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Type:
Change Request
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Resolution: Persuasive with Modification
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Priority:
Medium
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Genomics Reporting (FHIR)
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STU3
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Clinical Genomics
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(profiles) [deprecated]
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Enhancement
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Compatible, substantive
Add text from Section 10.8 of Implementation Guidance document to either a new Overview section or existing 1.3 Sequenced Variants section. Suggest specifically this section:
STU3 moves beyond FHIR DSTU2 Standard Genetics profile on Observation allowing increased granularity and less ambiguity by creating a new resource to be called Sequence. This resource will be used to hold clinically relevant sequence data in a manner that is both efficient and versatile integrating new and as yet undefined types of genomic and other -omics data that will soon be commonly entered into health records for clinical use. Sequence will be leveraged by other FHIR resources, including Observation. This is consistent with how all FHIR resources are designed and used.
The September 2014 Informative Ballot ("HL7 Clinical Genomics, Domain Analysis Model: Clinical Sequencing Release 1") provided guiding use cases, which initially informed development of the initial Standard Genetics profile that is found in FHIR DSTU2. The same use cases also led to a second Project to develop a Sequence resource ("Develop FHIR sequence resource for Clinical Genomics"). A preliminary effort to address these issues has been explored and published in context of the [Substitutable Medical Applications and Reusable Technologies
http://smarthealthit.org/an-app-platform-for-healthcare/about/] (SMART) Platforms Project and described in an article ("[SMART on FHIR Genomics: Facilitating standardized clinico-genomic apps |
http://jamia.oxfordjournals.org/content/early/2015/07/21/jamia.ocv045.long]"). |
Sequence is designed to hold genetic sequences in blocks relevant to actionable clinical decision-making. Extensions to Sequence address complex cases and can associate it with repositories for retrieving a patient's full sequence data, such as those defined by GA4GH. Other changes include a suite of genetics profiles for other FHIR resources. In addition, the Observation-genetics profile adds new references so that an Observation can report genetics test results to be integrated into the EHR. There are also new genetics-extension profiles for DiagnosticReport, ProcedureRequest and FamilyMemberHistory, respectively, to extend them to report genetics results. We have given all of these FHIR genetics profiles the suffix "-genetics" (e.g. "DiagnosticReport-genetics profile"). New profiles on top of DiagnosticReport have been created for reporting HLA genotyping results.