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Overview

  • Cancer-related genomics sequencing related diagnostic results.
  • The mCODE genomics profiles are intended to be a minimal subset of the HL7 Clinical Genomics (CG) Reporting IG, where possible.
    • Genomics changes were significant between mCODE 0.9.1 and mCODE 1.0 in order because of this alignment and feedback from the HL7 Clinical Genomics Working Group (CGWG).
    • CG Reporting IG STU2 release will potentially cause breaking changes with mCODE due to change of bindings to the Genomics SequenceOntology standard.
  • Genomics coding systems are the loosest ones in mCODE because of the many coding standard and knowledge base variations that exist in clinical genomics.

Profile: CancerGenomicsReport 

http://hl7.org/fhir/us/mcode/StructureDefinition-mcode-cancer-genomics-report.html

  • Base FHIR Resource: DiagnosticReport
  • Derived from: USCoreDiagnosticReportProfileLaboratoryReporting
  • Description: Genetic analysis summary report
  • mCODE-specific Attribute Constraints:
    • Code fixed to LOINC#81247-9 “Master HL7 genetic variant reporting panel”
    • Category fixed to v2-0074#GE “Genetics”
    • subject reference restricted to (Cancer Patient)
    • specimen reference restricted to (Genetic Specimen) and is must support
    • basedOn reference restricted to (ServiceRequest | CarePlan)
  • mCODE-specific Extensions: none
  • mCODE-specific Slices:
    • category sliced to conform to CG Reporting IG GenomicsReport as well as US Core Diagnostic Report profiles
    • result sliced to CancerGeneticVariant and GenomicRegionStudied
  • mCODE-specific ValueSets: none

Other Notes of Interest: 

  • Some molecular markers may be represented with either TumorMarker or the Genomics profiles
    • The primary decision to separate both TumorMarker and Genomics was pragmatically driven based on how some prognostic molecular marker results are sent by reference labs today.
    • TumorMarker represents tests for substances found in tissue, blood, or other bodily fluids
    • The Genomics profiles represent tests that measure DNA, RNA, or chromosomal changes
  • Genomics sequencing tests can contain groupings of multiple tests and panels of tests. Since groupings of genomics panels in a greater report is complex and currently evolving in CGWG discussions, mCODElimited it to one test to keep it minimal and simple.  mCODE could potentially change this for a STU2 release depending on mCODE TRG review and scoping.

Profile: GeneticSpecimen

http://hl7.org/fhir/us/mcode/StructureDefinition-mcode-genetic-specimen.html

  • Base FHIR Resource: Specimen
  • Derived from: USCoreSpecimen
  • Description: Genetic analysis summary report
  • mCODE-specific Attribute Constraints:
    • Type is must support
    • Collection.bodySite is must support
  • mCODE-specific Extensions:
    • mcode-laterality is must support
  • mCODE-specific Slices:
    • none
  • mCODE-specific ValueSets:
    • Type is bound to Genetic Specimen Type Value Set (preferred)

Other Notes of Interest: 

  • GeneticSpecimenVS was created to constain the entire list of possible specimens to those which are relevant for cancer related genomics tests.

Profile: GenomicRegionStudied

http://hl7.org/fhir/us/mcode/StructureDefinition-mcode-genomic-region-studied.html

  • Base FHIR Resource: Observation
  • Derived from: USCoreLaboratoryResultObservationProfile
  • Description: The area of the genome region referenced in testing for variants.
  • mCODE-specific Attribute Constraints:
    • Code is fixed to LOINC#53041-0 “DNA region of interest panel”
  • mCODE-specific Extensions:
  • mCODE-specific Slices:
    • Components generally describing the overall regions within the genomics test performed: GeneMutations, GeneStudied, DNARegionDescription, DNARangesExamined, GenomicRegionCoordinateSystem, GenomicReferenceSequenceId
    • All components are must support
  • mCODE-specific ValueSets:
    • All component LOINC answer lists assigned to the component LOINC code (see component slices).

Other Notes of Interest: 

  • A genomics report can contain multiple regions analyzed for variants. Each region can have many variants.
  • GenomicRegionStudied was added to mCODE based on ballot reconciliation feedback from the HL7 CGWG. Requested for better alignment with CG Reporting IG even if these data elements are more than "minimal" in the initial mCODE scope.

Profile: CancerGeneticVariant

http://hl7.org/fhir/us/mcode/StructureDefinition-mcode-cancer-genetic-variant.html

  • Base FHIR Resource: Observation
  • Derived from: USCoreLaboratoryResultObservationProfile
  • Description: An alteration in the most common DNA nucleotide sequence.
  • mCODE-specific Attribute Constraints:
    • Code is fixed to LOINC#69548-6 “Genetic variant assessment”
    • valueCodeableConcept bound to LOINC LL1971-2 (present/absent)
    • Method is must support and is bound to LOINC Answer List LL4048-6 (extensible)
    • specimen reference restricted to (GeneticSpecimen)
  • mCODE-specific Extensions: none
  • mCODE-specific Slices:
    • Components generally describing the overall regions within the genomics test performed: GeneMutations, GeneStudied, DNARegionDescription, DNARangesExamined, GenomicRegionCoordinateSystem, GenomicReferenceSequenceId
    • All components are must support
  • mCODE-specific ValueSets:
    • All component LOINC answer lists assigned to the component LOINC code (see component slices).

Other Notes of Interest: 

  • Components are only a subset of the HL7 Clinical Genomics Reporting IG to minimize scope and knowing that EHRs would not store all of the elements that could be generated from a Genomics Report.
  • per discussion with mCODE clinical community, oncologists oftentimes view relevant genomic markers as being "positive or negative" rather than having a variant that is "present or absent". Genomic reports focus on the presence of variants and position that "positive or negative" is relative to a clinical interpretation.
    • If available, mCODE represents "positive or negative" under Observation.interpretation and provides guidance through documentation.

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