FHIR IG analytics| Package | hl7.fhir.uv.genomics-reporting.r4b |
| Resource Type | Observation |
| Id | Observation-Pgx-var-1018.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-1018
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
method: Sequencing
component
code: Genomic reference sequence [ID]
value: b37 Chr10
component
code: Genomic coordinate system [Type]
value: 1-based character counting
component
code: Genomic allele start-end
value: 96612495-96612495
component
code: Genomic ref allele [ID]
value: C
component
code: Genomic alt allele [ID]
value: C
component
code: Genomic source class [Type]
value: Germline
component
code: Allelic state
value: homozygous
component
code: Gene studied [ID]
value: CYP2C19
component
code: DNA change type
value: wild type
component
code: Allelic read depth
value: >20
component
code: Variant Confidence Status
value: High
FHIR
FHIRsmith{
"resourceType": "Observation",
"id": "Pgx-var-1018",
"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"
}
]
},
"method": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA26398-0",
"display": "Sequencing"
}
]
},
"component": [
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48013-7"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.ncbi.nlm.nih.gov/refseq",
"code": "NC_000010.10",
"display": "b37 Chr10"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "92822-6"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA30102-0",
"display": "1-based character counting"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81254-5"
}
]
},
"valueRange": {
"low": {
"value": 96612495
},
"high": {
"value": 96612495
}
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "69547-8"
}
]
},
"valueString": "C"
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "69551-0"
}
]
},
"valueString": "C"
},
{
"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": "LA6705-3",
"display": "homozygous"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48018-6"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.genenames.org",
"code": "HGNC:2621",
"display": "CYP2C19"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48019-4"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO:1000002",
"display": "wild type"
}
]
}
},
{
"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"
}
]
}
}
]
}