FHIR IG analytics| Package | hl7.fhir.uv.genomics-reporting.r4b |
| Resource Type | Procedure |
| Id | Procedure-lungMass-analysis1.json |
| FHIR Version | R4B |
No resources found
No resources found
Note: links and images are rebased to the (stated) source
Generated Narrative: Procedure lungMass-analysis1
Genomic Study Analysis Method Type: Sequence analysis of the entire coding region
Genomic Study Analysis Source Class: Somatic
Genomic Study Analysis Change Type: SNV
Genomic Study Analysis Change Type: MNV
Genomic Study Analysis Change Type: delins
Genomic Study Analysis Genome Build: GRCh38
Genomic Study Analysis Specimen: Specimen: identifier = http://www.somesystemabc.net/identifiers/specimens#4; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2019-03-01 01:01:01+0000
Genomic Study Analysis Focus: John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117 (use: temp, period: 2021-01-01 --> (ongoing)))
Genomic Study Analysis Device
Genomic Study Analysis Regions
- studied: DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11117; status = current; docStatus = preliminary; description = WES_FullSequencedRegion_GRCh38: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted
- uncalled: DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11125; status = current; docStatus = preliminary; description = Representing a BED file that represents uncallable regions; securityLabel = Restricted
- called: DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11118; status = current; docStatus = preliminary; description = SimpleVariantAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted
Genomic Study Analysis Output
instantiatesUri: https://pubmed.ncbi.nlm.nih.gov/33927380/
status: Completed
category: Laboratory
performed: 2019-03-01 01:01:10-0600
| Function | Actor |
| Performer | Practitioner Jane Doel |
note: For technical reasons, PIK3CB was deemed uncallable using this method.
FHIR
FHIRsmith{
"resourceType": "Procedure",
"id": "lungMass-analysis1",
"meta": {
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis"
]
},
"text": {
"status": "extensions",
"div": "<!-- snip (see above) -->"
},
"extension": [
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs",
"code": "sequence-analysis-of-the-entire-coding-region",
"display": "Sequence analysis of the entire coding region"
}
]
}
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genomic-source-class",
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA6684-0",
"display": "Somatic"
}
]
}
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
"valueCodeableConcept": {
"coding": [
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"system": "http://www.sequenceontology.org",
"code": "SO:0001483",
"display": "SNV"
}
]
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"valueCodeableConcept": {
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"code": "SO:0002007",
"display": "MNV"
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}
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{
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"valueCodeableConcept": {
"coding": [
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"system": "http://www.sequenceontology.org",
"code": "SO:1000032",
"display": "delins"
}
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}
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genome-build",
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA26806-2",
"display": "GRCh38"
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}
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen",
"valueReference": {
"reference": "Specimen/genomicSpecimen"
}
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus",
"valueReference": {
"reference": "Patient/genomicPatient"
}
},
{
"extension": [
{
"url": "device",
"valueReference": {
"reference": "Device/triodenovo-software"
}
}
],
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device"
},
{
"extension": [
{
"url": "studied",
"valueReference": {
"reference": "DocumentReference/WES-FullSequencedRegion-GRCh38"
}
},
{
"url": "uncalled",
"valueReference": {
"reference": "DocumentReference/UncallableRegions"
}
},
{
"url": "called",
"valueReference": {
"reference": "DocumentReference/SimpleVariantAnalysis-called"
}
}
],
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions"
},
{
"extension": [
{
"url": "type",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs",
"code": "vcf",
"display": "VCF"
}
]
}
},
{
"url": "file",
"valueReference": {
"reference": "DocumentReference/genomicVCFfile-simple"
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}
],
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output"
}
],
"instantiatesUri": [
"https://pubmed.ncbi.nlm.nih.gov/33927380/"
],
"status": "completed",
"category": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory"
}
]
},
"subject": {
"reference": "Patient/genomicPatient"
},
"performedDateTime": "2019-03-01T01:01:10-06:00",
"performer": [
{
"function": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
"code": "PRF",
"display": "Performer"
}
]
},
"actor": {
"reference": "Practitioner/practitioner02"
}
}
],
"note": [
{
"text": "For technical reasons, PIK3CB was deemed uncallable using this method."
}
]
}