1. Development of A Digital Pathology Database for Annotation and Quality Management of a Brain Tumor Biorepository
Jeremy Molligan, MD
Pathology

2. How do we integrate and utilize all of this information?
Information Age
Collecting terabytes of information per patient
Next Generation Assays
Personalized Medicine Iniatives
Intelligent Biosensors
Investments in Basic, Clinical, & Translational Research
How do we integrate and utilize all of this information?

3. Objectives
Establish a CAP accredited, quality-controlled tissue bank for neuro-oncologic research
Integration of Informatics
Clinical, Radiology, Histopathology, Genomics
Platform for Translational Research

4. Tissue Specimens Collection directly from OR
Warm-ischemia Time < 5 min
Cold-ischemia Time < 15 min
SNAP Frozen
RNAlater - Nucleic Acids
FFPE with QC Slide

5. Direct collection from OR
Specimen Work Flow
Direct collection from OR
Aliquot
10% Formalin for FFPE
RNAlater
SNAP Frozen
Quality Control
Molecular Analysis
Research

6. Blood Specimens PAXGene tubes Immediate RNA & DNA stabilization
Kits for high-throughput processing
EDTA tubes
Standard Plasma, Buffy-coat

7. Quality Control 5-10% Sampling Audit Nucleic Acids Nanodrop: A260/280
Aigilent TapeStation: RIN (Digital Electrophoresis)
FFPE Slide verified by attending Neuropathologist
SPREC - Documentation of Pre- analytic Variables (cold-ischemia time, thaws, centrifuge speed)

8. RFID-based Tracking BioTillion - RFID Bioinventory Management System
Software integration with OpenSpecimen
Reduces cataloging errors

9. Data Capture NEURO DB LIS OPEN SPECIMEN ELECTRONIC MEDICAL RECORD
Clinical and demographic information is
gathered for diagnostic and therapeutic
purposes
NEURO DB
Clinical research paramteres are captured
prospectively and retrospectively
LIS
Anatomic Pathology Laboratory Information System
OPEN SPECIMEN
Biospecimen information and clinical annotation

10. Neuro DB
Security - Password-protected, user management system, Jefferson Firewall
Accessible - Any computer on Jefferson Campus, No software downloads
Customizable - Forms can be tailored to specific research interests
Fidelity - Designed to limit erroneous user input; Intuitive User Interface
Integrated - Link clinical data to biospecimens

11. Neuro DB

12. Neuro DB

13. OpenSpecimen OpenSpecimen - Bioinventory Management System
Open source web application
SQL Backend
Custom work flows
REST API

14. OpenSpecimen

15. Digital Pathology
Leica Aperio – High resolution, whole slide image capture
OpenSeadragon – Open source, web-based WSI viewer
Directly integrated into biorepository LIS
WYSIWYG for researchers
Infrastructure for future analytics: AI & Machine Vision Analysis

17. Data Work Flow NEURO DB I2B2 OPEN SPECIMEN APERIO EMR LIS
Clinical research data capture
I2B2
Data Integration
Biorepository specimen data capture
OPEN SPECIMEN
APERIO
Whole Slide Imaging (Digital Pathology)
EMR
Clinical Information
LIS
Anatomic Pathology
Information System

18. i2b2 i2b2- Web-based Query & Analysis Tool Data Aggregation
Integration of Clinical, Pathologic, Genomic, & Biospecimen Data

19. i2b2

20. Current Collected 250+ Cranial Base Neurologic Cases
Benign, Malignant, and Metastasis
>2500 individual specimens
Seven Neurosurgery & ENT surgeons
Pending CAP inspection & approval

21. Summary
Established a quality controlled digital pathology system for our brain tumor biorepository
Integrated clinical, pathologic, and genomic information systems
Serves as foundation for current and future translational research iniatives