# Presentation: 605591

## caTissue Core v1.1 Update 

- caTissue Core v1.1 Update
- July 2006

**Rakesh Nagarajan, M.D., Ph.D.**
**Mark A. Watson, M.D., Ph.D.**
**Washington Univ. / Siteman Cancer Center**

- http://caBIG.nci.nih.gov

_**Srikanth Adiga**_
_**Kapil Kaveeshwar**_
**Aarti Sharma**
**Gautam Shetty**
**Mandar Deshmukh**

## caTissue Core V1.1 Enhancements

-  Specimen Aliquoting
-  Storage Container Enhancements
- Automatic Specimen Assignment
- Association with Specimen Types and Collection Protocols
- User Annotation
- Virtual Storage Location
- Role Based Privileges
-  Participant Lookup
-  Arrays
-  Enhanced Events View
-  Quick Links for Common Tasks
-  Multiple Specimen Entry
-  Query Audit
-  Secure Password Functionality

## caTissue Core Home Page

**http://catissuecore.wustl.edu**

## Storage Creation

## Participant Match Check

## Accession Specimen

## Aliquot Creation

## caTissue Core:  Project Timeline

**PHASE I **
- Deploy majority of basic specimen tracking functions to seven adopter institutions
_**Phase Ia & Ib - 2005 Oct**_
- Working prototype with all basic functionality
_**Phase Ic – 2006 Feb**_
- Stable version with caBIG security model and feedback from adopters on prototype.

**PHASE II **
- Integration with other TBPT tools and full Grid enablement / Gold level compliance
**(Mar 2007)**

**2005 - 06**

**2006 - 07**

**2007 - 08**

_**PHASE Id – 2006 Nov.**_
- caTissue Core v1.1 with enhancements based on end-user feedback

## caTissue Core Module

- Other ***Critical*** Classes / Functionality ?

-  Consent Tracking
- Consent is an attribute of what class?
- What functionality is needed?
- What are the attributes of consent?
-  Reconsider Specimen Ontology and Vocabulary
-  Required Business Logic
- Date consistency
- Specimen / Protocol / Pathology Status consistency
-  Automated Specimen Request / Fulfillment
-  Increased Detail in Distribution Protocol
-  Family Object

## caTissue Core Module

- Other ***Critical*** Classes / Functionality ?

-  Remaining Workflow Issues
-  Temporal Queries
-  User / Department / Research Group / Institution Hierarchy
-  Billing Module
-  Shipping Module
-  Others...

## caTissue Specimen Vocabulary

## caTissue Pathology Vocabularies

**Breast**
**Prostate**
**Melanoma**
**Lung**
**Colorectal**
**Pancreatic**
**Head and Neck**
**Ovarian**
**Heme**
**Kidney**
**Bladder**
**Esophagus**
**Endometrial**
**CNS**
**Cervical**
**Thyroid**
**Gastric**
**Liver**
**Bone**

**Procedure**
**Histological Type**
**Histological Grade**
**Tumor Max. Dim.**
**T Stage**
**Pos. LN**
**Examined LN**
**N Stage**
**M Stage**
**R classification**
**LVI**
**PNI**
**Tissue Biomarkers**
**ER, PR, Her2. Ki-67, S100**
**Laterality**
**Site (within organ)**

## caTissue Clinical Data

-  Smoking History
- Attributes?
- Status, Years, PPD, Years Quit
-  Alcohol Use
-  Environmental Exposures
-  Family History of CA
- How represented?
-  Other Static Data
-  _**Dynamic Local Extensions**_

## caTissue Clinical Events

**Clinical Event**
- Event_Date
- Data_Source
- Date_Entered

**Participant**

**Treatment Event**

**Health Status Event**
- Relapse
- New DX

**ChemoRX**
- Agent
- Dose
- Start
- End

**RadRX**

**Lab Event**
- Biomarker
- Result

**SCG / Accession**
- i.e. results in biospecimen collection

**Specimen Annotation**

##   Work Flow Integration 

-  Query Integration
-   View Integration

## Object Integration

**Participant**
**Unique Participant Identifier (UPI)**
**Patient Demographic Data**

**Protocol Collection Event**
- Unique Event Identifier (UEI)
*Event Data*

**Specimen**
- Unique Specimen Identifier (USI)
*Specimen Data*
**Fluid Specimen**
**Tissue Specimen**
**Cell Specimen**
**Molecular Specimen**

**Participant**

**Accession**

**Part**

**Specimen**

**Surgical Pathology Report**

**Part**

**Specimen**

- caTissue Core

- caTIES

- caTissue CAE

## Object Integration Issues

- Remove “Clinical Diagnosis” from Core module-  Use CAE.
- Add “Clinical Status” to CAE Accession object.
- CAE must annotate cases as well as individual specimens.
- Some specimens must be represented in CAE with annotation, will have a unique SCG, but will not have a CAE “accession” because they are not clinical specimens.
- Core module SCG is protocol based, but CAE / TIES accessions are not.
- Others ?

## caTissue Data Entry Requirements

- Users should not be made to enter the same data repeatedly across applications.
- It should be possible to add clinical annotations to a Participant added via caTIES without having to renter the same information again.

**Core Module**

**CAE Module**

**New Participant**
**New SCG**
**New Specimen**

**Additional Annotation**

**TIES Module**

**Path Report**

**CAE Module**

**TIES Module**

**New Participant**
**Annotation**

**Core Module**

**Path Report**

**New Specimens**

**TIES Module**

**Core Module**

**New Participant**
**Path Report**

**CAE Module**

**New Specimens**

**Additional Annotation**

## Data Entry Integration

- SPR uploaded using caTIES tool
*Participant created;  Specimen Collection Group created*
*Check for existing*
- Clinical data uploaded in bulk or manually entered
*Participant created; Specimen Collection Group created*
*Check for existing*
- New specimen received in bank
*Check for existing (from TIES or CAE upload) or add participant*
*Check for existing (from TIES or CAE upload) or add SCG*
*Add specimen*
- New SPR uploaded using caTIES tool
*Check for match to previously received specimen and link to same SCG*
- New clinical or pathology data entered
*Find existing participant, SCG, or specimen (depending upon data to be entered) and link.*

## caTissue Data Entry Integration

## Query Integration

***Find all cases of prostate ductal carcinoma of Gleason grade 3+4 for which there are frozen tissue samples containing at least 50% neoplastic cellularity available.***

***Find all cases of squamous cell carcinoma of the tongue base with perineural invasion for which there is at least 5 ug of matching RNA from non-malignant tissue and tumor with at least 50% neoplastic cellularity. ***

- caTIES
- caTissue Core
- caTissue CAE

## Query Integration

***Find all cases of breast cancer with subsequent presentation of brain metastasis greater than 5 years after initial diagnosis for which a pretreatment bone marrow and primary tumor frozen tissue sample is available.  ***

***Find all cases of prostate cancer with pre-treatment PSA level > 14 and greater than 5 year disease free survival for which serial serum samples are available over 6 month intervals.***

- caTIES
- caTissue Core
- caTissue CAE

## Work Flow Integration

- Query all SP Archive

***“******Adenocarcinoma of the Small Bowel”***

- Request Tissue Specimens

**caTIES Shopping Cart Interface**

**caTISSUE CORE**

- Distribute to Honest Broker
- Specimen Accession / Link Block
- De-Identify
- Specimen Processing
- Specimen Distribution
- Return Block to SP or Store

**Research**

**Select Tissue Blocks for Distribution Using caTIES**

## caTissue Integrated Workflows

- Scientist I – Version A (Less Harmonious)

- Scientist logs into caTIES and uses caTIES query to search for desired cases based upon pathology report queries.
- Scientist requests cases via caTIES ordering system.
- Honest brokers obtains blocks from requested cases.
- Selected blocks are entered as Specimens into caTissue.
*Corresponding Participant and Specimen Collection Group already exist in caTissue because of model harmonization with caTIES.*
- Specimens are processed, tracked, and distributed to investigator using caTissue functionality.

## Work Flow Integration

- Query all SP Archive

***“******Prostate Adenocarcinoma with Gleason Score 3+3...”***

- Pass Query Results by:

**caTISSUE CORE**

- Filter for Cases with Frozen Tissue and Preoperative Serum

**SP Report #**

***“******...with frozen tissue and pre-operative serum available”***

**Research**

**Select Research Bank Specimens for Distribution Using caTIES Annotation**

## caTissue Integrated Workflows

- Scientist I – Version B (More Harmonious)

- Scientist logs into caTISSUE and uses query to search for desired cases based upon pathology report queries, specimen queries, or clinical annotation queries
*Queries would return results at the SCG/Accession level if specimens were currently not accessioned (e.g. archived blocks) or at the specimen level if individual specimens had been accessioned.*
- Scientist requests cases via new caTISSUE / caTIES hybrid ordering system.
- Honest brokers obtains blocks from requested cases (if blocks need to be accessioned).
- Selected blocks are entered as Specimens into caTissue.
*Corresponding Participant and Specimen Collection Group already exist in caTissue because of model harmonization with caTIES.*
- Specimens are processed, tracked, and distributed to investigator using caTissue functionality.

## Work Flow Integration

- Query for available specimens...

***“******Patient-matched frozen tumor and metastatic lymph node tissue...”***

**caTISSUE CORE**

**Select Research Bank Specimens for Distribution Using Annotation Module and TIES**

**caTISSUE CORE**

- ...based on clinical data

***“******...from nulliparous females with her2-, Stage II invasive lobular carcinoma...”***

**caTISSUE CORE**

- Review de-identified pathology details...

**caTIES**

**caTISSUE CORE**

- ...and request / distribute for research

***“******...with the presence of LCIS features”***

***“******...needing matched DNA (1 ug) and RNA (3 ug) samples.”***

## Query Integration

- caTissue Core

- caTIES

- caTissue CAE

## caTissue Query Integration

## View Integration