# Presentation: 186320

## caBIG Tissue Bank and Pathology Tools (TBPT) Workspace

- Ian Fore, D.Phil.
- NCI Center for Bioinformatics
- September, 2005

**caBIG Tissue Bank and Pathology Tools (TBPT) Workspace**
**Developing standards based interoperable technologies enabling translational research**

**Notes:**
I should highlight that this workspace addresses biospecimens of all kinds - not just tissue samples

Focus is on short term here. Tools which are available or will be so shortly.

## Tissue Banks and Pathology Tools Workspace: Goals

- Biospecimen and pathology tools to enable specimen and information sharing across Cancer Centers.
- Building tools for the collection and annotation of biospecimens
- Developing the means to share specimens between centers and over time
- Integrating existing biospecimen software

**Notes:**
3 goals

First - not only to collect specimens but to record the various kinds of annotation on them. The value of specimens is greatly increased by having clinical annotation about the patient from which the specimens came.

Second the goal is to make specimens available. The NCI spends about $50m annually on biospecimens as part of one project or another. An important aim is to see these specimen resources well used.

Thirdly, along with the general principle of caBIG we aim to integrate existing tissue bank software. I’d like to highlight t that Kim Johnson of CALGB is currently involved in this workspace to evaluate some of the commercial software available for Biospecimen banking

## TBPT Activities

- TBPT activities involve the development of a basic tissue inventory tracking module that can be annotated with 21st century specimen resources

- Wash University/Siteman Cancer Center

**Notes:**
The activities of the workspace are summarized here. From a set of applications the goal is to provide an informatics resource that will support translational research.

The aim is to handle a comprehensive set of sample types, provide them to labs carrying out a range of experimental techniques and associating the results from those experiments with clinical data

## TBPT applications

- caTissue Core
- Core specimen handling and tracking functions
- caTissue Clinical Annotation Engine
- Annotation of specimens with clinical data
- caTIES
- Text Information and Extraction System

**Notes:**
These are the applications currently in development

## A cooperative endeavor

- caTissue Core
- Washington University
- caTissue Clinical Annotation Engine
- University of Pittsburgh Medical Center
- caTIES
- University of Pittsburgh Medical Center
- Adopters at many centers

**Notes:**
It should be emphasized that thisis a cooperative endeavor

These three applications are being developed at Washington University 

## caTissue Core

- Core specimen handling and tracking

## caTISSUE Core - Features and Benefits

- A basic system that can be rapidly deployed to institutions with little or no specimen banking informatics
- Model to expose existing biospecimen informatics systems
- Plays well with others - via caBIG compatibility
- Usage derived from existing specimen banking systems
- Modular design so that additional functionality (biological annotations, billing and financial modules, etc.) can be added without architectural redesign

**Notes:**
caTISSUE Lite will be the primary database for tissue specimen inventory and tracking to be used by researchers from/universities/hospitals from different geographic areas

Develop Use Cases from existing systems to build the caTISSUE object model - Don’t reinvent the wheel.

 Create an open source object model, data elements, and vocabularies for biospecimen informatics management that are “caBIG Compliant.”

 Utilize best practices for data sharing, confidentiality, and patient consent tracking.

 Develop a modular architecture that allows the addition of other functionality in the future. 
Core biospecimen object model

 Data elements for specimen tracking, inventory, distribution, and QA.

 Use cases for specimen accessioning, data update, and querying based on core specimen data elements.

 Not pathology annotation.

 Not clinical annotation. 

 Not biological annotation (yet).

## Use what you have - or adopt caTissue

- Cross
- Institution
-  Query
- Interface

- caTissue
- Database

- Custom
- Mapping

- Standard
- Mapping

- Existing system

- caTissue Model

## caTISSUE Example Query

***Find all cases of prostate cancer with available RNA (> 5 ug) and DNA (> 5 ug) from tumor tissue with at least 50% neoplastic cellularity and participant-matching DNA (> 5 ug) from non-malignant prostate tissue or peripheral blood leukocytes.  ***
***Also identify the element location for these tumors on all available tissue microarray blocks made from corresponding surgical pathology specimens.***

- Wash University/Siteman Cancer Center

## Entering a new Specimen - Fluid Sample

**Entering a new Specimen - Fluid Sample**

## Specimen Event - Tissue Fixation

**Specimen Event - Tissue Fixation**

## caTISSUE Current Status

- Version 1.0
- Prototype Oct 2005
- Release Dec 2005
- Experimental Annotation Module
- 2006
- Possible future modules
- Ordering
- Financial - Billing

## caTIES

- Cancer Text Information Extraction System

## caTIES Features and Benefits

- Extraction of coded information from free text surgical pathology reports using caBIG compliant data structures and terminology
- Surgical pathology reports contain a wealth of information (in free text) including:
- Histologic Type
- Stage and Size
- Prognostic Factors (LN, ALI, PNI, Margins)
- Immunophenotype, Molecular Markers
- Ability to query, browse, and acquire annotated tissue data and physical material across centers
- Based on the Shared Pathology Information Network (SPIN) application

- UPMC Centers for Pathology & Oncology Informatics

## caTIES Query

## caTIES - Surgical Pathology Report coding

## caTIES Example Query

***Find all cases of gleason score 3+3 prostate carcinoma with neuroendocrine differentiation from patients who have also had a previous non-small cell lung tumor.***

**Notes:**
Eventual query

Dependent on temporal queries

## caTIES Current Status

- Version 1.0 - June 2005
- In use at U.Penn & UPMC
- caTIES caBIG Extensions
- CDEs described in the caDSR
- Terminologies available in the NCI Meta Thesaurus
- Version 2.0 –
- Available on the caBIG Grid
- New functions based on user feedback
- Ordering, and fulfillment, verification of report coding

## caTissue Clinical Annotation Engine

- Annotation of specimens with clinical data

## Clinical Annotation

**Clinical Annotation**

- Clinical annotation includes information of interest to tissue banks and their clients, that is not generated by the tissue bank
- Clinical annotation is generated over long periods of time in multiple clinical systems as part of the clinical process
- Clinical annotations are often contained in Pathology, Laboratory (AP-LIS, CP-LIS), Registry, and Clinical Trials Management Systems

- UPMC Centers for Pathology & Oncology Informatics

*Request for samples of high grade, organ confined prostatic adenocarcinoma primaries from patients less than 60 years old at diagnosis and no hormonal therapy prior to resection. Five year follow up with no chemical or anatomic recurrences*

**Notes:**
Anatomic Pathology Laboratory Information Services (AP-LIS) 
Clinical Pathology Laboratory Information Services (CP-LIS)
Pathology – Surgical Accessions, Specimens, Samples
Registry – Patient, Primary Tumor, Grade Stage, Progression, Outcome

## caTissue Clinical Annotation - example query

***Find all cases of prostate carcinoma with diagnostic PSA levels > 14 and subsequent patient survival greater than ten years***

## Clinical Annotation - current status

- Phase 1 – Clinical Annotation Engine
- Gathering requirements
- Integrating with caTissue Core
- Breast & Prostate Annotations
- Version 1.0 - Dec 2005

## Participation

- Biweekly workspace teleconference
- All projects open to wider participation
- Requirements & features
- Data elements
- Installing and using the software
- Web site
- https://cabig.nci.nih.gov/workspaces/TBPT/
- Contact
- Greg Eley - Booz Allen Hamilton
- eley_greg at bah.com