mCODE Release Notes / Change Log

mCODE 1.0 STU1

The following are changes made to the mCODE 0.9.1 September 2019 Ballot Release.

Enhancements

• The following profiles have been added: GeneticSpecimen, RegionStudied to support greater alignment between mCODE and the Clinical Genomics Reporting FHIR IG STU1..
• The GeneticVariant profile has additional components which conform to equivalent components in the CG Reporting IG Variant profile: GeneStudied, VariationCode, GenomicDNAChange, GenomicSourceClass, AminoAcidChange, AminoAcidChangeType, CytogeneticLocation, and CytogeneticNomenclature.
• The MedicationStatement profile name has changed to CancerRelatedMedicationStatement. This profile now constrains the reason reference to only primary and secondary cancer conditions.

Corrections and Modifications to Existing Content

• The following mCODE profiles no longer appear and instead document preferred use of FHIR base profiles: BloodPressure, BodyWeight, BodyHeight, CBCWAutoDifferentialPanel, ComprehensiveMetabolic2000SerumOrPlasmaPanel.
• Genomics-related profiles GeneticVariantTested and GeneticVariantFound are combined into one profile, GeneticVariant.
• GenomicsReport onco-core-RegionStudied-extension is migrated to a slice under DiagnosticReport.result with a reference to a new profile, RegionStudied.
• GenomicsReport obf-SpecimenType-extension is migrated to a slice under DiagnosticReport.result with a reference to a new profile, GeneticSpecimen.
• DiagnosticReport.category cardinality changed from 1..1 to 1..*
• Replaced references of CIMPL to references of FHIR Shorthand and SUSHI.
• ECOGPerformanceStatus Observation.code and Observation.interpretation changed to align with the LOINC equivalent of ECOG score (89247-1) and interpretation (LOINC Answer List LL529-9).
• KarnofskyPerformanceStatus Observation.code and Observation.interpretation changed to align with the LOINC equivalent of Karnofsky score (89243-0) and interpretation (LOINC Answer List LL4986-7).

mCODE 0.9.1 September 2019 Ballot Release

The following are changes relative to mCODE 0.9.0.

Enhancements

• Updated to FHIR Release 4 from DSTU 2.
• Changed base class of mCODE laboratory panels (CBC and CMP) from Observation to DiagnosticReport.
• Documented mCODE compliance criteria.
• Documented preferred value sets for extensible binding and affect on US Core compliance.
• Changed HistologyMorphologyBehaviorVS value set to descendants of SCT#367651003 (Malignant neoplasm of primary, secondary, or uncertain origin (morphologic abnormality)), from descendants of SCT#108369006 (Neoplasm (morphologic abnormality)), because the latter brought in some concepts that do not represent malignant neoplasms.

Corrections and Modifications to Existing Content

• Updated code systems to new FHIR R4 base URL, http://terminology.hl7.org (previously was http://hl7.org/fhir)
• Changed profile name from GeneticMutationTested to GeneticVariant.
• Corrected mapping so the reference to PrimaryCancerCondition in all staging-related observations uses the existing 'focus' attribute.
• Eliminated AnatomicalOrientation.
• Eliminated ClockDirection as a separate value set because values are incorporated in logically-defined SNOMED-CT AnatomicalOrientationVS.
• Re-wrote the introductory narratives to consolidate multiple pages.
• Changed clinicalStatus on PrimaryCancerCondition and SecondaryCancerCondition from 1..1 to 0..1.
• Typographical fixes to multiple documentation pages.
• Eliminated reference range from GeneticVariant and components of GeneticVariantFound.
• Improved the definition of "curative" and "palliative" in TreatmentIntentVS.
• Corrected the definition of TreatmentIntent.
• Improved the explanation of the relationships between the genomics-related profiles.
• Updated examples to validate against FHIR R4 and other changes to the profiles.
• Changed blood pressure test code to LNC#85354-9 "Blood pressure panel with all children optional" to align with FHIR
• Restored device attribute on TumorMarkerTest since laboratories do report it on occasion.
• Added string as an allowable datatype for TumorMarkerTest.value[x], since it is a valid datatype for some of the tests included in TumorMarkerTestVS.
• Changed cardinality of ECOGPerformanceStatus.value and KarnofskyPerformanceStatus.value to 1..1 and ECOGPerformanceStatus.dataAbsentReason and ECOGPerformanceStatus.dataAbsentReason to 0..0
• Changed cardinality of GeneticVariant.referenceRange to 0..0.
• Changed cardinality of referenceRange for GeneticVariantFound.component[VariantFoundIdentifier], GeneticVariantFound.component[VariantFoundHGVSName] and GeneticVariantFound.component[VariantFoundDescription] and to 0..0.
• Clarified description of HistologyMorphologyBehaviorVS regarding the use of ICD-O-3 behavior codes.
• Corrected descriptions for multiple codes in the ComorbidConditionVS.
• Updated Data Dictionary to reflect FHIR R4 and other changes to the Implementation Guide.
• Renamed PrimaryCancerConditionVS to PrimaryOrUncertainBehaviorCancerDisorderVS, for greater alignement with value set content.
• Renamed extension prefixes from `shr-core` to `obf-datatype`.
• Replaced onco-core-GeneStudied-extension with observation-geneticsGene standard extension in GeneticVariant.
• Corrected the definition of obf-RadiationDosePerFraction-extension.
• Renamed vital-precondition-extension to vital-preconditionCode-extension to distinguish from precondition whose datatype is Reference().
• Improved the definition for obf-RadiationFractionsDelivered-extension.
• Replaced locally defined LateralityVS with FHIR-defined laterality value set in obf-datatype-Laterality-extension.
• Improved definition of onco-core-EvidenceType-extension.
• Replaced obf-dateOfDiagnosis-extension with condition-assertedDate standard extension in PrimaryCancerCondition and SecondaryCancerCondition.
• Added logical definition to TNM-related value sets to include all codes from AJCC staging systems.
• Removed references to MedicationRequest on basedOn attribute for TNMClinicalPrimaryTumorCategory, TNMClinicalRegionalNodesCategory, TNMClinicalDistantMetastasesCategory, KarnofskyPerformanceStatus and ECOGPerformanceStatus.