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201901 Clinical Genomics

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Clinical Genomics Track

Zulip Chat

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

Zulip Chat

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.

Proposed Track Lead

Gil Alterovitz, Patrick Werner

Expected participants

Gil Alterovitz, James Jones, Kevin Power ...


FHIR Client

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

FHIR Server

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


Register a New Sequence and Observation

Register a New Genomics Report

Scenario 1 Pharmacogenomics

Scenario 2 Clinical Sequencing - Germline Testing

Scenario 3 Family Member History

Scenario 4 Clinical and Research Data Warehouses

Scenario 5 HLA Typing

Scenario 6 Comprehensive Pathology Report

PGx CDS Scenario

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]

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.

A swim-lane overview of the scenario is here ('GACS' is a Genomic Archiving and Communication System, used to store genomic test results):


What else?


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