Custom R Flexdashboard for molecular genetic pathology quality tracking

Abstract

The practice of modern-day laboratory medicine entails extensive, daily practice of tracking various quality metrics of every molecular test to ensure quality maintenance, as well as for laboratory management. While various third-party tools are commercially available, such represent a significant investment for publicly funded institutions. To automate aspects of this quality management, we developed a custom dashboard, written using R. We used R Studio, a freely available software, and employed the Shiny and Flexdashboard packages to develop the code base for the dashboard. Data for the dashboard were pulled from multiple Excel tracking spreadsheets for different clinical assays. The current dashboard allows for dynamic, automated reporting of case volume, and turn-around time, which are regularly reported metrics to CancerCare Ontario for reimbursement purposes. Workload tracking is also made possible, automating calculations regularly performed for billing purposes. The dashboard summarizes various quality metrics for each assay in a single table, viewable by multiple personnel within a single network. Additional features such as filtering quality metrics by date and customization of a variety of plots were also included. Whereas other informatics solutions may be available, our custom solution represents a low-cost system that alleviates a significant workload from various members of the laboratory medicine department, easing the currently significant administrative burden from the “hands-on” staff. Future work will be focused on further improving the accessibility of the dashboard and the integration of additional molecular assays for quality monitoring.