1. of Pathology Specimens for the VA Precision Oncology Program
Implementation of an Informatics Solution to Improve Management
of Pathology Specimens for the VA Precision Oncology Program
Danne C. Elbers MS, Robert B. Hall MS, Beth J. Katcher BS, Svitlana diPietro BS, Sung Feng-Chi MS,
Sergey D. Goryachev MS, Karen E. Pierce-Murray RN BA, Corri L. DeDomenico BS,
Lauren MacMullen BS, Helene Garcon MD, Nhan V Do MD, Louis D. Fiore MD
MAVERIC, VA Boston Healthcare System, Boston, MA
OVERVIEW
The Veteran Affairs (VA) Precision Oncology Program (POP) is a clinical care effort intended to bring personalized health care and cutting edge cancer treatment to Veterans by sequencing tumor samples. The program includes a research component (RePOP), which consents patients to share their clinical, genetic and imaging data. Program staff initially relied on MS Excel and InfoPath to handle the activities to identify patients diagnosed with cancer, track pathology samples with vendors, and enroll Veterans into the RePOP cohort.
As the program expanded across the VA a more scalable informatics approach was required to better manage current and future functions of the POP program. To meet these requirements we developed a workflow software application in-house called ProjectFlow with the VA Informatics and Computing Infrastructure (VINCI) group to manage this and other research activities. For the implementation we created an integrated system consisting of a database model, web services, stored procedures, ETL’s and workflows adhering to the BPMN20 standard.
REQUIREMENTS
Figure 3: High level system design
Streamline and facilitate business operations.
Capture data and track history for a large number of specimens and patients.
Provide ability to scale, grow and evolve.
Manage and improve accuracy of data for reporting, auditing and analysis purposes. .
RESULTS
The ProjectFlow application for POP was deployed in August of To date pathology specimens have been managed through the application among 55 sites. A series of reports and graphs have been generated from the POP data repository utilizing reporting services. On October 3rd 2017 the ProjectFlow application for RePOP was deployed. Since then 16+ patients have successfully completed the consent workflow.
SYSTEM DEPLOYMENT
BPMN20 workflows were designed for the ProjectFlow application to capture the attributes associated with the clinical and research operations, see figure 1. To keep our clinical (POP) and research operations (RePOP) separate, two ProjectFlow instances were deployed. A view from the POP database was placed in the RePOP database for easy unidirectional movement of eligible patients from POP to RePOP, see figure 2. For each instance and to assist the workflows in their execution a SQL relational database model was developed as well as stored procedures and a web service (PnP) to validate ProjectFlow’s input before storing data through stored procedures in the database schema, see figure 3. In addition to this we created a scheduled ETL that queries pathology electronic health records for VA Region 4 based on SNOMED and ICD codes and incorporated them into the POP database as a starting point for specimen identification.
CONCLUSION
The development of the ProjectFlow application demonstrates how a structured Informatics solution can facilitate and improve business operations in the precision medicine arena. The application allowed our developers to streamline business operations for the POP and RePOP program with less data errors and improved reporting and querying capabilities. Our workflow application provides a scalable approach that can handle a large number of pathology records and consents, and is extendible for modifications and additions. The team overcame challenges with incorporating VA pathology data and CDW patient records into the application. Our team continues to integrate with the POP and RePOP operations staff to improve and develop novel ways to implement new workflows, integrate more VA healthcare data, and enhance system usability.
Future plans involve real time tracking of the patient’s vital status for RePOP and the expansion of the ETL to query specimens beyond VA Region 4.
Figure 1: POP workflow to track specimens send out for sequencing
ACKNOWLEDGEMENTS
Funding was provided under the VA Cooperative Studies Program Study #2010. ProjectFlow was developed in collaboration between MAVERIC and the VA Informatics and Computing Infrastructure (VINCI).
The contents do not represent the views of the U.S. Department of Veterans Affairs or the United States Government.
Figure 2: Unidirectional patient flow from POP to RePOP