# Presentation: 287393

## Informatics Tools for Molecular-Based Specimen Banks

**Informatics Tools for Molecular-Based Specimen Banks**

** ****Current Resources**
** ****CaTIS Database**
** ****VGSR Concept**

**Mark A. Watson, M.D., Ph.D.**

## Informatics Limitations of Specimen Banks

-  Inefficient tracking of specimens and specimen quality to multiple different research projects.
-  Inability to perform real-time queries of readily available samples from secure data servers.
-  Lack of biological (research) data annotation for specimens.

**Informatics Limitations of Specimen Banks**

-  Inability to completely and accurately annotate specimens with clinical and pathological data.
-  Inefficient tracking of specimens and specimen quality to multiple different research projects.
-  Inability to perform real-time queries of readily available samples from secure data servers.
-  Lack of biological (research) data annotation for specimens.

## SCC Tissue Procurement Core Overview

-  24 studies
-  Archival bank
-  Institutional studies
-  American College of Surgeons Oncology Group (ACOSOG)
-  21,000 specimens / 8,000 patients (sporadic cancer)
-  Frozen Tissue / Paraffin Blocks / Serum
-  6,300 DNA and RNA samples
-  112 Sample distributions
-  Intra- and extramural investigators

**SCC Tissue Procurement Core Overview**

## SCC Tissue Procurement Bioinformatics

- Dir. Siteman Cancer Center Tissue Procurement Core Facility
- Dir. ACOSOG Central Specimen Bank
- Dir. Siteman Cancer Center Multiplexed Gene Analysis Facility
-  Rakesh Nagarajan, M.D., Ph.D.
- Asst. Dir.  Siteman Cancer Center Bioinformatics Core Facility
-  Jeff Milbrandt, M.D., Ph.D.
- Dir. Siteman Cancer Center Bioinformatics Core Facility
-  Richard Wilson, Ph.D.
- Dir. Washington Univ. Genome Sequencing Center
-  (5) Laboratory FTEs
-  Persistent Systems (Software Development)

**SCC Tissue Procurement Bioinformatics**

## SCC Tissue Procurement Core Capabilities

-  Multiple institutional sites
-  Outside institutions
-  Specimen Storage
-  LN2, -80C, 4C
-  Specimen Processing and QA
-  DNA and RNA samples
-  Sample Arraying
-  Tissue / DNA / RNA
-  Data Management (Tracking)

**SCC Tissue Procurement Core Capabilities**

## A Paradigm for Specimen Data Utilization

- Specimen Data

**Multi-Dimensional Data Space**

## CaTIS Specimen Database

-  MS Access Based
-  Non-networked
-  Scalable
-  Rapid customization
-  Functionality
-  Patient / Specimen / Sample Accession
-  Storage / QA data (tissues and samples)
-  Pathology data (manual entry)
-  Distribution data
-  Mapping to sample arrays / robotics
-  Tracking through to outside institutions (e.g. WU-GSC)
-  Mapping to experimental results

## CaTIS Specimen Database

## CaTIS Specimen Database

## CaTIS Specimen Database

## CaTIS Specimen Database

## CaTIS Specimen Database

## CaTIS Specimen Database

## CaTIS Specimen Database

**Patient Data**
- Patient Code Number
- Demographics
- Study / IRB

**Specimen Data**
- Patient Code Number
- Specimen Code Number
- Specimen Info / QC
- Submission Data
- Path Data

**Sample Data**
- Specimen Code Number
- Sample Code Number
- Sample QC
- Investigator Distribution
- Experimental Results

## Aim 1:  Commercialize and Distribute Key CaTIS Components

-  Migrate to web based data entry / query
-  Migrate to platform independence
-  Open interface to other pathology data systems
-  Open interface to genomics data systems (e.g. CHIPDB)
-  Use of caBIG-defined common data elements
-  Pathology
-  Molecular
-  Additional tools (e.g. pedigrees) suggested by adopters

**Aim 1:  Commercialize and Distribute Key CaTIS Components**

## Virtual Genomic Sample Repository (VGSR)

-  Most specimen resources do not allow querying by biological (experimental) data.
-  Caucasian male / > 60 YO / T2N0 NSCLC
-  T2N0 NSCLC / p53- / 50 ug DNA / _U133 Array # 4567_
-  Single specimens may be used for multiple studies at the genome / transcriptome / proteome level
-  Maximum specimen utility
-  Integrative systems biology

**Virtual Genomic Sample Repository (VGSR)**

## Virtual Genomic Sample Repository (VGSR)

-  Goal:	To develop an informatics system and 	scientific culture to facilitate the sharing of 	molecular biospecimens and biological data 	associated with their use.

##  VGSR – Conceptual Data Flow

- Institutional Tissue Banks

## VGSR - Components

-  Can samples be shared (IRB / MTA) ?
-  Will samples be shared (ownership / IP) ?
-  How will samples be shared (review / prioritization) ?
-  Sample QA / Data standards
-  Central Database Server
-  Web-based Applications
-  Sample Registration
-  Sample Query / Request
-  Sample Manager
-  Data Registration

**VGSR - Components**

## VGSR – Key Features

-  Cooperative Group Tissue Banks
-  Pathology Database Tools
-  Unique opportunity to test the ‘Virtual Specimen Bank’ concept
-  Numerous points of interoperability with caBIG systems
-  Based on caBIG Architecture Workspace recommendations
-  Use of caBIG vocabularies and common data elements
-  Integrated with NCICB tools (caIMAGE)
-  Works with other software developed in Integrative Cancer Research Tools Workspace (e.g. *Function Express, Mutation Viewer)*

**VGSR – Key Features**

## CaTIS / VGSR – Required Resources

** ****Consensus building / SOPs / CDEs**
** ****Personnel**
** ****1 Architect (Shared with Architecture Workspace)**
** ****1 Project manager (50%- Shared with Integrated Cancer Research Tools Workspace)**
** ****1 DBA (50%- Shared with Integrated Cancer Research Tools Workspace)**
** ****2 Programmers**
** ****Hardware**
** ****Enterprise-class server  / programmer workstations**
** ****Software**
** ****Rational Rose/XDE, ClearCase (CVS), ClearQuest**
** ****JBuilder, C++ Builder, Ant**
** ****RDBMS (e.g. Oracle, DB2, MSSQL, etc.)**

**CaTIS / VGSR – Required Resources**

## CaTIS – Project Timeline

-  Conversion of CaTIS to “Commercialized” CaTIS
-  Month 7-12
-  Deploy CaTIS API to extramural sites (adopters)

**CaTIS – Project Timeline**

## VGSR – Project Timeline (1-12 months)

-  Consensus / Policy building
-  Architecture design / CDEs and vocabularies
-  Month 9-12
-  Database building
-  Web tools design

**VGSR – Project Timeline (1-12 months)**

## CaTIS / VGSR Outcome Measures

-  Successful registration of samples to VGSR
-  Utilization of VGSR samples by new collaborative research teams for translational cancer research
-  Funding opportunities
-  Publications track record

**CaTIS / VGSR Outcome Measures**