1. An End-to-End Donor Repository System in an Academic Environment
Kerry Wiles, Dr. Kay Washington
Department of Pathology, Microbiology and Immunology
Vanderbilt University Medical Center – Nashville, TN
Abstract
Materials and Methods cont.
Results cont.
Lifecycles
The Cooperative Human Tissue Network Western Division at Vanderbilt University Medical Center (CHTN-VUMC) is a federally funded prospective procurement service-oriented grant that provides high quality human specimens to researchers to accelerate the advancement of discoveries in cancer diagnosis and treatment. The CHTN provides biospecimens and associated data to academic and commercial investigators for research and development. The CHTN grant funding covers approximately 62 percent of operating costs with the remaining 38 percent being supported through cost recovery. Therefore, operations require that we streamline tissue and data collections to ensure that grant funds are used responsibly. This requires a robust and agile IT solution. Responding to the challenges and complexity of biospecimen data management, the CHTN-VUMC DQuest II application was built to cover all aspect of a tissue procurement workflow. This was accomplished by utilizing many existing informatics systems by leveraging Web Services technology. Traditional methods for integrating to other systems are typically tightly coupled, resulting in rigidity and difficulty in adapting rapidly to changing conditions. Web Services provide a mechanism to integrate with external systems in a loosely coupled manner, allowing functionality to be replaced, optimized or consumed in various ways without impacting the core functionality of the repository system. The resulting CHTN-VUMC DQuest II is a true end-to-end repository solution that provides mechanisms for improvements and enhancements, provides a reporting tool for metrics and provides investigators with the capabilities to access de-identified data in a variety of formats associated with their orders as well as manage their investigator request file to ensure their research dollars are spent responsibly.
The Donor 2 RESTful Services provide REST interfaces to the Donor Portal Application, GI SPORE LIMS (Laboratory Information Systems) and the ORMIS (VUMC Operating Room System). Diagram 1.
Invoice Search Service provides a search for Investigator Invoices based on the Investigator ID, Invoice ID or Shipment Date Range. This service returns a list of Invoices matching the given parameters.
File Retrieval Service accepts an Invoice ID and has endpoints to return Pathology Reports, Chart Reviews, Packing Slips, and Digital Slide Images. Files such as IRB documentation, CHTN Standard Operating Procedures, Scheduled tissue collection notifications, Shared Research Results and CHTN Investigator File documents and requests are available.
Specimen Search Service allows the GI SPORE Application to retrieve specimen data collected by the CHTN-WD.
Scheduling Service is an interface developed to isolate the DQuest II application from the underlying details of any scheduling system.
In additional to providing functionality through Web Services, the DQuest II application uses Web Services to retrieve information from third party resources as well. The CHTN Investigator System provides two SOAP Web Services, the Investigator Service and the Disease List Service.
The Investigator Service provides a list of approved CHTN investigators, the associated CHTN Division and the information associated with the investigator such as; primary address, lab address, contacts, shipping address and information, project details, IRB approvals and tissue requests.
The Disease List Service returns a list of diagnosis, categories, anatomic sites, and anatomic sub-sites. A list of valid combinations of these list items is also available.
The DQuest II application consumes SOAP services provided by the CHTN Investigator System, which was developed to provide an application for all CHTN divisions to manage investigators. This includes, but is not limited to, investigator requests, addresses, billing information, investigator status and primary division. A common disease vocabulary is also managed by the CHTN-IS. The CHTN-IS provides two SOAP Web Services, the Investigator Service and the Disease List Service.
The DQuest II Application provides RESTful Services to the Donor Portal Application, which is exposed outside the Vanderbilt network. Donor Portal provides a Web Application interface for CHTN-WD served investigators to retrieve files associated with specimens they have received. It makes us of the Invoice Search and File Retrieval services. The investigator is provided a login and password to retrieve information pertaining to their orders. This alleviates the need to transmit huge files through or physical media and allows for the data integration with their own LIMS in real time.
Screen Shot 4 Specimen Entry
Screen Shot 5 QAQC Submission
Screen Shot 7 Investigator Notification of Samples
Screen Shot 5 QAQC Submission
IT Procurement Lifecycle
Study participants are identified by the collaboration of the treating clinician or surgeon and scheduled for surgery.
The patient is identified on the Operating Room Schedule within our DQuest IT system and a consent decision is rendered and the patient appears on the scheduled collection page for planned collections (Screenshot 1).
Procurement personnel can add notes regarding the possible collection, donor parameters such as tumor size, grade (Screenshot 1, #1), indicate a reason if collection did not occur (Screenshot 1, #2), and select a workflow (Screenshot 1, #3).
Consent record is captured (Screenshot 2) and managed and patient history is captured (Screenshot 3).
Specimens enter the surgical pathology suite to be evaluated, patient diagnosis obtained and then research specimens are distributed to the biorepository and entered (Screenshot 4). Specimens are assigned a “status” as they move through the Biorepository to ensure quality (Screenshot 5 and 6). Specimens that fail any status are reported in an online error-reporting module, hosted within the application. This audit trail allows us to review error-reports by area of operation and by category (Minor, Major or Critical) and make determinations to revise SOPs, retrain staff or re-evaluate the work process.
Investigators are notified of procured specimens (Screenshot 7) and orders are scheduled and shipped by assigned CHTN staff (Screenshot 8).
Investigators are provided a user name and password to the secure “Donor Portal” (Screenshot 9) to download or view the orders associated with their account and the specimens details, final pathology reports, chart reviews and other features, such as searching for investigators who may have received the same donor and submitting a request to share research results, view CHTN SOPs or view surgery schedules (de-identified) and notify the CHTN procurement technicians if interested in a particular surgery which may yield specimens required for their research.
Screen Shot 8 Specimen Shipping
Screen Shot 9 Donor Portal
Introduction
Biorepository solutions are often large monolithic applications, incorporating functionality for all business functions required to collect, manage and distribute different types of human specimens and associated clinical data. Often times, the biorepository tries to not only provide the collection data associated with the biorepository, but also the research and results arm of the institution. Often times the result is a large, complex system with little code documentation and platforms that do not support modern upgrades and are not secure.
The biorepositories core offerings and function become lost with the institutions and investigators personal research needs.
Responding to the challenges and complexity of biospecimen data management, the CHTN-VUMC DQuest II application was built to cover all aspects of a tissue procurement workflow. This was accomplished by utilizing many existing informatics systems by leveraging Web Services technology. Traditional methods for integrating to other systems are typically tightly coupled, resulting in rigidity and difficulty in adapting rapidly to changing conditions. Web Services provide a mechanism to integrate with external systems in a loosely coupled manner, allowing functionality to be replaced, optimized or consumed in various ways without impacting the core functionality of the repository system.
Conclusion
Today, the ability to seamlessly exchange information effectively is vital for the success of any Biorepository. Existing investments in systems development and infrastructure can be combined to add additional value to mission-critical application. Web Services automate connections across applications offering an alternative approach far more flexible than traditional methods. The DQuest II application is a state of the art application providing a level of functionality that would not have been possible without leveraging many existing systems. DQuest II provides a level of integration for clients that would not be possible without Web Services. Web services hold the promise of integrating software application from heterogeneous platforms in a simple, standardized manner. The resulting DQuest II Biorepository management system will allow the end-user to be shielded from all the complexity of interacting with the various resources and also allow organization to quickly reap the benefits of this powerful technology.
Results
Biospecimen management complexity escalates when systems need to connect to multiple external systems, thus making it difficult for any out-of-the-box solution to work effectively for our biorepository. CHTN-VUMC has designed a suite of products that can be used to both manage the investigator and their requests as well as a system to manage: consent, solid tissue and bio-fluid procurement, QAQC procedures, shipping, invoicing, auditing, error reporting and file retrieval.
The design and agile development of our IT system has allowed us to quickly transform an idea to workable product, maintain security and institutional regulations and streamline operations to operate as lean as possible.
The CHTN-VUMC DQuest II application utilizes Web Services to reap significant business benefits, more flexibility and more leverage in terms of accessing third party resources, providing functionality that may not have been possible due to time and money constraints. By consuming external Web Services, the DQuest II application can easily integrate with CHTN investigator information, CHTN Disease List Vocabulary and VUMC Operating room scheduling system. More broadly, functionality behind a Web Service interface can be replaced or changed without affecting the DQuest II system itself.
Screen Shot 1 Participant ID and Decision
Screen Shot 2 Consent Record
Materials and Methods
The DQuest II Web Services, developed for the CHTN Western Division at VUMC, make use of two leading Web Service standards to integrate the Donor 2 application with other systems, regardless of platform or programming language.
SOAP: XML representation of requests and responses
RESTful: Incorporates standard HTTP Methods to respond to requests. REST responses can be XML, JSON (JavaScript Object Notation), Plain Text and other various representations.
Acknowledgements
Screen Shot 3 Patient History
We thank the CHTN VUMC staff for their efforts and support: Erik Brooks, Kiley Wease, Ying Jin, Manu Manrao, Stephanie Shelton, Brittney Fain, Grace Ordung, Linda Sircy, Bob Burnell, Alle Crider, Regina Jenkins, Kelsey Shaffer and former CHTN staff member Matthew Clement.
This project was supported by NCI/NIH 1UM1CA