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.
  • 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