minimal Common Oncology Data Elements (mCODE) Implementation Guide
2.1.0 - Pre-STU 3 Development United States of America flag

minimal Common Oncology Data Elements (mCODE) Implementation Guide, published by HL7 International Clinical Interoperability Council. This is not an authorized publication; it is the continuous build for version 2.1.0). This version is based on the current content of https://github.com/HL7/fhir-mCODE-ig/ and changes regularly. See the Directory of published versions

Release Notes

The following changes occurred between STU 2 publication (January 2022) and mCODE version 2.1, STU 3 ballot (January 2023). For a history of previous changes, please see the prior change logs in the appropriate versions.

Use of AJCC-equivalent SNOMED Codes for Staging

mCODE STU 3 accepts SNOMED equivalents of AJCC codes, in addition to AJCC codes as in STU 2. This provides maximum interoperability across AJCC licensed and unlicensed systems, but does not break existing applications.

Based on a new licensing agreement between SNOMED International and the American College of Surgeons, SNOMED CT now contains equivalents of AJCC staging codes. For example, SNOMED CT concept 1229967007 represents AJCC’s cN0 category. To be clear, a clinician would never see the SNOMED codes. The user interface would work with the familiar AJCC staging codes, whil the SNOMED equivalents would exist only in the back-end system.

Due to copyright restrictions still in effect, specific AJCC codes cannot be enumerated in HL7 standards. Because of this restriction, staging value sets were only vaguely defined in mCODE STU 2. In STU 3, however, mCODE has taken advantage of the new licensing agreement by redefining the staging value sets in terms of SNOMED CT’s AJCC-equivalent codes, allowing specific enumeration of codes in staging-related profiles. The following value sets are now defined in terms of SNOMED CT:

This change addresses the issue https://jira.hl7.org/browse/FHIR-37593.

The binding strength for these value sets remains “preferred”, meaning that the SNOMED codes are not required. However, any alternative codes MUST be AJCC codes. This has been implemented through addition of maximum value sets to the bindings. The maximum value sets are:

Staging Profiles

Previously, the CancerStageGroup profile contained optional elements specific to TNM staging. This was misleading because CancerStageGroup could be used for non-TNM staging. To avoid this ambiguity, CancerStageGroup no longer contains the optional TNM-specific content. A separate child profile, TNMStageGroup, has been added as a template for TNM-specific staging. This change is backward compatible, since any resource complying with the STU 2 version of CancerStageGroup will comply with STU 3 CancerStageGroup, and every resource complying to TNMStageGroup automatically complies to CancerStageGroup.

Staging Value Sets

To support the separation of TNMStageGroup from more generic CancerStageGroup profile, several value sets were renamed. In FHIR, renaming value sets has little or no impact on implementations, since value set names are not directly used in information exchanges. The following TNM value sets were renamed for clarity:

In addition, the following value sets are now associated with the non-TNM CancerStageGroup profile:

  • CancerStagingSystemVS was renamed CancerStagingMethodVS, because it populates Observation.method.
  • CancerStagingTypeVS was introduced to populate the Observation.code element in the CancerStageGroup profile.
  • CancerStageVS was introduced to populate the Observation.valueCodeableConcept element in the CancerStageGroup profile.

Value Set Content Changes

  • The following improvements were made to CancerStagingMethodVS (formerly CancerStagingSystemVS) value set:
    • Certain children of Tumor staging (SCTID: 2542920070) (see https://jira.hl7.org/browse/FHIR-34448) were removed because they represent stage values rather than staging methods.
    • The following staging methods were added (see https://jira.hl7.org/browse/FHIR-37860):
      • SCT#1149162008 “International Staging System for multiple myeloma (staging scale)”
      • SCT#1149163003 “Revised International Staging System for multiple myeloma (staging scale)”
      • SCT#246165003 “Extent of disease (attribute)”
  • New SNOMED Codes that have been issued since the STU 2 publication have replaced STU 2 temporary codes. These new terms include:
    • #1204242009 “External beam radiation therapy using particle scanning technique (procedure)” //USCRS-33517
    • #1217011006 “non-adjacent (qualifier)” // formerly USCRS-33144
    • #1217123003 “Radiotherapy Course of Treatment (regime/therapy)” //USCRS-33529
    • #1201745009 “Internal Target Volume (observable entity)” //USCRS-33520
    • #1201746005 “Internal Gross Tumor Volume (observable entity)” // USCRS-33521
    • #551001000124108 “Cancer in partial remission (finding)” // USCRS-352237
    • #550991000124107 “Cancer in full remission(finding)” //USCRS-352236
    • #1162492000 “Tumor bed (morphologic abnormality)”
    • #1162782007 “Three dimensional external beam radiation therapy (procedure)”
    • #1162586008 “Irradiated volume of organ at risk (observable entity)”
    • #1162616006 “Lymph node level IA (qualifier value)”
    • #1162617002 “Lymph node level IB (qualifier value)”
    • #1162620005 “Lymph node level IVA (qualifier value)”
    • #1162621009 “Lymph node level IVB (qualifier value)”
    • #1162622002 “Lymph node level VA (qualifier value)”
    • #1162623007 “Lymph node level VB (qualifier value)”
    • #1162624001 “Lymph node level VC (qualifier value)”
    • #1162625000 “Lymph node level VIA (qualifier value)”
    • #1162626004 “Lymph node level VIB (qualifier value)”
    • #1162628003 “Lymph node level VIIA (qualifier value)”
    • #1162627008 “Lymph node level VIIB (qualifier value)”
    • #1162618007 “Lymph node level VIII (qualifier value)”
    • #1162619004 “Lymph node level IX (qualifier value)”
    • #1162614009 “Lymph node level X (qualifier value)”
    • #1162615005 “Lymph node level XA (qualifier value)”
    • #1162613003 “Lymph node level XB (qualifier value)”

Profile Categories

Required categories (Observation.category) have been added to PrimaryCancerCondition, SecondaryCancerCondition, TumorMarkerTest, and five staging-related profiles. The purpose is to make it easier to retrieve mCODE resources. Having fixed categories provide a firmer “handle” to retrieve relevant mCODE resources, without relying on the “code in value set” (code:in=[value set]) operation that is not implemented by all FHIR servers. Updated sample queries have been provided. These changes are not backward compatible.

The following are now required values in Condition.category or Observation.category:

  • PrimaryCancerCondition now requires category SNOMED CT 372087000 “Primary malignant neoplasm (disorder)”
  • SecondaryCancerCondition now requires category SNOMED CT 128462008 “Metastatic malignant neoplasm (disorder)”
  • TumorMarkerTest now requires category SNOMED CT 250724005 “Tumor marker measurement (procedure)”
  • The five staging profiles (CancerStageGroup, TNMStageGroup, TNMPrimaryTumorCategory, TNMRegionalNodesCategory, and TNMDistantMetastasesCategory) now require category SNOMED CT 385356007 “Tumor stage finding (finding)”

    As an example of how to assign these categories in instances, the JSON for a principal cancer condition would include:

    "category" : [
        {
          "coding" : [
            {
              "system" : "http://terminology.hl7.org/CodeSystem/condition-category",
              "code" : "problem-list-item"
            }
          ]
        },
        {
          "coding" : [
            {
              "system" : "http://snomed.info/sct",
              "code" : "372087000"
            }
          ]
        }
      ]
    

    The first of these categories satisfies the US Core requirement from US Core Condition Problems and Health Concerns Profile and the second category satisfies the mCODE requirement. The other categories are similar.

Comorbidity Redesign

Based on user feedback on the complexity of the STU 2 design, comorbidities have been redesigned into a more compact, practical form. As a full redesign, this change is not backward compatible.

  • Comorbidities are no longer based on the Elixhauser framework. Users now have the freedom to name any condition as a comorbidity.
  • Comorbid conditions can be designated either by providing a disorder code or reference to a FHIR resource. To allow this, the data types on the RelatedCondition extension have been expanded to allow a choice of Reference(Condition) or CodeableConcept.
  • Conditions mentioned in the Comorbidities profile can still be designated as present or absent, but this is accomplished by populating different extensions. A new extension, RelatedConditionAbsent, has been introduced to support negation of a comorbidity (if needed to assert a significant negative).
  • Value sets, extensions, code systems, and profiles related to STU 2 Elixhauser comorbidities that are no longer required have been eliminated.

Update to US Core 5.0.1

mCODE has been updated to the current version of US Core, STU 5. Because there are new profiles in STU 5 that should be used as parent profiles, some mCODE profiles were affected. In particular, the parent profiles of KarnofskyPerformanceStatus and ECOGPerformanceStatus were switched from Observation to the newly-introduced US Core Observation Clinical Test Result Profile.

Dependency on Genomics Reporting IG

mCODE is now is explicitly dependent on the Genomics Reporting IG STU2 (v2.0.0) (GRIG). This eliminates the duplication of profiles that existed in STU 1 and STU 2, and assures that the two IGs remain in synchronization. The following changes were made:

  • GenomicsReport, GenomicRegionStudied, and GenomicVariant now inherit from the corresponding profiles in GRIG.
  • Inheritance from US Core was removed from these profiles, since FHIR does not allow a profile to have two parents. Instances MUST be consistent with US Core but the FHIR IG Publisher does not recognize US Core compliance because it does not derive from inheritance.
  • Component names in genomics examples were aligned to the component names in GRIG.
  • The diagnosticImplication component of GenomicVariant (present in STU 2) does not exist in GRIG. Users should express diagnostic implications of a variant using the GRIG DiagnosticImplication profile.
  • Value sets that are no longer required because equivalents are defined externally in GRIG were removed: HGNCVS, HGVSVS, GenomicMolecularConsequenceVS, ClinvarVS, and DNAChangeTypeVS.

Maturity Indicators

Maturity indicators, based on the FHIR Maturity Model (FMM) have been added to profiles and value sets. These indicators show up in the IG but have no functional affect on implementations.

CancerDiseaseStatus Focus

Radiotherapy subject matter experts requested a way to link CancerDiseaseStatus to a RadiotherapyVolume through the Observation.focus element. This broadens the choices of STU2, which were Reference(PrimaryCancerCondition or SecondaryCancerCondition or Tumor) and are now Reference(PrimaryCancerCondition or SecondaryCancerCondition or Tumor or RadiotherapyVolume). This allows a change in disease status to point to a specific area of the body, not just a specific Tumor or condition.

Users requested a link between TumorMarkerTest and the condition the test is related to. Optional RelatedCondition extension was added to TumorMarkerTest. See https://chat.fhir.org/#narrow/stream/229074-CodeX/topic/Reference.20between.20tumor.20characteristics.20and.20cancer.20diagnosis

Multiple Specimen Profiles Simplified

A specimen is a specimen. There was no real reason to distinguish specimens obtained for genomic analysis from those obtained for other uses. A single profile, HumanSpecimen, was created to represent any specimen from a human subject. Since this profile is no longer associated with a single domain (Disease or Genomics), specimens were added to the Patient domain.

Technical Corrections

  • PrimaryCancerCondition’s stage.type value set binding was corrected. It should have indicated the staging method that gave rise to the value appearing in stage.summary (such as AJCC Version 8).
  • Corrected extended example, which formerly used invalid stage “pM0”. Replaced with a data absent reason “not applicable”.
  • “SNOMED-CT” was changed to the preferred form “SNOMED CT” in narratives

Examples