Short Description

The purpose of this track is to validate the exchange of genomics reporting data from a genomics lab information system to consuming healthcare applications.


Long Description

The activities in this track will help inform implementation considerations for data exchange. The track will involve an analysis of the minimal set of data elements needed in genomics data exchange for the purpose of diagnosis, treatment, and monitoring. 

This track will also provide an "on-ramp" opportunity to learn about how genomics data is represented in FHIR and how to search and retrieve FHIR-based genomics reporting data. Basic knowledge of FHIR is also necessary but the on-ramp activities may be accomplished with or without the use of development or programming tools. Knowledge of basic genomics concepts is also highly preferred, but introductory materials could be provided to learn enough to participate in on-ramp activities.

Type

Test an Implementation Guide

Related Tracks?


Call for participants

Representing organizations:

  • EHR Vendors
  • Laboratory Information Systems
  • Health systems

Roles/Skills:

  • Clinical SMEs
  • Clinical informaticians and Bioinformaticians
  • Software architects and developers
  • Systems Integrators

Track Prerequisites

Basic knowledge of

  • FHIR - navigating a FHIR specification and implementation guide
  • Genomics data standards, code systems, and nomenclatures

Track Lead(s)

May Terry , Srikar Chamala  

Track Lead Email(s)

mayT@mitre.org, schamala@chla.usc.edu

Specification Information


Zulip stream

https://chat.fhir.org/#narrow/stream/179197-genomics/topic/CG.20Connectathon.20Track

Track Kick off Call

Kick-off call will be held April 25, 2023, 11-11:30am ET. 

Track kick-off slides here. 

Track kick-off recording here. 

Specification Information

HL7 Clinical Genomics Reporting Implementation Guide (Continuous Integration Build) 

System Roles

  • EHR (order from clinician/specialist) or clinical application
  • Laboratory Information System (LIS)
  • Integration or translation engine - it is possible that this could be co-located in either the EHR or the LIS.

Testing Scenario:

Day 1 Track Introduction slides here. 

Scenario: Determining the actionable and minimal set for genomics discrete data elements

Actors:

  • Lab Information System (LIS1)
  • FHIR Server (FS1) - receives resources from the reference lab; receives requests from clinical application clients and returns resources.
  • Clinical application (CA1) - an application such as an Electronic Health Record (EHR) or clinical portal which accepts genomic test results for the end user. CA1 could use that data to display to the patient, or further process discrete data from the results for decision support.
  • End-User (EU1) - a person who views the results for the purpose of diagnosing, treating, and monitoring patients.

Pre-Requisites:

Activities

Participants engage in one or more activities in the scenario below.

Activity #1: Identify and implement an actionable and minimal set of genomics data elements to include in a genomics report

A genomics reference lab will analyze their own internal genomics reporting data representation, identify the elements that could be structurally and semantically mapped from their system, and create an example FHIR instance that conforms to the HL7 Clinical Genomics Reporting Implementation Guide.

Action:

  • a starter list of minimal elements in a genomics will be provided in a spreadsheet.
    • Starter set examples of at least 3 somatic reports translated from proprietary format to FHIR will be shared.
  • LIS1 participants
    • will use this starter list as a guide to translate/convert their proprietary reports to FHIR and post to the FHIR server (FS1).
  • CA1 participants
    • will be given a list of patients (name and stable identifier) ahead of time to either configure in their system or to use in their request for their genomic reports.
    • will use this data to query and retrieve the patient's genomic reports.
    • will parse the FHIR resources necessary to process in their client application.

Success Criteria:  

  • LIS1 actors will have generated genomics report FHIR examples that successfully validate against FHIR validation tools.
  • CA1 actors will be able to parse the following FHIR resources:
    • Core FHIR resources:
    • FHIR resources that conform with the genomics reporting IG profiles:
      • GenomicsReport
      • Variant
      • DiagnosticImplications
      • TherapeuticImplications
  • Clinical SMEs in attendance will confirm that the data represented in a set of FHIR resources is useful in the diagnosis, treatment, and monitoring of patients with a certain clinical condition.

Participants and observers in this track will provide feedback on the IG.


TestScript(s):

To be determined.


Security and Privacy Considerations:

At this stage, security and privacy are not a focus.  The objective is to test the data structures and workflows and get implementers comfortable using FHIR.  Security layers will be folded in as part of future events.