improve understanding

  4. IS THIS PATHOLOGY REPORT IN ENGLISH OR QUOKKA, MATE?? Quokka- A nocturnal marsupial unique to Western Australia.

  5. Utility of a Simulated Pathology Report Database THE PATIENTS ARE FICTIONAL, NON-EXISTENT • Test software safely (De-identification, data mining, search engines etc) • Provide cases for implementation of pathology information systems • Education of medical personnel • Experimentation with pathology report formats and functions

  6. Pros and Cons of a Simulated Pathology Report Database PROS (“IN VITRO ENVIRONMENT”) • No real patient data and privacy (e.g. HIPAA) concerns • Control the content in the reports • Scalable to large numbers of reports CONS • Different complexity than a real database

  7. VBA Microsoft Access DB Simulated reports in MS Word Pathology Report Generation • Data elements are entered into MS Access • Programming in Visual Basic for Applications (VBA) pulls together data elements • Final output as Microsoft Word files

  8. Data Elements for Synthesizing Simulated Brain Tumor Reports • 83 brain tumors types from the WHO classification • Microscopic descriptions and Comments (Standard) • Tumor layman explanations (Annotated Reports) • Locations in brain (e.g. Left occipital lobe) • Median or mean age of each tumor • World Health Organization (WHO) grades • Incidence of tumors (Central Brain Tumor Registry of the United States 2005-2006 statistical report)

  9. A READER-APPROPRIATE EXPLANATION IS CREATED FOR EACH TUMOR

  10. THE 83 TUMOR TYPES ARE MAPPED AGAINST 84 BRAIN SITES

  11. Pathology Report Generator Menu # of reports to generate Vary proportions of tumors Annotation feature, can be turned on or off

  12. Simulated Report

  13. Annotations Writing in blue indicates annotations

  14. Large databases of reports are easily created • 13,999 SIMULATED BRAIN TUMOR PATHOLOGY REPORTS (1.0-3.5 minutes/report) • CBTRUS Proportionate Database: 10,000 • Proportionate plus rare cases forced in: 1,000 • Proportionate with/without annotation: 2,002 • (1001 standard, 1001 annotated) • Equal distribution Database: 997

  15. Distribution of Tumor Types in the Proportionate Database is appropriate

  16. Greek

  17. Conclusions • This prototype Simulated Pathology Report Generator can produce simulated brain tumor reports in large numbers. • The brain tumor reports mimic real pathology reports in content but without the privacy concerns. • The automated conversion of data elements in the standard report to a reader-appropriate version is feasible.  • We suggest that Simulated Report Generators and Simulated Report databases have substantial potential for many types of informatics experimentation

  18. Acknowledgments • Bei Hu • Tomer Schechori • Xuemo Fan • Alberto Marchevsky • Steven Silver the Computer Cowboy Sponsored in part by NCI U01 CA91429 William Yong M.D. Dept of Pathology and Laboratory Medicine (Neuropathology) UCLA Medical Center David Geffen School of Medicine at UCLA wyong@mednet.ucla.edu (310) 825-0825

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