FHIR IG analytics| Package | hl7.fhir.uv.genomics-reporting.r4b |
| Resource Type | Observation |
| Id | Observation-Pgx-var-1019.json |
| FHIR Version | R4B |
No resources found
No resources found
Note: links and images are rebased to the (stated) source
Generated Narrative: Observation Pgx-var-1019
status: Final
category: Laboratory, Genetics
code: Genetic variant assessment
subject: Adam B. Everyman Male, DoB: 1951-01-20 ( Medical Record Number: m123 (use: usual, ))
effective: 2019-04-01
performer: Organization some lab
value: Present
note: This variant was confirmed with SANGER sequencing
method: Sequencing
component
code: Genomic DNA change (gHGVS)
value: NC_000016.9:g.31096368G>T
component
code: Genomic source class [Type]
value: Germline
component
code: Allelic state
value: heterozygous
component
code: Gene studied [ID]
value: VKORC1
component
code: DNA change type
value: substitution
component
code: Allelic read depth
value: >20
component
code: Variant Confidence Status
value: High
FHIR
FHIRsmith{
"resourceType": "Observation",
"id": "Pgx-var-1019",
"meta": {
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text": {
"status": "generated",
"div": "<!-- snip (see above) -->"
},
"status": "final",
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory"
}
]
},
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v2-0074",
"code": "GE"
}
]
}
],
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "69548-6"
}
]
},
"subject": {
"reference": "Patient/CGPatientExample01"
},
"effectiveDateTime": "2019-04-01",
"performer": [
{
"reference": "Organization/ExampleOrg"
}
],
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA9633-4",
"display": "Present"
}
]
},
"note": [
{
"extension": [
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/coded-annotation-types-cs",
"code": "result-confirmation"
}
]
}
}
],
"text": "This variant was confirmed with SANGER sequencing"
}
],
"method": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA26398-0",
"display": "Sequencing"
}
]
},
"component": [
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81290-9"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://varnomen.hgvs.org",
"code": "NC_000016.9:g.31096368G>T"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48002-0"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA6683-2",
"display": "Germline"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "53034-5"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA6706-1",
"display": "heterozygous"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48018-6"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.genenames.org",
"code": "HGNC:23663",
"display": "VKORC1"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48019-4"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO:1000002",
"display": "substitution"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "82121-5"
}
]
},
"valueQuantity": {
"value": 20,
"comparator": ">"
}
},
{
"code": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code": "variant-confidence-status"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/variant-confidence-status-cs",
"code": "high"
}
]
}
}
]
}