caTissue Suite 1.2 TPBT Face to Face Michelle Lee, MBA, Ph.D. Ian Fore, D. Phil. December, 2009

2 Agenda High Level Objectives of caTissue 1.2 What’s new Create new services Integrating with existing services Integrate with PSC, C3PR, caArray, BRD Implement CBM Enhancements Community involvements

High Level Objectives Improve interoperability of caTissue Suite with caBIG tools/applications and other biospecimen informatics systems Integrate caTissue Suite with caBIG Clinical Trial Suite, caArray, and Biospecimen Research Database Improve caTissue Suite Usability Improve caTissue Suite Performance, scalability and reliability Improve caTissue Suite Security 3

Interoperability Integrate with other applications/tools through services Create new services, i.e. A suite of Biospecimen Services, Specimen Id Service Integrate with existing services, i.e. COPPA Coordinate with other groups to create and integrate new services, i.e. Subject Management, Subject Scheduling, Planned Calendar, Scheduled Calendar. 4

Interoperability Architecture graph of caTissue 1.2: specify that caTissue, caArray, CTS will use SMS, COPPA services. 5

6 Specimen Management Services SMS Family will provide the core services for specimen management for both clinical and research areas. Specimen Service Family’s capabilities provided include: Collecting, processing, storing, tracking, ordering, and distributing specimen Management Annotation Reporting etc. They fit into different layers of the NES service periodic table. They may use other services. ESST Sf Specimen Family N/D SMS will provide the core specification for specimen management from both the clinical and research perspectives regardless of the nature of specimen transactions that occur or the type of specimens involved in the transaction. O Organization R Registration C Correlation Sc Schedule P Person Su Subject Mgmt Sc Specimen Collection So Specimen Ordering S Specimen Sd Specimen Distribution Sp Specimen Process Sa Specimen Annotation Si Specimen Id Sc Container Mgmt

7 Specimen Id Service Each biospecimen must be identified uniquely to promote tracking its comprehensive life history and its derivatives across multiple sites. The goal is to glue specimens and their related entities across multiple sites/applications, so they can interoperate. It may use Id Mgmt service. Responsibilities: Global Unique Id management High Availability Mgmt Inventory Mgmt Batch Processing Ancestral Relationship Mgmt (all the way to patient global id.) ESST Si Specimen Id Service N/D Batch process High availability mgmt Inventory Mgmt System Relationship tracking Batch process High availability mgmt Inventory Mgmt System Relationship tracking Si provide services to global unique ids for specimen. Id Management

C3PR invokes Subject Service to register a patient A subject is being considered for study registration for which a central pathology review is required to determine eligibility (or any other protocol-specific central review requirement). When a CRA (Clinical Research Associate) uses C3PR to pre-register the patient, C3PR invokes the Subject Registration Service to pre- registers the patient and give the patient a unique patient identifier by utilizing Id Management service. Then, specimens are collected, labeled and sent in a protocol-specific kit to a central laboratory which is using caTissue. The central laboratory personnel use caTissue, which in turn uses Biospecimen Service to collect and process the tissue according to collection protocol. The status and results are stored in the specimen service data storage. When CRA uses C3PR next time, C3PR will get the process result from Specimen Service. If the results indicate that the subject is eligible, the CRA registers the subject on the study. Otherwise, the subject registration for this patient is cancelled. Use Case 1: Services Connect caTissue & CTS – Pre-Registration 8 caTissue Chinese Tissue Tool Specimen Service Specimen Id C3PR PSC Subject Registration Scheduled Calendar COPPA 1: Pre – register Patient 2: Pre-register patient &Create Patient Id 3: Process Specimen 3: Collection Protocol 4: Get specimen process Result; Register Patient

Use Case 2: Services Connect caTissue & CTS – Study Calendar C3PR invokes Subject Service to register a patient When a subject is registered to a study, there will be a subject-specific study calendar created. All activities planned for this subject on the study will be displayed to the Clinical Research Associate (CRA). The CRA reviews and validates this information in PSC and activates the study calendar event at the appropriate time. When the patient arrives the pathology lab for the tissue collecting. caTissue will query the specimen collection request from subject scheduling service and collecting specimen according to requirements. It will update the patient registration service status when it is done. PSC will get updated status and move to the next step of the study. 9 caTissue Chinese Tissue Tool Specimen Service Specimen Id C3PR PSC Subject Registration Scheduled Calendar COPPA 1: CRA review & activate PSC 5: CRA get Specimen Collection Status and move to the next step 3: Get Specimen Collection order from Scheduling Srv. Update the status when it is done 2: Activate PSC event 4: Update event status

Structured Standard Operating Procedure (SOP) Structured Standard Operating Procedure A series of defined steps that dictate how to procure or process biospecimens. E.g. tissue collection protocols, surgical procedures used to obtain a biopsy or tissue resection, protocols to isolate DNA or RNA from primary biospecimens. 10

BRD Biospecimen Research Database, supported by OBBR Identify best practices in biospecimen procurement and processing so as to minimize experimental bias. Best practices will be documented as SOPs in BRD to use in clinical trials and collection protocols. Store and share SOPs in structured data. Provide services for consumers to query, import and manage SOPs. 11

Integrate with BRD Query a list SOPs from BRD according to specified criteria e.g. identify SOPs to procure protein samples with minimal alteration to phosphorylated sites find SOPs to purify high quality RNA from paraffin sections Query structure data details for a SOP from BRD Import SOPs from BRD 12

Manage SOPs in caTissue Manage and represent SOPs associated with individual collection protocols Capture information when biospecimens are procured as per the SOP Capture information when biospecimens are collected with deviations to one or more variables in the SOP Create, Read, Update SOPs in caTissue Expose SOPs as grid service 13

Use Case 3: Integrate with BRD Integration graph with BRD: caTissue and BRD will integrate using web services/grid services 14 caTissue Specimen Service Specimen Id BRD SOP Service A PI search for SOPs Import a selected SOP Show SOP list and detail data Import SOP Local SOP template is created A Scientist search & view SOPs Available through Grid Services

Integrate with caArray Export annotations for selected specimens to MAGE-TAB format for eventual linkage with microarray experiment information Import to caArray. 15

Enhancements Enhance existing architecture. User configurable workflow to fit specific business needs for different organizations Improve usability Improve performance Improve the capacity and scalability Security Enhancements Provide more grid services Address grid compatibility of Dynamic Extensions. 16

Configurable Workflow Configure page flow to support all types of tissue banking workflows. This ranges from simple use cases required by smaller repositories to more complex multi- site repositories across an organization. Single page specimen entry 17

Improve Usability Fix major defects reported by community Google-like keyword search allows users to perform free text searches on the caTissue database. Auto prompted dropdowns Improve screen layout, auto scale Dynamic screen layout auto show or hide certain fields according to the value of other fields. Avoid page refresh Improve visual effect (font, color, layout) … 18

Others Features Bulk operations: legacy data migration, bulk disposal, bulk participant registration, bulk transfer, bulk specimen edit, etc. Edit collection protocols, Enhance summary page, Direct distribution User based dashboard 19

Tentative Service Schedule Tentative service schedule different services that might be used by caTissue. This is the tentative schedule for services in caTissue 1.2 and services they might depend on.

Engaging Communities Engaging Different Adopters caTissue institutional adopters Center deployment adopters SPORE adopters Adopters at large Channels Site visits Screenshot, prototype reviews Usability study Forum Knowledge Center Workspace meetings, CDL meetings … 21

Questions? 22