caTISSUE

1
caTISSUE Annotations Update for caBIG TBPT
F2F

• Mike Becich, MD PhD, becich_at_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

• Tissue Banking Informatics
• Managing Information on the for Pathologic,
  Genomic, Proteomic Analysis on Patients Tumors
  for Biomarker Development
• Extracting Clinical Information Outcomes
  Annotation to Enable Discovery

Pathologic and Tissue Banking (Annotation of
Biospecimens)
Research Environment Tissue Banking
Information De-Identified Data
Clinical Environment Pathology Reports Identified
Data
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 NCIs
  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 biospecimensCompleted!

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/publicatio
  ns/MG/MG120/
• Blueprint for NBN publicly available at
  http//www.ndoc.org/about_ndc/reports/pdfs/FINAL_N
  BN_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
NCIs 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 TBPT

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.e
du
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
doesnt have to be this way.Dr. A.C. von
Eschenbach, M.D.Director, National Cancer
Institute The Nations Investment in Cancer
Research (2003)