FHIR IG analytics| Package | hl7.fhir.uv.genomics-reporting.r4 |
| Resource Type | Procedure |
| Id | Procedure-analysisTumorNormalDNA.json |
| FHIR Version | R4 |
No resources found
No resources found
Note: links and images are rebased to the (stated) source
Generated Narrative: Procedure analysisTumorNormalDNA
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
- studied: ABL1
- studied: ALK
- studied: APC
- uncalled: DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11146520; status = current; docStatus = preliminary; description = Regions deemed uncallable (generally due to low coverage).; securityLabel = Restricted
Genomic Study Analysis Method Type: Sequence analysis of the entire coding region
Genomic Study Analysis Method Type: Deletion/duplication analysis
Genomic Study Analysis Change Type: SNV
Genomic Study Analysis Change Type: MNV
Genomic Study Analysis Change Type: delins
Genomic Study Analysis Change Type: CNV
Genomic Study Analysis Genome Build: GRCh38
Genomic Study Analysis Specimen: Specimen: identifier = http://www.somesystemabc.net/identifiers/specimens#222333; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2023-01-23 01:01:01+0000; note = Tumor: 20%
Genomic Study Analysis Specimen: Specimen: identifier = http://www.somesystemabc.net/identifiers/specimens#444555; status = available; type = Blood specimen (specimen); receivedTime = 2023-01-23 01:01:01+0000
Genomic Study Analysis Focus: Substance Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567 (use: temp, period: 2021-01-01 --> (ongoing)))
Genomic Study Analysis Output
status: Completed
category: Laboratory
performed: 2023-02-02 01:01:10-0600
note: For technical reasons, BCR gene was deemed uncallable.
FHIR
FHIRsmith{
"resourceType": "Procedure",
"id": "analysisTumorNormalDNA",
"meta": {
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis"
]
},
"text": {
"status": "extensions",
"div": "<!-- snip (see above) -->"
},
"extension": [
{
"extension": [
{
"url": "studied",
"valueReference": {
"reference": "DocumentReference/WES-FullSequencedRegion-GRCh38"
}
},
{
"url": "studied",
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.genenames.org",
"code": "HGNC:76",
"display": "ABL1"
}
]
}
},
{
"url": "studied",
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.genenames.org",
"code": "HGNC:427",
"display": "ALK"
}
]
}
},
{
"url": "studied",
"valueCodeableConcept": {
"coding": [
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"system": "http://www.genenames.org",
"code": "HGNC:583",
"display": "APC"
}
]
}
},
{
"url": "uncalled",
"valueReference": {
"reference": "DocumentReference/WES-UncallableRegions-GRCh38"
}
}
],
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions"
},
{
"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-method-type",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs",
"code": "deletion-duplication-analysis",
"display": "Deletion/duplication analysis"
}
]
}
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO:0001483",
"display": "SNV"
}
]
}
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO:0002007",
"display": "MNV"
}
]
}
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO:1000032",
"display": "delins"
}
]
}
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO:0001019",
"display": "CNV"
}
]
}
},
{
"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"
}
]
}
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen",
"valueReference": {
"reference": "Specimen/tumorSpecimen"
}
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen",
"valueReference": {
"reference": "Specimen/normalSpecimen"
}
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus",
"valueReference": {
"reference": "Patient/somaticPatient"
}
},
{
"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/somaticVCFfile"
}
}
],
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output"
}
],
"status": "completed",
"category": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory"
}
]
},
"subject": {
"reference": "Patient/somaticPatient"
},
"performedDateTime": "2023-02-02T01:01:10-06:00",
"note": [
{
"text": "For technical reasons, BCR gene was deemed uncallable."
}
]
}