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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
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
… 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
The Other Problem
• Medical Centers support multiple
Patient tissue banks
• Samples from a single patient (or a
Accession Accession single operation) are stored in
multiple tissue banks
• Each bank operates and annotates
Collection
Collection
Collection
Collection
Collection
differently
• And there is chaos…
UPMC Pathology and Oncology Informatics
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
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
The Archive and the Bank Interact
• The Banked and Archived Tissue are
related through the tissue donor
Pre Diagnostic Biopsy
Diagnostic Biopsy • The Archive contains
Resection – Clinical Discards – Diagnostic & Pre Diagnostic Biopsies
Progression Bx
– Diagnostic Tissue Samples
Protocol Bx
• The Bank tends to have frozen tissue -
protocol samples and clinical discards
Time
• One needs both the Archive and the
Bank to get a complete view
UPMC Pathology and Oncology Informatics
caTISSUE
A Tissue Bank Centric Model
caTISSUE Lite Annotation Services
Lab Data
Tissue Processing and
Storage
Standards Based Pathology Data
Tissue Bank Database
Clients and Projects
Outcomes and Rx
Tissue Bank Viewer
On the caBIG
Core Bank Activities Enterprise Activities
Washington University University of Pittsburgh
UPMC Pathology and Oncology Informatics
Annotation Services Model
Enterprise Activities
Tissue Processing and
Clients and Projects
Outcomes and Rx
Pathology Data
Lab Data
Storage
Standard Data
Data
Tissue Bank Data Mapping
Aggregation
For Annotation
Request for Information
Tissue Bank Activities
UPMC Pathology and Oncology Informatics
Enterprise View of Tissue
Outcomes and Rx
Pathology Data
Lab Data
Standard Tissue Processing Data
Tissue Processing,
Tissue Bank
Inventory and Availability
Enterprise Annotation Services
Tissue Processing,
Tissue Bank
Inventory and Availability
Tissue Processing, Aggregator
Tissue Bank
Inventory and Availability
Tissue Processing,
Tissue Bank
Inventory and Availability
Enterprise Tissue Dataset
Extend Local Dataset
Enterprise wide Patient/Specimen centric view of tissue
UPMC Pathology and Oncology Informatics
UPMC System
Identified “Clinical” Data in Silos
Clinical Anatomic Cancer Tissue Clinical
LIS LIS Registry Banks Trials
Outcomes Permission Status in trials
Tumor Synoptic
Progression & Rx Procession
Markers Reports
Datawarehouse
Merging Data Mapping to disease Mapping to Canonical Elements
Error Correction De-identification
Mapping to Client Elements
Data Data Data Data
Mart Mart Mart Mart
Integrated, Standard De-identified Data for Researchers
UPMC Pathology and Oncology Informatics
Enterprise Tissue Management
• Standard Clinical Annotation provided
centrally
Enterprise View of Tissue
Outcomes and Rx
•
Pathology Data
A small number of processing data
Lab Data
Standard Processing Data
elements are provided from each bank
Tissue Processing,
Tissue Bank
•
Inventory and Availability
Enterprise Annotation Services One can provide a standard, enterprise
Tissue Bank
Tissue Processing,
Inventory and Availability
view of all tissue samples
Tissue Processing, Aggregator
Tissue Bank
•
Inventory and Availability
The enterprise view can be mapped to
Tissue Bank
Tissue Processing,
Inventory and Availability
standard national data elements and
Enterprise Tissue Dataset
published to the caBIG
Extend Local Dataset
•
Enterprise wide Patient/Specimen centric view of tissue
Any local bank can extend the central
annotation
UPMC Pathology and Oncology Informatics
Enterprise Tissue Management
• Standard Clinical Annotation provided
centrally
Enterprise View of Tissue
Outcomes and Rx
•
Pathology Data
A small number of processing data
Lab Data
Standard Processing Data
elements are provided from each bank
Tissue Processing,
Tissue Bank
•
Inventory and Availability
Enterprise Annotation Services One can provide a standard, enterprise
Tissue Bank
Tissue Processing,
Inventory and Availability
view of all tissue samples
Tissue Processing, Aggregator
Tissue Bank
•
Inventory and Availability
The enterprise view can be mapped to
Tissue Bank
Tissue Processing,
Inventory and Availability
standard national data elements and
Enterprise Tissue Dataset
published to the caBIG
Extend Local Dataset
•
Enterprise wide Patient/Specimen centric view of tissue
Any local bank can extend the central
annotation
UPMC Pathology and Oncology Informatics
Institution is a RIM entity that
Represents the medical or research
Institute responsible of the TCE
A person is a RIM entity
A Collection Authority is a RIM
Institution Entity. It has the power to allow
Person The Tissue Collector is a Surgeon-like A project to collect and store tissue
1 Role. There may be more than one Samples for research. There are
“collector” for each TCE. usually two authorities, the IRB
0..* (representing the patient) and
The Institution (representing the
1 0..* 0..* 1..* institution
Tissue Donor Tissue Collection Event Tissue Collector
Collection Authority
A Tissue Donor is a Patient-like
Role. Note however, that a Tissue 1 1
1..*
Donor may or may not be ill or Collected and Labeled Specimen
Receiving care. Further, a donor may
Or may not have given consent Authority
0..* 1..*
For banking. Document
May be associated with
Clinical
Pathology Report/Part
Specimen 0..* 0..*
1..* Sponsoring Project
1 1
1
A specimen can be clinical or research 1
Across its lifetime.
Research
A sample can be split or Specimen 0..*
Converted to another type All research specimens have a sponsoring
1..* Project that has the authority to “bank” tissue
1 0..*
For research, and is responsible for the
0..*
Appropriate use of that specimen.
A research project uses the tissue (or data)
It requires IRB authority and permission from Research Project
The Sponsoring Project(s)
0..*
1..*
Research Authority
Authority
Document
Draft
Center for Pathology & Oncology Informatics
UPMC Pathology and Oncology Informatics
Data Dictionaries
Source AP LIS Registry CP LIS TIES CTMA
Applications
API or Reports Application Adapters
Tissue Bank
Applications
Consent
Aggregator Data
Tissue Bank [identify patients/samples data across sources]
Mapping
Tissue Bank Patient Accession Sample
Merged Annotation in “Containers”
Tissue Bank
Download
API/XLM Canonical
Dictionary
Containers in Canonical Object Model
Metadata
DE
Mapping
Consent Download
Data
caDRS
Data Mapped to “caBIG CDE”
Published Data De-identification
API/XLM Institutional Firewall
API
Tissue Enterprise
Q/A Data SPORE CaBIG caBIG
Bank Presentation
Presentation Presentation Presentation GRID
Presentation Tissue Res.
UPMC Pathology and Oncology Informatics
Data Dictionaries
Source AP LIS Registry CP LIS TIES CTMA
Applications
Data Containers Identification
Metadata
Donor ID Rx History Tumor Marker Hx Pathology Hx Progression
Mapping and Transformations
Disease
Business Rules Local Systems
Metadata
Mapping
Clean Canonical Patient Model Canonical
Metadata
Mapping and Transformation
CaBIG
Tissue Bank Enterprise CaBIG Metadata
Presentations Presentation Presentation
UPMC Pathology and Oncology Informatics
