# Presentation: 937632

## caTissue Suite 1.1 

## caTissue Big Picture

**Web based open source application**
**Track receipt, processing, storage, quality review, and distribution of biospecimens.**
**Certified on **
- JBoss App. Server(4.2.2 GA)
- Oracle(10.2.0.2) and MySQL(5.0.45) databases
- Windows and Linux servers
- Internet Explorer, Firefox and Safari (on Mac)

## Features

**Customizable user roles and privileges structure to support multiple repositories within single caTissue instance**
**Flexible storage container hierarchy**
**Enhanced Collection Protocol Definition**
- Pre-define specimen processing schemes
- Define multiple study arms and time points
**Patient registry & in-built duplicate check algorith**
**Specimen accession,  derivatives, and processing**
**Pathology Annotation (CA)**
- CAP protocol pathology annotation for major organ systems
**caTIES-like Pathology Report Annotation**
**Custom Annotation (Dynamic Extensions)**
**Advanced Query “Wizard”**
- Create and save complex, pre-defined or parameterized searches
**Specimen Requisition and Request Tracking  **
**caGrid data share and API access**

## Biospecimen Functional Outline

## Functional Outline

**Log In**

## ADMINISTRATIVE FUNCTIONS

## Privileges at user level

**Privileges at user level**

*2. Select Sites*

*1. Select Role*

*3. Select CPs*

*4. Select Privileges*

## Multi-Site Repository

| Role | Description |
| --- | --- |
| Super Administrator | A Super Administrator can perform any operation within the application.  |
| Administrator | An Administrator registers new users, containers, and collection protocols and distribution protocols into the system. |
| Supervisor | A Supervisor adds participants and registers them to collection protocols. |
| Technician  | A Technician adds specimens into the system. |
| Scientist | A Scientist performs a query and orders specimens and specimen arrays of interest. |
| Custom | The role can be customized and certain required privileges can be assigned to the user.  |

**User Roles**

## Multi-Site Repository

**User Provisioning**

| Privilege | Description | Role |
| --- | --- | --- |
| User Provisioning | Create a user and assign privileges. | Administrator |
| Storage Administration | Add and edit storage containers. | Administrator |
| Protocol Administration | Add and edit CP
Assign privileges for each protocol | Administrator |
| Registration | Add or edit a Participant without registration
Register Participants, Consents, and Specimen Collection Group(SCG)
Add and edit Specimen and Consents | Administrator or Supervisor |
| Specimen Processing | Aliquot and Derive 
Add Events
Add Specimen Annotations
Create Specimen Array
Specimen Array Aliquots | Administrator, Supervisor, or Technician |
| Distribution | View orders
Process Ordering Requests(changing status of specimen orders)
Distribution  | Administrator, Supervisor, or
Technician |
| Read Denied | Disallow read access to data under a CP.  | Scientists except the Principal Investigator or the coordinators of the CP. By default Scientists have de-identified read privilege to everything. |

## Multi-Site Repository

**Bank A**

**Bank B**

**Protocol B**

**A Protocol**

**Protocol C**

**B Banker**

**A Banker**

***Shipping / Tracking***

*Register a participant to “A” Accession a tissue         Ship tissue to Bank B*

*Receive tissue                ****X**** Query tissue         Derive into RNA         Ship RNA back to Bank A*

## Creating a storage container

**Creating a storage container**

*1. Select a container Type*

*2. Select parent location details*

*3. Name the container*

*4. Restrict a container to a specific protocol*

*5. Restrict what the container can hold*

## Storage Container Map

## Creating a Collection Protocol

**Ability to define consent questions, time points and specimen collected per time point**
**Ability to define derivatives and aliquots that needs to be created on the specimens collected**
**System will use this information to create *****anticipated***** specimens for each participant registration**
**Support for complex protocols with arms and phases**

## Enhanced Protocol Definition

**Enhanced Protocol Definition**

**Pre-define Specimen requirements and properties at multiple time points in a collection protocol.**

*Calendar Clock*

*Define required specimens,*
*Derivatives, and aliquots *
*expected at collection event*

## Privileges at CP level

## Complex protocol

**Notes:**
Study arms are alternative pathways with alternative visit timelines, and participants are assigned to one of these alternative arms by inclusion criteria and/or randomization.  
Study phases are successive pathways that may or may not apply in the cause of a treatment for one participant. Some phases may apply to all participants and some phases are used for unplanned course of disease progression or relapse. 

## BIOSPECIMEN MODULE

## Collection Protocol Based View

**Collection Protocol Based View**

*CP registration*

*Register New*

*Participant demographics *

*Participants registered to the selected protocol*

*Specimens collected/to be collected under a registration for a time point*

## Facilitated Bio-specimen Accession

**Facilitated Bio-specimen Accession**

*Label printing*

*Creation of all expected specimens, derivatives, and aliquots based on CP definition*

*1.Indicate expected specimens collected *

*2.Indicate expected derivatives / aliquots created *

*3. Pre-defined / editable labels, quantities, and storage destination. *

## Other specimen operations

**Other specimen operations**

- Whole Blood

- Spin

- Derive

- Cell pellets

- DNA samples

**Create child specimens: Aliquot or derivatives**
**Add specimen events : spin, thaw, freeze, check in, check out, transfer, embedded and so forth**
**Add clinical or pathology annotations**
**Bulk specimen operations**

## Consent Tracking

**Consents tiers can be defined at collection protocol level**
**Consents can be tracked at participant registration, specimen collection group and each specimen level.**
**Consents are verified during distribution for concurrence**

## Consent Tracking

*Capturing participant responses for consent tiers *

## LOADING SURGICAL PATHOLOGY REPORTS

**LOADING SURGICAL PATHOLOGY REPORTS**

## caTIES-Like Path Report Annotation

**Surgical Pathology Report loading pipeline:**
- HL7 reports are loaded
- The identified information in the report can be de-identified  using different de-id tools.
- Reports are concept coded using NCI's EVS meta-thesaurus.
- These reports are associated with the Participants and Specimen Collection Groups within caTissue.
- Finally the reports can be viewed and queried with caTissue.

- Path reporting system (coPath)

- Concept Coder

- De-ID Tool Plug-In

## De-identified report with highlighted concept codes

## ANNOTATIONS – CLINICAL AND PATHOLOGY

## Clinical & Pathological Annotations

**CAP (College of American Pathologists) checklist based annotations**
**Can be collected at participant and specimens**
**Clinical: Smoking and Alcohol Use, Family History, Lab Values, Treatment Information, Comorbidities, Followup Information**
**Pathology: Breast, CNS, Colorectal, Heme, Kidney, Lung, Melanoma, Pancreas, Prostate**

## Forms hooked to different entities

| Participant | Specimen Collection Group | Specimen |
| --- | --- | --- |
| 
Lab Annotation
Family History Annotation
Treatment Annotation
Rad RX Annotation
Chemo RX Annotation
Treatment Regimen
Environmental Exposure Health Annotation
Alcohol Health Annotation
Smoking Health Annotation
Health Examination Annotation
New Diagnosis Health Annotation
No Evident Disease Health Annotation
Recurrence Health Examination Annotation
Local  Recurrence Health Examination Annotation
Distant  Recurrence Health Examination Annotation | 
Base Solid Tissue Pathology Annotation
Base Hematology Pathology Annotation
Radical Prostatectomy Pathology Annotation
Needle Biopsy Prostate Pathology Annotation
Retropubic Enucleation Pathology Annotation
Transurethral Prostatic Resection Pathology Annotation
Pancreas Pathology Annotation
Lung Biopsy Pathology Annotation
Lung Resection Based Pathology Annotation
Kidney Biopsy Based Pathology Annotation
Kidney Nephrectomy Pathology Annotation
Melanoma Pathology Annotation
CNS Pathology Annotation
Breast Pathology Annotation
Local Excision Based Colorectal Pathology Annotation
Excisional Biopsy Based Colorectal Pathology Annotation
Resection Based Colorectal Pathology Annotation | 
Specimen Based Solid Tissue Pathology Annotation
Colorectal Specimen Pathology Annotation
Pancreas Specimen Pathology Annotation
Melanoma Specimen Pathology Annotation
CNS Specimen Pathology Annotation
Prostate Specimen Pathology Annotation
Kidney Specimen Pathology Annotation
Lung Specimen Pathology Annotation
Breast Specimen Pathology Annotation |

## Local Extensions

**Add new forms on the fly – without any code changes**
**Can be used to collect local or custom data elements**
**Automatically generates forms without any programming efforts**
**Can add, edit and query for dynamic data elements along with static data elements**

*Example annotation loaded using this feature:*

## Workflow

## Dynamic Form Builder

## QUERY CAPABILITIES

**QUERY CAPABILITIES**
**SIMPLE QUERY INTERFACE**
**ADVANCED QUERY INTERFACE**

## Query Interface

**caTissue query interface supports following features:**
- Query any data in caTissue allowing both simple and complex conditions/associations
- Filtering results based on the access rights based on HIPAA compliance
- Save query – Canned and parameterized
- Export query results as a CSV file
- Define results view
- Select specimens from multiple queries and create a list for further actions(Ordering, shipping, bulk operations )

## Simple Query Interface

**Simple Query Interface**

*Form the query*

*Results view*

## Advance Query Wizard

**Advance Query Wizard**

*1. Find object of interest in data model*

*2.  **Define search conditions for selected object*

*3. Create complex query based on combinations of selected objects and conditions*

## Advanced Query results:

*Tree view of results*

*Results table view with pre-defined data elements*

**Advanced Query results:**

## Temporal Queries

**Advanced Search Query Builder**

**Build the Query with Data Types**

**Select the subjects of the query**

**Define the temporal expression and name the result field**

## Advance queries

**Through Advance Query Interface, complex queries are possible. Some examples are:**
- Query with complex criteria - Malignant breast DNA specimens from African American participants who are registered to protocol with the “Breast" in the title.
- Query on reports - Find all surgical pathology reports that have text content ‘viral’ present.
- Technician query - Find all the specimens that are to be collected today.
- Query across static and dynamic data - Find male participants suffering from prostate tumor whose biospecimen samples were tested two weeks after recording the PSA value.
- Temporal query - Find all the biospecimens which were fixed within 30 minutes of collection.

## Shipping & Tracking

**Shipping & Tracking**

** ****Users can send/receive bio-specimens from one site to another. **
**The specimens will be placed in a shipment having a unique shipment label and optionally a barcode.**
**The system tracks the shipments moving between the sites and sends email notifications to appropriate personnel at both sites.**

- Site-A

- Site-B

- Send/Receive Bio-Specimens

## Creating a shipment

*Specimens to be shipped*

*Containers to be shipped*

*Shipment details*

## Receiving shipment

*Accept shipment and allocate storage*

## Ordering and Distribution

- Allows scientist to query for specimens of interest and place order.
- Allows ordering specimens, specimen arrays, tissue blocks from pathology reports.
- Tissue bank staff can view the order list and process the distribution.
- Generates distribution report which can be exported in CSV format.

## Biospecimen Ordering

**Biospecimen Ordering**

*Step1: Create specimen list*

*Step2: Provide Order title and protocol title*

*Step3: Provide order details*

## Biospecimen Distribution

*Order List Dash Board*

*Processing the distribution*

*Once distributed, report is generated which can be exported*

*Verify* *consents before Distribution*

## For More Information...

** ****The TBPT KC site- **
- _[https://cabig-kc.nci.nih.gov/Biospecimen/KC/index.php/Main_Page](https://cabig-kc.nci.nih.gov/Biospecimen/KC/index.php/Main_Page)_
** ****Log on and try out the demo site for caTissue Suite v1.1- **_[http://catissue.wustl.edu:8080/catissuecore/](http://catissue.wustl.edu:8080/catissuecore/)_** **
** ****For additional questions, post them to the KC Forum- **
- _[https://cabig-kc.nci.nih.gov/Biospecimen/forums/](https://cabig-kc.nci.nih.gov/Biospecimen/forums/)_** **