minimal Common Oncology Data Elements (mCODE) Implementation Guide
3.0.0 - STU3 Release
minimal Common Oncology Data Elements (mCODE) Implementation Guide
3.0.0 - STU3 Release
This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v3.0.0: STU 3) 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
{
"resourceType" : "Observation",
"id" : "gx-genomic-variant-somatic-bap1-indel",
"meta" : {
"profile" : [
"http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-variant"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"gx-genomic-variant-somatic-bap1-indel\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource Observation "gx-genomic-variant-somatic-bap1-indel" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-mcode-genomic-variant.html\">Genomic Variant Profile</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: 69548-6 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69548-6)</span></p><p><b>subject</b>: <a href=\"Patient-gx-cancer-patient-adam-anyperson.html\">Patient/gx-cancer-patient-adam-anyperson</a> " ANYPERSON"</p><p><b>effective</b>: 2019-04-01</p><p><b>performer</b>: <a href=\"Practitioner-us-core-practitioner-owen-oncologist.html\">Practitioner/us-core-practitioner-owen-oncologist</a> " ONCOLOGIST"</p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA9633-4)</span></p><p><b>method</b>: Sequencing <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA26398-0)</span></p><blockquote><p><b>component</b></p><p><b>code</b>: 48018-6 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></p><p><b>value</b>: BAP1 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgnc.html\">HUGO Gene Nomenclature Committee Genes</a>#HGNC:950; gene#3815)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: 51958-7 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_004656.4 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_004656)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: 48004-6 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: NC_000003.11(NM_004656.4):c.1768C>T <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#NM_004656.4:c.1768C>T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: 48005-3 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48005-3)</span></p><p><b>value</b>: NP_004647.1:p.(Gln590Ter) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#NP_004647.1:p.(Gln590Ter))</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: 48002-0 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48002-0)</span></p><p><b>value</b>: Somatic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6684-0)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: 81258-6 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81258-6)</span></p><p><b>value</b>: 57.4 %<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code % = '%')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Molecular Consequence <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://hl7.org/fhir/uv/genomics-reporting/STU2/CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#molecular-consequence)</span></p><p><b>value</b>: stop_gained <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (#SO:0001587)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: 62374-4 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#62374-4)</span></p><p><b>value</b>: GRCh37 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA14029-5)</span></p></blockquote></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69548-6"
}
]
},
"subject" : {
"reference" : "Patient/gx-cancer-patient-adam-anyperson"
},
"effectiveDateTime" : "2019-04-01",
"performer" : [
{
"reference" : "Practitioner/us-core-practitioner-owen-oncologist"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"method" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26398-0",
"display" : "Sequencing"
}
]
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:950",
"display" : "BAP1"
},
{
"system" : "https://www.ncbi.nlm.nih.gov/gene",
"code" : "3815",
"display" : "BAP1"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51958-7"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/refseq",
"code" : "NM_004656",
"display" : "NM_004656.4"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48004-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"code" : "NM_004656.4:c.1768C>T",
"display" : "NC_000003.11(NM_004656.4):c.1768C>T"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48005-3"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"code" : "NP_004647.1:p.(Gln590Ter)",
"display" : "NP_004647.1:p.(Gln590Ter)"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48002-0"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6684-0",
"display" : "Somatic"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81258-6"
}
]
},
"valueQuantity" : {
"value" : 57.4,
"unit" : "%",
"system" : "http://unitsofmeasure.org",
"code" : "%"
}
},
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "molecular-consequence"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.sequenceontology.org/",
"code" : "SO:0001587",
"display" : "stop_gained"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "62374-4"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA14029-5",
"display" : "GRCh37"
}
]
}
}
]
}
IG © 2019+ HL7 International / Clinical Interoperability Council. Package hl7.fhir.us.mcode#3.0.0 based on FHIR 4.0.1. Generated 2023-10-25
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