# Presentation: 246366

## caTISSUE – Annotations: Update for caBIG TB&PT F2F

- Mike Becich, MD PhD, _[becich@pitt.edu](mailto:becich@pitt.edu)_
- Rebecca Crowley, MD (caTIES Faculty Lead)
- John Gilbertson, MD
- Rajnish Gupta (Lead Developer)
- John Milnes, Programmer/Analyst
- Yimin Nie, MD
- Anil Parwani, MD PhD
- Ashok Patel, MD
- Linda Schmandt, MS (caBIG Project Manager)
- University of Pittsburgh Cancer Institute

## Tissue Banking Informatics
Managing Information on the for Pathologic, Genomic, Proteomic Analysis on Patient’s Tumors for Biomarker Development
Extracting Clinical Information & Outcomes Annotation to Enable Discovery

**Managing Information on the for Pathologic, Genomic, Proteomic Analysis on Patient’s Tumors for Biomarker Development**
**Extracting Clinical Information & Outcomes Annotation to Enable Discovery**

**The Role of Tissue Banking in Cancer Research**

**Genomics**
**(Genotype)**

**Proteomics**

**Pathologic and Tissue Banking**
**(Annotation of Biospecimens)**

**ICR Workspace**

**caTISSUE Core**

**Clinical Environment**
**Pathology Reports**
**Identified Data**

**caTISSUE Core**

**Research Environment**
**Tissue Banking Information**
**De-Identified Data**

**caTISSUE **
**Annotation**

**caTIES**

**Notes:**
Data we can use

## caTISSUE-Annotation (Phase 1)

**Annotates biospecimens**** in tissue banks with pathology, tumor marker, staging, grading and clinical outcome data**
**HIPAA compliant de-identification, secure sharing**** and high quality annotation of specimens to facilitate researcher query of collected materials for translational research. (E-Bay for biospecimens)**
**The system upon which caTISSUE Annotation is based currently integrates:**
**Over 10,400 cancer patients biospecimens**
**Includes estimated 100,000 highly annotated paraffin blocks**
**20,000 frozen tissue specimens**
**150,000 serum samples available for cancer research**
**Over 3,000,000 clinical data points associated with these banked materials.**
**Based on system developed with funding by NCI’s Cooperative Prostate Cancer Tissue Resource (**_[http://www.prostatetissues.org](http://www.prostatetissues.org/)_**) and PA Department of Health - Pennsylvania Cancer Alliance Bioinformatics Consortium (**_[http://](http://pcabc.upmc.edu/)__[pcabc.upmc.edu](http://pcabc.upmc.edu/)_**)**

## caTISSUE-Annotations (v1.0)

**Automated Extraction of Data from Clinical Systems** – Automated extraction of data from Pathology Laboratory Information Systems (LIS)  and legacy databases
**Query Interface** – “E-Bay” resource to browse, explore and request tissues for research
**caTISSUE Integration** – Harmonized object (data) model with caTIES and caTISSUE-Core and provide key IDs for biospecimens...Completed!

## caTISSUE-Annotation (Phase 1)

**The annotation toolkit consists of:**
**Tools for the ****automated extraction of data**** from Pathology Information Systems**
**An ****XML data repository**** based on star design concepts for data warehousing**
**A ****metadata engine****, partially complaint (today) to ISO data sharing standards,  **
**User interface, ****data translation/mapping and data publishing components that use XML and Java**

## caTISSUE Annotation (see poster #11) 

## caTISSUE-Annotations Data Services

**Identified (Clinical) Data - This API will use a metadata engine to present identified data for honest brokers.   Customized role based access. **
**De-identified (Research) data - This API will identified data presentation and predefined de-identification rules from metadata engine.  De-identification rules can be defined by adopter of the system (e.g. local standards) and driven by national security and privacy rules (e.g. national standards).**
**Manual Annotation - Will help in quality assurance, data correction, reviewing and expert annotation and allows capture of local data items**
**caTISSUE-Core and ca-TIES Automated Annotation Services -  Accepting request for annotation and sending annotation in XML packet.**
**Data Publishing Services**
**Queries (user defined searches and predefined sets of standard queries)**
**Data export and downloading**
**Data publishing to caBIG Grid services**

## caTISSUE-Annotation Task Order Update

**Vision and Scope Document completed (4/15/05)**
**Currently being circulated for comments**
**Use Cases completed (5/1/05)**
**Will be circulated for comments this week**
**Traceability Matrix – currently being worked on, will be completed by 5/15/05**
**Specifications Document – will be completed by 5/20/05**
**Writing 2****nd**** Task Order (Final Development Plan) – will be completed by 5/20/05**

## caTISSUE-Annotation Adopter Update

**Discussions with adopters are underway:**
**Bob Lanese and Case Western Reserve have agreed to be our first adopter site**
**Close proximity (2 hour drive)**
**Established relationship with Pathology Department**
**Warren Kibbe and Northwestern University have agreed to be an adopter as well**
**Member of Prostate SPORE program**
**Strong relationship with Pathology Department**
**TJU – have a relationship with Jack London via PCABC**
**U Penn – already have strong relationship via PCABC, CPCTR and caTIES adopter with Mike Feldman and David Fenstermacher**
**Will be approaching at this meeting:**
**Indiana – already have a strong relationship via SPIN program**
**Dartmouth – familiar with Cancer Center program and director**
**Duke – have relationships with pathology department**
**Wake Forest – working on relationship**

## NBN Prostate SPOREs Pilot

**NCI and C-Change (formerly National Dialogue on Cancer) initiative in partnership with Industry**
_**Goal**_**:  Provide tissues with high degree of clinical annotation as well as “analysis center” approach to additionally providing biomarker data sets (*****tissue bank and biomarker bioinformatics*****)**
**Not for profit with national distribution mechanism/governance**
**Based on “Best Practices” in Tissue Bank report by Rand Corporation**
**For full report see **_[http://www.rand.org/publications/MG/MG120/](http://www.rand.org/publications/MG/MG120/)__  _
**Blueprint for NBN publicly available at **_[http://www.ndoc.org/about_ndc/reports/pdfs/FINAL_NBN_Blueprint.pdf](http://www.ndoc.org/about_ndc/reports/pdfs/FINAL_NBN_Blueprint.pdf)_**  **
**Pilot program initiated with Prostate SPOREs**
**RFP Published by NCI Resource Contract Branch on 3/31/05 at **_[http://rcb.cancer.gov/rcb-internet/appl/rfp/51018/toc.pdf](http://rcb.cancer.gov/rcb-internet/appl/rfp/51018/toc.pdf)__ _
**RFP responses due 5/4/05**

## NCI’s Cooperative Prostate Cancer Tissue Resource

**Prostate tissue and serum from 6000 cancer patients  (frozen, paraffin, blood derivatives, tissue microarrays)**
**Provide a high level clinical annotation on the research resources, standard collection and distribution SOPs**
**Based on ISO compliant common data elements**
**On line browsable de-identified set of clinical, pathologic and demographic (HIPAA compliant) data elements to identify research cohorts (supports many of NBN goals)**
**Shared with over 100 investigators to date**
**See **_[http://cpctr.cancer.gov/todatabase.html](http://cpctr.cancer.gov/todatabase.html)_
**Basis of caTISSUE-Annotation for caBIG TB&PT**

## Join us for APIII

**10****th**** Annual Meeting**
**2005 Meeting: Aug 24-26****th**
**Themed on Practical Tools for Pathology/Oncology:**
**Pathology Imaging Jamboree, **
**HL7 and SNOMED in Practice,**
**HIPAA, Honest Broker and IRB Practical Approaches,**
**caBIG as a Change Element, **
**Lab Portals, Impact of EMRs,**
**& Vendor Visions of the Future**
**New Venue: Lake Tahoe, CA**
**Granlibakken Conf Ctr**
**Abstract Sessions**
**Trainee Travel Awards**
- _[http://apiii.upmc.edu](http://apiii.upmc.edu/)_** **

## The NCI 2015 challenge goal:... eliminate death and suffering due to cancer

- “When I look into the eyes of a patient losing the battle with cancer, I say to myself, It doesn’t have to be this way.”Dr. A.C. von Eschenbach, M.D.Director, National Cancer Institute
*The Nation’s Investment in Cancer Research* (2003)