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
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.
As with general genomics reporting, germline reports are centered around findings (variants, haplotypes, genotypes, biomarkers) and annotations derived from those findings (diagnostic implications, risk assessments). These constructs are assembled within the broader context of the Genomics Report, which generally contains information about the specimen(s), providers and organizations involved in the ordering and testing process. The report may also contain details about the genomic study analyses used to obtain the findings.
Some germline reports differ from typical genomics reports in patterns of structure and hierarchy. For example, prenatal reports indicate the risk of inheriting a genetic disease or defect depending on variants coming from two prospective parents. In such cases, genomic reports for multiple individuals are nested in a dependent structure so that results are still encapsulated by one single, overarching report.
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.extensions.r4#1.0.0
This IG defines the global extensions - the ones defined for everyone. These extensions are always in scope wherever FHIR is being used (built Sun, Mar 26, 2023 08:46+1100+11:00)
Guidelines for reporting of clinical genomics results using HL7 FHIR. (built Mon, Dec 18, 2023 22:39+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.
Copyright HL7. Licensed under creative commons public domain
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.
Most of the information on the CDC and ATSDR websites is not subject to copyright, is in the public domain, and may be freely used or reproduced without obtaining copyright permission.For information and exceptions regarding use of CDC material please see https://www.cdc.gov/other/agencymaterials.html.
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/TermsOfUse
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.
GenomeX Data Exchange FHIR IG
