Flype: Integrating Molecular and Pharmacogenomic Results to Enhance Oncology Patient Care in a Community-Based Academic Cancer Center.

Background/

Objectives

We describe how our in-house bioinformatics platform, Flype, has evolved from being a variant repository to an enterprise role as an electronic medical record (EMR) content provider, powering molecular pathology reporting, pharmacogenomics reporting, sending discrete data to our EMR, aggregating internal and external molecular test results and powering our molecular tumor board (MTB).

Methods

In response to critical pain points, we developed Docket, a sample tracking system in Flype, which manages multiple individual in-house molecular tests for NGS assays, pharmacogenomic (PGX) assays and additional molecular testing. To help with interpretation and integration of all internal and external assays, we developed a clinical outcomes view in Flype. To improve the efficiency of our molecular pathologists reporting results, we developed Convo 2.0, which integrates OncoKB interpretations and other information. Flype can also be used by our pathologists to submit patient molecular results to NCI's ComboMATCH and retrieve clinical trial recommendations.

Results

Flype was used during our Kellogg Cancer Genomic Initiative for reporting PGX integration, MTB review and integration of EMR prescription information with internal and external molecular test results. Integrating PGX results led to several recommendations against the use of drugs metabolized by, for example, CYP2D6 or TPMT, along with warnings about altered pain relief. Enhancements in report sign-out and the use of file transfer scripts have led to reduced turnaround time.

Conclusions

Flype supports hundreds of users performing different roles in molecular diagnostics. We discuss lessons learned adapting our software to support continuously changing test requirements.