Abstract
Objectives Pharmacogenomics (PGx) is often considered a low-hanging fruit for genomics–electronic
health record (EHR) integrations, and many have expressed the notion that drug–gene
interaction checking might one day become as much a commodity in EHRs as drug–drug
and drug–allergy checking. In addition, the U.S. Office of the National Coordinator
has recognized the trend toward storing complete sequencing data outside the EHR in
a Genomic Archiving and Communication System (GACS) and has emphasized the need for
“pilots that test Fast Healthcare Interoperability Resources (FHIR) Genomics for GACS
integration with EHRs.” We sought to develop a PGx clinical decision support (CDS)
service, leveraging the emerging FHIR and CDS Hooks standards, and based on an assumption
that pharmacogene sequencing data would be stored alongside the EHR in a GACS.
Methods We developed a PGx CDS service as a functional prototype. The service is triggered
by a medication order in the EHR. When evoked, the service looks for relevant genetic
data in a GACS and returns corresponding recommendations back to the ordering clinician.
Where the patient has no genetic data on file, the service can recommend pretreatment
genetic testing where applicable.
Results Overall, we were able to meet our objectives and deploy a functional prototype, interfaced
with a commercial EHR. We identified several areas where FHIR or CDS Hooks lacked
necessary semantics or have implementation ambiguity. Primary FHIR challenges included
multiple ways to say the same thing, which exacerbated the complexity of variant to
allele conversion and lack of representation of deoxyribonucleic acid region(s) studied.
Primary CDS Hooks challenges included the complexity of executing an authenticated
query against one system (GACS) upon being triggered by a different system (the EHR),
and limitations in the types of actionable recommendations that can be returned to
the EHR.
Conclusions In conclusion, we have found that PGx CDS based on FHIR and CDS Hooks appears to
represent a promising means of genomics–EHR integration. More real-world testing along
with a set of use-case driven GACS interface requirements will push us closer to the
U.S. National Human Genome Research Institute vision of a plug-in PGx app.
Keywords
pharmacogenetics - pharmacogenomics - HL7 - FHIR - CDS hooks - clinical decision support
