FHIR IG analytics| Package | hl7.fhir.uv.genomics-reporting.r4b |
| Resource Type | Observation |
| Id | Observation-SNVexample.json |
| FHIR Version | R4B |
No resources found
No resources found
Note: links and images are rebased to the (stated) source
Generated Narrative: Observation SNVexample
status: Final
category: Laboratory, Genetics
code: Genetic variant assessment
subject: Anonymous Patient (no stated gender), DoB Unknown
effective: 2023-06-01
performer: Organization Some lab
value: Present
method: Sequencing
specimen: Identifier: http://slk-kliniken.de/fhir/namingSystem/tissueID/16-123456-23
component
code: Gene studied ID
value: AR
component
code: Cytogenetic (chromosome) location
value: chrX
component
code: Human reference sequence assembly version
value: GRCh37
component
code: Genomic source class
value: Somatic
component
code: DNA change (c.HGVS)
value: NM_000044.6:c.7G>A
component
code: Amino acid change (pHGVS)
value: NP_000035.2:p.Val3Met
component
code: Transcript reference sequence [ID]
value: NM_000044.6
component
code: Sample VAF
value: 0.44 decimal
component
code: Allelic read depth
value: 120 reads per base pair (Details: UCUM code1 = '1')
FHIR
FHIRsmith{
"resourceType": "Observation",
"id": "SNVexample",
"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",
"display": "Genetic variant assessment"
}
]
},
"subject": {
"reference": "Patient/ExamplePatient"
},
"effectiveDateTime": "2023-06-01",
"performer": [
{
"reference": "Organization/ExampleLab"
}
],
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA9633-4",
"display": "Present"
}
]
},
"method": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA26398-0",
"display": "Sequencing"
}
]
},
"specimen": {
"identifier": {
"system": "http://slk-kliniken.de/fhir/namingSystem/tissueID",
"value": "16-123456-23"
}
},
"component": [
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48018-6",
"display": "Gene studied ID"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.genenames.org",
"code": "HGNC:644",
"display": "AR"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48001-2",
"display": "Cytogenetic (chromosome) location"
}
]
},
"valueCodeableConcept": {
"text": "chrX"
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "62374-4",
"display": "Human reference sequence assembly version"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA14029-5",
"display": "GRCh37"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48002-0",
"display": "Genomic source class"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA6684-0",
"display": "Somatic"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48004-6",
"display": "DNA change (c.HGVS)"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://varnomen.hgvs.org",
"code": "NM_000044.6:c.7G>A"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48005-3",
"display": "Amino acid change (pHGVS)"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://varnomen.hgvs.org",
"code": "NP_000035.2:p.Val3Met",
"display": "NP_000035.2:p.Val3Met"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "51958-7",
"display": "Transcript reference sequence [ID]"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.ncbi.nlm.nih.gov/refseq",
"code": "NM_000044.3",
"display": "NM_000044.6"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81258-6",
"display": "Sample VAF"
}
]
},
"valueQuantity": {
"value": 0.44,
"unit": "decimal",
"system": "http://unitsofmeasure.org"
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "82121-5",
"display": "Allelic read depth"
}
]
},
"valueQuantity": {
"value": 120,
"unit": "reads per base pair",
"system": "http://unitsofmeasure.org",
"code": "1"
}
}
]
}