minimal Common Oncology Data Elements (mCODE) Implementation Guide
2.0.0 - STU 2

This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v2.0.0: STU 2) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

Example Observation: genomic-variant-jenny-m

Generated Narrative

Resource "genomic-variant-jenny-m"

Profile: Genomic Variant Profile

status: final

category: Laboratory (Observation Category Codes#laboratory)

code: Genetic variant assessment (LOINC#69548-6)

subject: Patient/cancer-patient-jenny-m " M"

effective: 2018-03-15

value: Present (LOINC#LA9633-4)

method: Sequencing (LOINC#LA26398-0)

component

code: Gene studied [ID] (LOINC#48018-6)

value: PALB2 (HUGO Gene Nomenclature#HGNC:26144)

component

code: Discrete genetic variant (LOINC#81252-9)

value: NM_024675.3(PALB2):c.3549C>A (p.Tyr1183Ter) (clinvar#128144)

component

code: Genomic DNA change (gHGVS) (LOINC#81290-9)

value: NC_000016.10:g.23603471G>T (Human Genome Variation Society nomenclature#NC_000016.10:g.23603471G>T)

component

code: Genomic source class [Type] (LOINC#48002-0)

value: Somatic (LOINC#LA6684-0)

Notes:

Instance: genomic-variant-jenny-m
InstanceOf: GenomicVariant
Title: "genomic-variant-jenny-m"
Description: "Extended example: example showing genomic variant found by breast cancer genomics panel"
Usage: #example
* status = #final
* category = http://terminology.hl7.org/CodeSystem/observation-category#laboratory
* code = http://loinc.org#69548-6 "Genetic variant assessment"
* subject = Reference(cancer-patient-jenny-m)
* effectiveDateTime = "2018-03-15"
* valueCodeableConcept = http://loinc.org#LA9633-4 "Present"
* method = http://loinc.org#LA26398-0 "Sequencing"
* component[0].code = http://loinc.org#48018-6
* component[=].valueCodeableConcept = http://www.genenames.org#HGNC:26144 "PALB2"
* component[+].code = http://loinc.org#81252-9
* component[=].valueCodeableConcept = http://www.ncbi.nlm.nih.gov/clinvar#128144 "NM_024675.3(PALB2):c.3549C>A (p.Tyr1183Ter)"
* component[+].code = http://loinc.org#81290-9
* component[=].valueCodeableConcept = http://varnomen.hgvs.org#NC_000016.10:g.23603471G>T
* component[+].code = http://loinc.org#48002-0
* component[=].valueCodeableConcept = http://loinc.org#LA6684-0 "Somatic"