Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-ballot built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

Change Log

Page standards status: Informative

Version = STU3

  • FHIR version: 4.0.1

Summary of updates

  • Introduction of new operations along with extensive implementation guidance and examples. Refer to here for details.
  • Addition of support for GenomicStudy to capture structed, study level metadata. This is back porting a resource introduced in R5 as a set of profiles, code systems, and value sets into this R4 based IG. This includes structured extensions to capture region studied details, and the existing profile was removed. See here for more information.
  • Broadening support for biomarker observations by introducing a new, more generic MolecularBiomarker profile, along with refactoring existing profiles and examples. Explore the new profile here.
  • Improved guidance on the Somatic Reporting page, including a detailed synthetic report and additional example instances. See the new page here.
  • Update in the representation of molecular consequences through the creation of a new Molecular Consequences observation profile that is treated as an Implication. This is a non-passive change, as several Variant(Observation).component and DiagnosticImplication(Observation).component slices were moved to the new profile. See here for the new profile. A list of changes includes:
    • Variant
      • rename component:coding-hgvs to component:representative-coding-hgvs (same LOINC code)
      • rename component:transcript-ref-seq to component:representative-transcript-ref-seq (same LOINC code)
      • rename component:protein-hgvs to component:representative-protein-hgvs (same LOINC code)
      • delete component:amino-acid-change-type
      • move component:molecular-consequence to Molecular Consequence profile, renamed component:feature-consequence
    • DiagnosticImplication
      • move component:functional-effect to Molecular Consequence profile
  • Support repeat expansions on the Variant profile. See here for guidance on the new slices.

Trackers

JIRA                 Summary
FHIR-25170 Send related artifacts at the Observation.component level
FHIR-28943 Introduced new MolecularBiomarker artifacts
FHIR-31030 Add pattern for GenomicReport.code for LOINC 51969-4
FHIR-31506 Add genetics category to observation profiles
FHIR-32101 Observation.component to capture variant inheritance basis
FHIR-32696 Improved somatic reporting guidance
FHIR-34418 Support repeat expansions
FHIR-35864 Add GenomicStudy to support study-level metadata
FHIR-36041 New operations, additional guidance
FHIR-37892 Add phase data to find subject variants operation
FHIR-37893 Add ranges parameter to subject phenotype operations
FHIR-40320 Create a new MolecularConsequence profile
FHIR-40805 Support copy number range and decimal in Variant profile
FHIR-41245 Merge predicted-therapeutic-implication slice into therapeutic-implication
FHIR-41246 Remove prognosis slice from implications, and prognostic-implication TBD code
FHIR-41247 For therapy- and medication-assessed extensions, move extensions to corresponding component slices
FHIR-41248 Add region studied meta data to Genomic Study and remove existing profile
FHIR-41355 Add new molecular consequence phenotype operations
FHIR-41587 Additional meta data for Genomic Study for regions: studied, called, uncalled
FHIR-41610 Guidance for consistently representing Variant value (especially for pertinent negatives)
FHIR-42850 Cleanup guidance for star alleles
FHIR-43574 Resolve discrepancies on Somatic page
FHIR-43517 Enhance somatic table of examples
FHIR-43744 Add additional GenomicStudyAnalysis metadata
FHIR-43745 Advance several GenomicStudyAnalysis value sets to Preferred
FHIR-45434 Add clarity to representation of Significance and Evidence in implication profiles
FHIR-43691 Remove Overall Interpretation profile and provide guidance for GenomicsReport attributes for conclusion and conclusionCode.
FHIR-43745 Advance several GenomicStudyAnalysis value sets to Preferred