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

Extended Example

In addition to providing examples of mCODE profiles, this extended example demonstrates how to represent a clinically realistic scenario.

  • When information in the scenario does not map on to mCODE profiles, we provide examples using USCore or standard FHIR resources.
  • We condense some repeated patterns. For example, we only show one example of MedicationAdministration when in reality, there could be multiple cycles, the only difference being the day of the administration.

Patient description

Note: patient and clinical data in the narrative example below are linked to the relevant FHIR examples using this styling.

Patient Jenny M. is a 55 year old non-Hispanic white female with a past medical history significant for depression, a 20-pack-year history of smoking (current smoker), anxiety, and hypertension. Her family history was significant for a maternal aunt with ovarian cancer at age 69, a sister with breast cancer at age 64, and deceased paternal uncle due to pancreatic cancer.

During a routine screening mammography in February 2018, an abnormality was detected as a possible mass and suspected breast cancer. The gynecologist performing the biopsy refers the patient to an oncologist for further workup. An ultrasound-guided biopsy was performed along with prognostic tumor marker tests with ER positive, PR negative, and HER2 negative. The patient is referred to an oncologist who clinically reviews the mammogram and tumor marker results, and clinical staged the cancer diagnosis as cT3N0.

Genetic counseling ordered a 7 gene panel, and the panel results revealed a pathogenic variant in PALB2 (c.3549C>A).1

A partial mastectomy was performed, revealing a 2.5 cm tumor with no lymph-vascular invasion and negative margins of excision. Three sentinel lymph nodes were excised and were negative for metastatic carcinoma. The tumor specimen was sent to the pathologist. The pathology report revealed a 2.5cm malignant tumor histological grade 2 invasive ductal adenocarcinoma with prognostic tumor markers ER positive, PR negative, and HER2 negative. The patient is pathologically staged as pT3 pN0, stage group IIB.

A 21-gene RT-PCR assay yielded a recurrence score of 47.

Treatment options were discussed between the patient and the medical oncologist. With an ECOG performance score of 0, the patient agrees to receive an AC-T chemotherapy regimen. She received four cycles of doxorubicin (60 mg/m² IV) and cyclophosphamide (600 mg/m² IV) followed by paclitaxel (175 mg/m² IV) (AC-T), administered on a dose-dense schedule. She subsequently received whole breast radiation therapy with regional nodal irradiation.

One month following the completion of first-line therapy, the patient is evaluated and with her disease status improving. The patient will undergo surveillance imaging and monitoring.

A timeline of the narrative is illustrated in the following diagram:

Example Timeline

FHIR instances from mCODE elements

Instance Description mCODE Profile
Cancer Diagnosis PrimaryCancerCondition
Cancer Disease Status: Condition Improving CancerDiseaseStatus
Cancer Patient: Jenny M CancerPatient
Clinical Cancer Stage Group: 2B TNMStageGroup
Clinical Primary Tumor Category: cT3 TNMPrimaryTumorCategory
Clinical Regional Lymph Nodes Category: cN0 TNMRegionalNodesCategory
Clinical Distant Metastases Category: cM0 TNMDistantMetastasesCategory
Comorbidities: Anxiety, Depression, Hypertension Comorbidities
Genomic Region: BRCA1 GenomicRegionStudied
Genomics Report GenomicsReport
Genomic Variant Results: Pathogenic Variant in PALB2 GenomicVariant
Human Specimen: Left Breast HumanSpecimen
mCODE Patient Bundle: Jenny M MCODEPatientBundle
Medication Administration: Cyclophosphamide CancerRelatedMedicationAdministration
Medication Administration: Paclitaxel CancerRelatedMedicationAdministration
Medication Administration: Doxorubicin CancerRelatedMedicationAdministration
Medication Request: Doxorubicin CancerRelatedMedicationRequest
Medication Request: Cyclophosphamide CancerRelatedMedicationRequest
Medication Request: Paclitaxel CancerRelatedMedicationRequest
Oncotype DX Breast Recurrence Score Assay: 47/High TumorMarkerTest
Pathologic Cancer Stage Group Group: stage IIB TNMStageGroup
Pathologic Primary Tumor Category: pT3 TNMPrimaryTumorCategory
Pathologic Regional Lymph Nodes Category: pN0 TNMRegionalNodesCategory
Pathologic Distant Metastases Category: pM0 TNMDistantMetastasesCategory
Performance Status: ECOG ECOGPerformanceStatus
Radiation Treatment Summary RadiotherapyCourseSummary
Seven Gene Panel: BRCA1, BRCA2, CDH1, PALB2, PTEN, STK11, TP53 GenomicRegionStudied
Surgical Procedure: Partial Mastectomy CancerRelatedSurgicalProcedure
Tumor Marker ER Positive TumorMarkerTest
Tumor Marker PR Negative TumorMarkerTest
Tumor Marker Her2 Negative TumorMarkerTest
Tumor Size: 2.5cm TumorSize
Tumor Specimen: Left Breast HumanSpecimen

FHIR instances from non-mCODE elements

Instance Description Profile/Resource
Smoking History: 20 Pack-Years R4Observation
Aunt With Ovarian Cancer R4FamilyMemberHistory
Sister With Breast Cancer R4FamilyMemberHistory
Uncle With Pancreatic Cancer R4FamilyMemberHistory
Comorbidity: Anxiety Diagnosis USCoreConditionProblemHealthConcern
Comorbidity: Depression Diagnosis USCoreConditionProblemHealthConcern
Comorbidity: Hypertension Diagnosis USCoreConditionProblemHealthConcern
Pathology Report USCoreDiagnosticReport
DCIS intraductal extension Report USCoreLaboratoryResultObservation
Histologic Grade in Specimen: Grade 2 USCoreLaboratoryResultObservation
Tumor Invasion Report USCoreLaboratoryResultObservation
Tumor Margins Report USCoreLaboratoryResultObservation
Sentinel Lymph Nodes Report: Negative USCoreLaboratoryResultObservation
Oncologist Owen USCorePractitioner
Breast Biopsy Procedure USCoreProcedure
Mammogram Procedure USCoreProcedure
Smoking Status: Smokes Daily USCoreSmokingStatus
  1. For the purposes of this example, we are assuming that a single relevant variant was returned by the clinical genomics laboratory. In practice, genomics testing may return (many) more variants. The standards for representing genomics data are currently under development by the HL7 Clinical Genomics Work Group. The expectation is that mCODE will adopt those standards when they are completed.