caTISSUE – Annotations: Update for caBIG TB&PT F2F

1. caTISSUE – Annotations: Update for caBIG TB&PT F2F Mike Becich, MD PhD, 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

2. The Role of Tissue Banking in Cancer Research Pathologic and Tissue Banking (Annotation of Biospecimens) Research Environment Tissue Banking Information De-Identified Data Clinical Environment Pathology Reports Identified Data 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 caTIES caTISSUE Annotation caTISSUE Core caTISSUE Core ICR Workspace Genomics (Genotype) Proteomics

3. 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) and PA Department of Health - Pennsylvania Cancer Alliance Bioinformatics Consortium (http://pcabc.upmc.edu)

4. 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!

5. 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

6. caTISSUE Annotation(see poster #11)

7. 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

8. 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 2nd Task Order (Final Development Plan) – will be completed by 5/20/05

9. 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

10. 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/ • Blueprint for NBN publicly available at 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 • RFP responses due 5/4/05

11. 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 • Basis of caTISSUE-Annotation for caBIG TB&PT

12. Join us for APIII 10th Annual Meeting 2005 Meeting: Aug 24-26th 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

13. 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)