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201905 Clinical Genomics

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Clinical Genomics Track

Zulip Chat

The Zulip Chat will be used to coordinate among participants during the connectathon:

Submitting WG/Project/Implementer Group


Genomic data are of increasing importance to clinical care and secondary analysis. After initial Feedback from the first ballot of the Clinical Genomics Implementation Guide, considerable updates have been made, and the recently balloted IG and profiles should be tested in the Connectathon for more feedback and trial use.

Track Lead

Gil Alterovitz

Expected participants


FHIR Client

Support the sending of the MolecularSequence resource and genetics profiles operations: create, history, read, search and update.

FHIR Server

Support the receiving and processing of the MolecularSequence resource/genetics profiles operations: create, history, read, search and update.


This represents the main areas of interest in the recent connectathon. A couple new use cases may be considered as approved by the CG workgroup and time permits.

Scenario 1 Registering New IG-compliant Resources

Action: (FHIR Client) Creates FHIR genomics resources compliant with the Implementation Guide and sends them to the (FHIR Server).
Precondition: The instances do not exist in server prior to action.
Success Criteria: Instances created correctly on server and in the desired format.
Bonus point: Resources tailored to individual use cases can be sent and received, validating and generating further examples for the IG. Additionally, automated conversion of genomic data from other sources (eg V2, VCF) can be tested.

Scenario 2 Querying FHIR Resources/GACS Operations

More on Scenario 2 and the Clinical Genomics, Release 1, July 2018 Informative Publication

Action: Following use cases outlined in the DAM, (FHIR Client) queries (FHIR Server) for relevant compliant genomic resources.
Precondition: Relevant resources and query methods are supported in FHIR Server.
Success Criteria: Appropriate bundles of genetics resources are returned.
Bonus point: Server can explore GACS operation functionality, including on-demand conversion to FHIR.

Scenario 3 EHR Integration with PGx using CDS Hooks

This scenario demonstrates an implementation of CPIC Pharmacogenomic Guidelines [1] based on FHIR, CDS Hooks [2], and genomics results formatted per our latest HL7 FHIR Clinical Genomics Reporting guide [3]

Action: In this scenario, a medication order arises in the EHR (which is also a CDS Hooks client), triggering a notification to a PGx CDS Service (which is also a CDS Hooks server). The "medication-prescribe" hook also provides the PGX CDS Service with a FHIR Medication resource that includes an RxNorm code for the ordered drug. Having been triggered by the “medication-prescribe” CDS hook, the PGx CDS Service now executes a decision support rule that [1] determines if the ordered drug has a known gene interaction; [2] determines, where there is a known drug-gene interaction, whether or not the patient has genetic test results on file; [3] determines, where there are genetic test results on file, if the patient has an interacting genotype; [4] determines, where there are not genetic test results on file, if the patient needs pre-testing. The PGx CDS Service returns a CDS hooks “suggestion card” back to the EHR, with appropriate recommendations.
Precondition: Genomic observation(s) are available for some patients.
Success Criteria: Retrieve relevant observations (variants, haplotype, genotype, etc) on a pharmacogene where they exist.
Bonus point: Correctly identify that there are no observations for the gene in question.


The supporting TestScripts and corresponding fixtures have been committed to the FHIR documents Github repository at:

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