GenomeX Data Exchange FHIR IG, published by MITRE. This guide is not an authorized publication; it is the continuous build for version 0.2.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/CodeX-HL7-FHIR-Accelerator/GenomeX-DataExchange/ and changes regularly. See the Directory of published versions
GenomeX Data Exchange
| Official URL: http://mitre.org/gdx/ImplementationGuide/fhir.gdx | Version: 0.2.0 | |||
| Draft as of 2024-09-12 | Computable Name: GenomeXDataExchange | |||
Background
There is an ongoing need to expand and standardize genomic test results that are exchanged between laboratories, EHR vendors and other interested stakeholders. The work of the HL7 Clinical Genomics Working Group (CGWG) and their HL7 Genomics Reporting FHIR Implementation Guide (GRIG), to design and build, scalable FHIR genomics interfaces, is enabling the appropriate data to be sent to EHRs and genomics repositories.
The Genomics Reporting IG is a comprehensive guide, but is too broad for the specific needs of the GenomeX Data Exchange community. More specific guidance is needed to constrain the GRIG to meet the scope of the Data Exchange use case.
The Data Exchange effort differs from the work of the CGWG in its focus on real-world implementations. The emphasis is on providing a narrow scope which identifies the set of elements that are actionable and minimal for clinical use. This effort will begin with a starter set of elements that support the participating laboratories genomic test results for oncology focused reports. In addition to the FHIR specifications, this IG will also address the transport mechanisms and workflow-related guidance necessary for implementation in today's existing laboratory infrastructure, which is currently out of scope of the FHIR focused CGWG.
This FHIR implementation guide (IG) is intended to organize modeling guidance for consensus among the GenomeX Data Exchange community. It is not intended for ballot at this time, although it may be considered in the future. Parts of the documented findings in this IG may be incorporated into the GRIG in the future.
Scope
This first draft will focus on the following:
- Genomics Reporting FHIR IG 3.0.1
- mCODE STU 3.0.0
- FHIR R4
- a basic set of data elements usable by providers for diagnosis, treatment, and monitoring
- somatic tests
- oncology-related GRIG profiles - Tumor mutation burden (TMB) and microsatellite instability (MSI)
The following topics may include guidance but are not definitively in-scope at this time:
- therapeutic drug implications
- applicable clinical trials
- germline tests
- genomic operations
Assumptions and Caveats
To enable the work within the GDX use case, a set of assumptions and caveats were needed to allow the community to work on the more pressing issue of representing genomic testing data using the scope defined above. Those assumptions and caveats are provided below:
- EHR-Lab workflows may vary in a way that obviates the need for some data elements to be included in the report. For example, Some genomics reports will not include expanded patient demographics like name or date of birth. Rather, a patient-related identifier is provided that can be matched by an external system.
- Not all terminologies will be supported
Approach
The Data Exchange community is working to build traction for the use of FHIR to exchange genomic data in real-world settings. To enable members to bridge from their current workflows into the higher requirements laid out in the Genomics Reporting IG, this supplemental IG will provide a glide path to allow members to increase capabilities and conformance over the first few iterations. This version of the IG represents the initial state that is attainable by our members with a target state laid out for many of the data elements. The intent is to meet the minimum standards provided by the GRIG as quickly as possible.
The Data Exchange effort has put an emphasis on achieving real-world implementations to allow the Data Exchange community to deliver minimum viable products (MVPs) for their commercial offerings. This emphasis has encouraged the community to prioritize making tangible progress using currently available infrastructure and minimal data sets to accelerate commercial implementation. To that end two tracks of activities were undertaken as part of Data Exchange use case:
- payload
- transport
More specific details regarding the structure of the use case and the sub-groups can be found on the Overview page.
Genomic Data Payload
The payload sub-group focuses on developing the FHIR-based representation of the genomic test result reports. The sub-group develops consensus between the multiple report producers regarding the data elements that are critical for use when delivering reports for specific genetic testing categories. That consensus can range from indicating must support for the report receiver, to the code system best suited for a specific data element, to which data elements are required for genomic test result reporting.
Details for scope of content in the genomics report are described in Payload
Genomic Data Transport
The transport sub-group focused on the mechanism to exchange the FHIR payload between the sending and receiving systems. This group focused on identifying a transport mechanism that can be realized today given the available technology and infrastructure. The near-term solution relies on the HL7v2 ordering and resulting infrastructure that is currently available in labs across the United States.
Details for Transport are described in Transport Messaging
Dependencies
| IG | Package | FHIR | Comment |
|---|---|---|---|
  GenomeX Data Exchange FHIR IG | fhir.gdx#0.2.0 | R4 | |
 HL7 Terminology (THO) | hl7.terminology.r4#6.0.2 | R4 | Automatically added as a dependency - all IGs depend on HL7 Terminology |
| FHIR Extensions Pack | hl7.fhir.uv.extensions.r4#5.1.0 | R4 | Automatically added as a dependency - all IGs depend on the HL7 Extension Pack |
 Genomics Reporting Implementation Guide | hl7.fhir.uv.genomics-reporting#2.0.0 | R4 |
Package hl7.fhir.uv.extensions.r4#5.1.0 This IG defines the global extensions - the ones defined for everyone. These extensions are always in scope wherever FHIR is being used (built Sat, Apr 27, 2024 18:39+1000+10:00) |
Package hl7.fhir.uv.genomics-reporting#2.0.0 Guidelines for reporting of clinical genomics results using HL7 FHIR. (built Mon, May 9, 2022 16:52+0000+00:00) |
Global Profiles
There are no Global profiles defined
Cross Version Analysis
This is an R4 IG. None of the features it uses are changed in R4B, so it can be used as is with R4B systems. Packages for both R4 (fhir.gdx.r4) and R4B (fhir.gdx.r4b) are available.
IP Statements
This publication includes IP covered under the following statements.
- It is a condition of HGNC funding from NIH and the Welcome Trust that the nomenclature and information provided is freely available to all. Anyone may use the HGNC data, but we request that they reference the "HUGO Gene Nomenclature Committee at the European Bioinformatics Institute"
and the website where possible.Show Usage
- See https://clinicaltrials.gov/about-site/terms-conditions
for the Terms and Conditions that apply for use of ClinicalTrials.gov data.Show Usage
- The UCUM codes, UCUM table (regardless of format), and UCUM Specification are copyright 1999-2009, Regenstrief Institute, Inc. and the Unified Codes for Units of Measures (UCUM) Organization. All rights reserved. https://ucum.org/trac/wiki/TermsOfUseShow Usage
- This material contains content from LOINC. LOINC is copyright © 1995-2020, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license. LOINC® is a registered United States trademark of Regenstrief Institute, Inc.Show Usage
- This material contains content that is copyright of SNOMED International. Implementers of these specifications must have the appropriate SNOMED CT Affiliate license - for more information contact https://www.snomed.org/get-snomed or info@snomed.org.Show Usage
- This material derives from the HL7 Terminology (THO). THO is copyright ©1989+ Health Level Seven International and is made available under the CC0 designation. For more licensing information see: https://terminology.hl7.org/licenseShow Usage
- This material derives from the HL7 Terminology (THO). THO is copyright ©1989+ Health Level Seven International and is made available under the CC0 designation. For more licensing information see: https://terminology.hl7.org/license.htmlShow Usage
- Using RxNorm codes of type SAB=RXNORM as this specification describes does not require a UMLS license. Access to the full set of RxNorm definitions, and/or additional use of other RxNorm structures and information requires a UMLS license. The use of RxNorm in this specification is pursuant to HL7's status as a licensee of the NLM UMLS. HL7's license does not convey the right to use RxNorm to any users of this specification; implementers must acquire a license to use RxNorm in their own right.Show Usage
Credits
Our thanks to the contributors to the CodeX/GenomeX data exchange work stream which drive the guidance in this IG.