Incorporation of externally generated next-generation tumor genotyping into clinical and research workflows: Successes and lessons learned.

Abstract

156 Background: The future of oncology will increasingly utilize information about tumor genomics. A growing number of tumor subtypes require genomic information as standard of care to inform treatment decisions. Clinical decision support (CDS) systems are able to improve healthcare and ensure best practices, but rely on machine-readable data. Typically, 3rd party genotyping results are returned in PDF reports that are not computable for standard presentation, CDS, or research purposes. Proposed oncology CDS platforms (such as CancerLinQ) will require computable tumor genomic information. Methods: A 3rd party CLIA-certified laboratory performed targeted exome tumor sequencing for a subset of cancer patients seen at Vanderbilt University (VUMC). The variants considered “actionable” were packaged into a standardized extensible markup language (XML) message and transmitted securely to a clinical server on a daily basis; the full PDF report was also transferred electronically. These messages were automatically received and parsed to match patients and display mutation data in their electronic medical record (EMR) for clinicians. This information was also placed into the VUMC Research Derivative (see Danciu et al. J Biomed Inform 2014 for more details). Results: The XML message, including specimen metadata, was successfully created by the 3rd party lab and received by VUMC after an iterative testing process was conducted. Clinicians were notified automatically when results were ready, within their EMR workflow. Because the primary purpose of the test is clinical, variants of unknown significance were not included in the XML transfer (these were however available in the PDF report). Conclusions: To our knowledge, this is the first demonstration of the automated incorporation of tumor genotype information from a 3rd party lab into a clinical EMR. Electronic transfer of genotype data enables rapid consumption of results by clinicians within their standard workflow, passive CDS (e.g. pointers to external knowledge bases), active CDS (e.g. standard and clinical trial treatment recommendations), and secondary use: all activities that improve the quality of cancer care.

Pragmatic precision oncology: the secondary uses of clinical tumor molecular profiling

“…While there exists an HL7 V2.5.1 standard for the transmission of some clinical genomic results, the use cases for molecular profile reporting are not implemented widely. 10 Previously, we have described a clinical transmission system of tumor molecular profiling reports from a thirdparty sequencing laboratory into an EHR 11,12 for real-time clinical practice. In addition, this structured data feed allows molecular results to be parsed, restructured, and stored into a database that can be used to further inform the science and practice of precision oncology.…”