FHIR IG analytics| Package | hl7.fhir.uv.cg-incubator |
| Resource Type | GenomicStudy |
| Id | GenomicStudy-example-lungMass.json |
| FHIR Version | R6 |
No resources found
No resources found
Note: links and images are rebased to the (stated) source
Generated Narrative: GenomicStudy example-lungMass
Language: en
identifier: http://example.org/identifiers/genomicstudies/urn:uuid:1111-1111-1111-1112 (use: temp, )
status: Registered
type: Sequencing of entire coding region of gene (procedure)
encounter: Encounter: status = in-progress; class = inpatient encounter
startDate: 2019-03-01
basedOn: ServiceRequest Carrier detection, molecular genetics (procedure)
referrer: Practitioner John Doel
interpreter: Practitioner Jane Doel
| Concept |
| Lung mass (finding) |
note:
For technical reasons, PIK3CA was deemed uncallable.
description:
Whole exome sequencing of lung biopsy. 300 genes are examined for simple variants (SNV, MNV, InDel), and 170 genes are also examined for CNVs. For technical reasons, PIK3CA was deemed uncallable.
analysis
identifier:
http://example.org/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1112 (use: official, )methodType: Nucleic acid sequencing (procedure)
changeType: SNV, MNV, delins
genomeBuild: GRCh38
genomicSourceClass: Somatic
title: Simple variant analysis
date: 2019-03-01 01:01:10-0600
note:
For technical reasons, PIK3CA was deemed uncallable using this method.
Metrics
ReadDepth SequencingCoverage Description 120 x (Details: UCUM code1 = '1') 98 % (Details: UCUM code% = '%') 120x average read depth with 98% coverage of target regions. genomicRegion
type: Studied
Locus
genomicRegion
type: Called
Locus
genomicRegion
type: Uncalled
Locus
Concept PIK3CA Outputs
Type VCF Performers
Actor Role Practitioner Jane Doel Performer Devices
Device Function Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object) Sequencing
analysis
identifier:
http://example.org/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1115 (use: official, )methodType: Nucleic acid sequencing (procedure)
changeType: CNV
genomeBuild: GRCh38
genomicSourceClass: Somatic
title: CNV analysis
date: 2019-03-01 01:01:10-0600
genomicRegion
type: Studied
Locus
genomicRegion
type: Called
Locus
genomicRegion
type: Uncalled
Locus
Concept PIK3CA description: PIK3CA was deemed uncallable using this CNV method due to technical limitations of the assay.
Outputs
Type VCF Performers
Actor Role Practitioner Jane Doel Performer
FHIR
FHIRsmith{
"resourceType": "GenomicStudy",
"resourceDefinition": "http://hl7.org/fhir/StructureDefinition/GenomicStudy|0.1.0-ci-build",
"id": "example-lungMass",
"language": "en",
"text": {
"status": "generated",
"div": "<!-- snip (see above) -->"
},
"identifier": [
{
"use": "temp",
"system": "http://example.org/identifiers/genomicstudies",
"value": "urn:uuid:1111-1111-1111-1112"
}
],
"status": "registered",
"type": [
{
"coding": [
{
"system": "http://snomed.info/sct",
"code": "443968007",
"display": "Sequencing of entire coding region of gene (procedure)"
}
]
}
],
"subject": {
"reference": "Patient/genomicPatient"
},
"encounter": {
"reference": "Encounter/genomicEncounter"
},
"startDate": "2019-03-01",
"basedOn": [
{
"reference": "ServiceRequest/genomicServiceRequest2"
}
],
"referrer": {
"reference": "Practitioner/practitioner01"
},
"interpreter": [
{
"reference": "Practitioner/practitioner02"
}
],
"reason": [
{
"concept": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "309529002",
"display": "Lung mass (finding)"
}
]
}
}
],
"note": [
{
"text": "For technical reasons, PIK3CA was deemed uncallable."
}
],
"description": "Whole exome sequencing of lung biopsy. 300 genes are examined for simple variants (SNV, MNV, InDel), and 170 genes are also examined for CNVs. For technical reasons, PIK3CA was deemed uncallable.",
"analysis": [
{
"identifier": [
{
"use": "official",
"system": "http://example.org/identifiers/genomicAnalyses",
"value": "urn:uuid:1111-1111-1111-1112"
}
],
"methodType": [
{
"coding": [
{
"system": "http://snomed.info/sct",
"code": "117040002",
"display": "Nucleic acid sequencing (procedure)"
}
]
}
],
"changeType": [
{
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO:0001483",
"display": "SNV"
}
]
},
{
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO:0002007",
"display": "MNV"
}
]
},
{
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO:1000032",
"display": "delins"
}
]
}
],
"genomeBuild": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA26806-2",
"display": "GRCh38"
}
]
},
"genomicSourceClass": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA6684-0",
"display": "Somatic"
}
]
},
"title": "Simple variant analysis",
"specimen": [
{
"reference": "Specimen/genomicSpecimen"
}
],
"date": "2019-03-01T01:01:10-06:00",
"note": [
{
"text": "For technical reasons, PIK3CA was deemed uncallable using this method."
}
],
"metrics": {
"readDepth": {
"value": 120,
"unit": "x",
"system": "http://unitsofmeasure.org",
"code": "1"
},
"sequencingCoverage": {
"value": 98,
"unit": "%",
"system": "http://unitsofmeasure.org",
"code": "%"
},
"description": "120x average read depth with 98% coverage of target regions."
},
"genomicRegion": [
{
"type": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
"code": "studied",
"display": "Studied"
}
]
},
"locus": [
{
"reference": {
"reference": "DocumentReference/WES-FullSequencedRegion-GRCh38"
}
}
]
},
{
"type": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
"code": "called",
"display": "Called"
}
]
},
"locus": [
{
"reference": {
"reference": "DocumentReference/SimpleVariantAnalysis-called"
}
}
]
},
{
"type": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
"code": "uncalled",
"display": "Uncalled"
}
]
},
"locus": [
{
"concept": {
"coding": [
{
"system": "http://www.genenames.org",
"code": "HGNC:8975",
"display": "PIK3CA"
}
]
}
}
]
}
],
"output": [
{
"type": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
"code": "vcf",
"display": "VCF"
}
]
}
}
],
"performer": [
{
"actor": {
"reference": "Practitioner/practitioner02"
},
"role": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
"code": "PRF",
"display": "Performer"
}
]
}
}
],
"device": [
{
"device": {
"reference": "Device/NGS-device"
},
"function": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA26398-0",
"display": "Sequencing"
}
]
}
}
]
},
{
"identifier": [
{
"use": "official",
"system": "http://example.org/identifiers/genomicAnalyses",
"value": "urn:uuid:1111-1111-1111-1115"
}
],
"methodType": [
{
"coding": [
{
"system": "http://snomed.info/sct",
"code": "117040002",
"display": "Nucleic acid sequencing (procedure)"
}
]
}
],
"changeType": [
{
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO:0001019",
"display": "CNV"
}
]
}
],
"genomeBuild": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA26806-2",
"display": "GRCh38"
}
]
},
"genomicSourceClass": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA6684-0",
"display": "Somatic"
}
]
},
"title": "CNV analysis",
"specimen": [
{
"reference": "Specimen/genomicSpecimen"
}
],
"date": "2019-03-01T01:01:10-06:00",
"genomicRegion": [
{
"type": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
"code": "studied",
"display": "Studied"
}
]
},
"locus": [
{
"reference": {
"reference": "DocumentReference/WES-FullSequencedRegion-GRCh38"
}
}
]
},
{
"type": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
"code": "called",
"display": "Called"
}
]
},
"locus": [
{
"reference": {
"reference": "DocumentReference/CNVAnalysis-called"
}
}
]
},
{
"type": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
"code": "uncalled",
"display": "Uncalled"
}
]
},
"locus": [
{
"concept": {
"coding": [
{
"system": "http://www.genenames.org",
"code": "HGNC:8975",
"display": "PIK3CA"
}
]
}
}
],
"description": "PIK3CA was deemed uncallable using this CNV method due to technical limitations of the assay."
}
],
"output": [
{
"type": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
"code": "vcf",
"display": "VCF"
}
]
}
}
],
"performer": [
{
"actor": {
"reference": "Practitioner/practitioner02"
},
"role": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
"code": "PRF",
"display": "Performer"
}
]
}
}
]
}
]
}