# Presentation: 358203

## CaBIG Adopter Overview

- Cancer Institute
- Oregon Health and Science University
- February 19, 2004

## Global Vision of the Grid

- Cancer Research Network to elucidate the underlying molecular mechanisms of the disease and identify therapeutic targets
- Rapid development of applications, algorithms and tools to achieve this goal
- Facilitate cross-institution collaboration and sharing of expertise
- “Greater than the sum of its parts”

## OHSU Cancer Institute

**OHSU Cancer Institute**
**Matrix Cancer Center (NCI-designated since 1997)**

## OHSU Cancer Institute Shared Resources

_**Biostatistics and Bioinformatics***_
**Cell Culture Media**
_**Clinical Research Management***_
**Flow Cytometry**
_**Gene Microarrays***_
**Molecular Biology (DNA sequencing)**
_**Cancer Pathology***_
**Transgenic/Gene Knockout**
_**Proteomics (in development)***_

- _*CaBIG Elements_

## Other Key OHSU Resources

- Evidence Based Medicine Center
- Biomedical Information and Communication Center
- Rural Health Network
- General Clinical Research Center

## IT Infrastructure @ OHSU

- Information Technology Group (ITG)
- Single IT department for University with 325 staff in four major divisions
- Three major Data Centers, geographically dispersed with approximately 350 Servers with over 7 TB of data
- High-speed, dual redundant Gigabit Ethernet backbones on campus and Gigabit Ethernet Metropolitan Area Network (MAN) to Crown Data Center and West Campus
- Internet2 connected via University of Washington at 155 Mbps
- High Performance Computing (HPC) Grid
- Provides access to 59 genomics and proteomics applications compiled on both 32-bit and 64-bit platforms as well as a number of statistical and simulation packages.
- Houses instances of the Swiss-Prot, TrEMBL, PDB, GenBank 133, Unigene and PEDSYS databases, which have been formatted for a number of applications.

## Clinical Research Vision of the Grid

- Expand capability of cancer clinical trials
- Ability to collaborate with other GRID participants and to conduct multi-site clinical trials
- Virtual clinical trials
- Improved patient care and education
- Shared protocols and patient education materials, ability to place patients on protocols offered by other GRID participants
- Standardization of clinical trials data reporting
- To develop standards for case reporting and data exchange in alliance with other cancer centers and pharmaceutical companies

## Clinical Research Contributions to the Grid

- Participation in working groups
- Uniform Clinical Trials Reporting
- Allies/Constituencies-SEER, CDC, Pharma, FDA
- Data Integrity and Quality Assurance
- Data warehousing/mining
- Guidelines for supportive care and surveillance
- Clinical trial data/ translational expertise
- Study information
- Adverse event information
- Limited subject information
- Annotated clinical data for specialized tissue banks
- Beta testing of tools for unmet needs

## Cancer Prevention and Control Vision of Grid

- Utilize grid to identify and access cases and controls (e.g., virtual patient registry)
- Enhance collaboration to conduct multi-site population-based studies
- Access to diverse populations
- Standardized instruments
- Web-based data capture system (e.g., patient surveys)
- Expand translational scope by establishing a virtual serum and tissue bank for population-based studies

## Cancer Prevention and Control Contributions to Grid

- Potential sharing of data and biological specimen (tissue and serum) from large epidemiological studies
- Serum samples from 600 cases and controls of older men living in NW (case control study of prostate cancer)
- Standardized instruments
- Nutritional intake (omega 3 fatty acids)
- Quality of Life in pediatric populations
- Participate in the validation studies for these instruments across participating cancer centers
- Rural Health Research Infrastructure

## Bioinformatics and Biostatistics at OHSU

- Center for Biostatistics, Computing and Informatics in Biology and Medicine
- Tremendous Domain Expertise across OHSU
- Division of Biostatistics, Department of Public Health and Preventive Medicine
- Department of Medical Informatics and Clinical Epidemiology
- Evidence-Based Practice Center
- Department of Computer Science and Engineering, OGI School of Science and Engineering
- Database and Object Technology Center, Machine Learning, Visualization and Scientific Computing
- National Heart Lung & Blood Institute (NHLBI) Microarray Center Grant
- Participation in Microarray Gene Expression Data (MGED) Working Groups to develop data standards

## IT Infrastructure

- Sun(Sparc) and Linux(Intel) hardware used for majority of development
- Software utilized by resource
- Oracle 8.1.7 RDBMS, 9i*AS*, SAS 8e, Splus 6.0, MatLab 6.5, Java, Perl and others
- Suite of open source packages including:  Apache, Tomcat, R, MySQL, CVS and others.
- Support of hardware and databases performed by OHSU Information Technology Group

## Communities Served

- Individual researchers
- From study design to software development and complex analysis
- Clinical Research Management (CRM)
- provides centralized services for the initiation, conduct and quality assurance of cancer related clinical trials.
- Gene Microarray Shared Resources (GMSR)
- Affymetrix Microarray Core (AMC)
- Spotted Microarray Core (SMC)
- Individual researchers from CI and all other departments
- National Heart, Lung, Blood, Institute (NHLBI)
- Individual investigators funded by NHLBI for research involving microarray technologies

## Key Projects: BIOSTATISTICS & BIOINFORMATICS

- Experimental design, consultations, and analysis
- Surveyor support
- Normalization workflow
- Implementation of R statistical protocol in collaboration with SMC
- Development of tools
- Annotation tools for Gene Ontology (GO)
- Filtering and transformation tools for microarray investigators
- Pattern analysis tools
- QA/QC reporting for CRM, GMSR
- Education
- One-on-one consultation and trainings
- Numerous workshop and seminars

## Key Projects: BIOINFORMATICS

**OHSU Affymetrix Microarray Database (AMCDB)**
- Status: release 12/2002, version 1.1 expected release date 8/2003
- Operational database for storing microarray data generated on the Affymetrix platform (MIAME supportive)
- web portal
- Investigators can submit project and sample information, access microarray raw and subsequent analysis data files, and also utilize filtering, transformation, and annotation tools

- Current number of users:  **139**
- Current number of projects loaded:**122**
**Of those ~50 cancer related**
- Current number of tuples in database:  **694,392,925 **
- Current size: approximately** 50GB**
- Affymetrix GenChips represented: **1440 **
- Subsequent analysis represented:** 4402**

- Approximate download time from standard desktop on OHSU network
- CHP file **11 seconds**.  HGU133A chip**
- CEL file **56 seconds**. HGU133A chip**
- **Times vary slightly up or down depending on the chip type.
- Note:  HGU133A is currently the largest chip type we have in the database and thus typically has the longest download times.

**Statistics as of August 2003**

## Slide 16

## Key Projects: BIOINFORMATICS

- Fanconi Anemia Transcriptome Consortium (FATC)
- Fanconi Anemia is a rare recessive disorder which can lead to bone marrow failure (aplastic anemia)
- Multi-site Model for Rare Diseases
- Goal is to create a bioinformatics center to provide a comprehensive database of Fanconi anemia transcriptomes. This is a multi-site model for rare disease research.  The database along with bioinformatic and meta-analysis tools will serve all members of the consortium.
- At this time, samples are being collected from 4 sites: OHSU , Brazil , Cincinnati, & Minnesota.  Stanford has recently joined the consortium.
- All data is run through the Affymetrix Core Facility at OHSU

## Key Projects: BIOINFORMATICS

- Spotted Microarray Database (SMCDB)
- Status: In development expected release date 12/2003
- MIAME compliant operational database for storing microarray data generated from cDNA spotted microarray platforms
- web portal
- Investigators can:
- submit project and sample information
- Access scanned image files, as well as raw and normalized data
- Utilize filtering, transformation, and annotation tools

## Slide 19

## Key Projects: BIOINFORMATICS

- Web resources
- MIAME supporting materials for all microarray publications
- Educational resources
- On-line tutorials
- Technical reports
- Multi-media

## New Proteomics Initiative

- University wide Initiative
- Provost and VP Research, OHSU School of Dentistry, OHSU School of Medicine, Vaccine and Gene Therapy Institute, OHSU Cancer Institute and others
- Special informatics needs
- 	Current proprietary solutions do not cross-talk well making inclusion in a grid initiative difficult
- 	Multi-platform solution needed for grid collaboration
- Possible solution:
- Institute for Systems Biology _[http://www.systemsbiology.org](http://www.systemsbiology.org/)_

## Bioinformatics and Biostatistics Visions for the Grid

- Biostatistical and Informatic Resource Network
- Access to large, combined data repositories
- Rapid application and algorithm development due to multi-site collaboration
- Elimination of redundant development projects at multiple institutions
- Potential for large-scale meta-analysis studies
- Shared ontologies and data standards to aid data mining and integration of clinical and research studies

## Bioinformatics and Biostatistics Contributions

- Experienced tightly integrated Bioinformatics and Biostatistics faculty and staff
- Existing applications, databases and tools
- AMCDB
- FATC
- AGLU (annotation tool for microarray data)
- Cancer related microarray data
- Cancer related Clinical trials data
- Expertise in meta-analysis in partnership with EPC

##  >3700 tissue samples collected from >1500 patients (OHSU and PVAMC).
Well Annotated Samples
Confirmed pathologic diagnosis
Tumor quality and purity
Tumor grade
TNM stage
Patient Age and Sex

- Well Annotated Samples
- Confirmed pathologic diagnosis
- Tumor quality and purity
- Tumor grade
- TNM stage
- Patient Age and Sex

- Tissue Pathology at OHSU Cancer Institute

## Well-represented in OCI bank: Cancers of the ovary, prostate, stomach, pancreas, liver, colon, testis, skin, head & neck, soft tissue, lymph nodes and bone marrow

Needs for OCI bank:  Cancers of the breast, brain, lung, bone

- Needs for OCI bank:  Cancers of the breast, brain, lung, bone

- Oregon Cancer Institute Tissue Bank

## Pathology View of Grid

- Virtual Tissue Repository among tissue pathology cores in all cancer centers
- Need for data standards for tissue collection, validation, diagnosis coding
- Ideal would be standardized microscopic images to allow virtual review of material
- Also ideal would be annotation with regard to any NCI- or Intergroup-sponsored clinical trials

## Pathology Contributions to Grid

- Current Tissue bank with annotated samples
- Willingness to test or implement a virtual tissue repository to share samples among centers
- Participation in working groups to determine data standards for tissue collection and  preparation

## Areas of Participation:Beta Testing / Implementation

- Clinical Research Management (Treatment Outcome Capture etc)
- Proteomics (LIMS, Cross-Platform Analysis of Proteomic Data)
- Virtual Patient Registry
- Virtual Tissue Repository

## Systems Development Project

- Develop conceptual model
-  (end user process model)

- Develop Implementation model
-  (developer technical specification)

- Beta system creation

- Develop administrative
- and user documentation

- Develop administrative
- and user documentation

- Revision requests
- controlled through service plan

**Process**

**Process**

**= Process**

**= Outcome**

**= Interaction**

-  Flow Chart

## Summary

- OHSU Cancer Institute is an enthusiastic supporter of the Grid concept
- Dedicated to open source, open development mission of the Grid to advance cancer research
- Open to participation at any level (Development or Implementation in a node, Working Group contributions etc)