minimal Common Oncology Data Elements (mCODE) Implementation Guide
2.1.0 - STU 2.1 United States of America flag

This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v2.1.0: 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-somatic-single-nucleotide

Generated Narrative: Observation

Resource Observation "genomic-variant-somatic-single-nucleotide"

Profile: Genomic Variant Profile

status: final

category: Laboratory (Observation Category Codes#laboratory)

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

subject: Patient/cancer-patient-john-anyperson " ANYPERSON"

effective: 2019-04-01

value: Present (LOINC#LA9633-4)

interpretation: Positive (qualifier value) (SNOMED CT#10828004)

method: Sequencing (LOINC#LA26398-0)

component

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

value: STK11 (HUGO Gene Nomenclature Committee Genes#HGNC:11389)

component

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

value: NC_000019.8:g.1171707G>A (ClinVar Variant ID#619728)

component

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

value: NC_000019.8:g.1171707G>A (Human Genome Variation Society nomenclature#NC_000019.8:g.1171707G>A)

component

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

value: Somatic (LOINC#LA6684-0)

Notes:

Instance: genomic-variant-somatic-single-nucleotide
InstanceOf: GenomicVariant
Title: "genomic-variant-somatic-single-nucleotide"
Description: "mCODE Example for Genomic Variant"
Usage: #example
* status = #final
* category = http://terminology.hl7.org/CodeSystem/observation-category#laboratory
* code = http://loinc.org#69548-6
* subject = Reference(cancer-patient-john-anyperson)
* effectiveDateTime = "2019-04-01"
* valueCodeableConcept = http://loinc.org#LA9633-4 "Present"
* interpretation.coding.version = "http://snomed.info/sct/900000000000207008"
* interpretation.coding = http://snomed.info/sct#10828004 "Positive (qualifier value)"
* method = http://loinc.org#LA26398-0 "Sequencing"
* component[0].code = http://loinc.org#48018-6
* component[=].valueCodeableConcept = http://www.genenames.org#HGNC:11389 "STK11"
* component[+].code = http://loinc.org#81252-9
* component[=].valueCodeableConcept = http://www.ncbi.nlm.nih.gov/clinvar#611264 "NM_000455.5(STK11):c.725G>A (p.Gly242Glu)"
* component[+].code = http://loinc.org#81290-9
* component[=].valueCodeableConcept = http://varnomen.hgvs.org#NM_000455.5:c.725G>A
* component[+].code = http://loinc.org#48002-0
* component[=].valueCodeableConcept = http://loinc.org#LA6684-0 "Somatic"