FHIR IG analytics| Package | hl7.fhir.uv.cg-incubator |
| Resource Type | GenomicStudy |
| Id | GenomicStudy-example-trio2.json |
| FHIR Version | R6 |
No resources found
No resources found
Note: links and images are rebased to the (stated) source
Generated Narrative: GenomicStudy example-trio2
Language: en
identifier: http://example.org/identifiers/genomicstudies/urn:uuid:1111-1111-1111-1113 (use: temp, )
status: Available
type: Trio analysis
encounter: Encounter: status = in-progress; class = inpatient encounter
startDate: 2022-05-01
basedOn:
referrer: Practitioner John Doel
interpreter: Practitioner Jane Doel
| Concept |
| Cystic fibrosis, prenatal detection (procedure) |
note:
This de novo mutation is urgent and important for establishing the treatment plan.
description:
De novo mutation study of the patient. The Prenatal Trio Whole Exome Sequencing (Prenatal Trio WES) test is ordered by a physician and must be accompanied with a consent form and detailed clinical information. In general, the test is used when prenatal imaging detects an anomaly that strongly suggests that there is an underlying genetic etiology. Prenatal Trio WES is often considered only after fetal chromosome microarray analysis has been non-diagnostic.
analysis
identifier:
http://example.org/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1112 (use: temp, )genomicSourceClass: Germline
title: Maternal Sequence Variation Detection Using Next Generation Sequencing
date: 2022-07-01 01:01:10-0600
note:
This is a next generation sequencing analysis of a mother of a proband.
Performers
Actor Role Practitioner Jane Doel Performer Devices
Device Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)
analysis
identifier:
http://example.org/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1113 (use: temp, )genomicSourceClass: Germline
title: Paternal Sequence Variation Detection Using Next Generation Sequencing
date: 2022-07-01 01:01:10-0600
note:
This is a next generation sequencing analysis of a father of a proband.
Performers
Actor Role Practitioner Jane Doel Performer Devices
Device Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)
analysis
identifier:
http://example.org/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1114 (use: temp, )title: De Novo Mutation Detection and Interpretation
focus:
- Child Junior Doe (official) Unknown, DoB: 2021-01-01 ( Medical record number: 11111 (use: temp, period: 2021-01-01 --> (ongoing)))
- RelatedPerson John Father Doe (official)
- RelatedPerson Jane Mother Doe (official)
date: 2022-07-01 03:01:10-0600
note:
This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences.
input
type: BAM
input
type: BAM
input
type: BAM
Outputs
Performers
Actor Role Practitioner Jane Doel Performer Devices
Device Device: identifier = http://example.org/identifiers/devices#11112; status = active; manufacturer = Vanderbilt Genetics Institute; type = Software (physical object)
FHIR
FHIRsmith{
"resourceType": "GenomicStudy",
"resourceDefinition": "http://hl7.org/fhir/StructureDefinition/GenomicStudy|0.1.0-ci-build",
"id": "example-trio2",
"language": "en",
"text": {
"status": "generated",
"div": "<!-- snip (see above) -->"
},
"identifier": [
{
"use": "temp",
"system": "http://example.org/identifiers/genomicstudies",
"value": "urn:uuid:1111-1111-1111-1113"
}
],
"status": "available",
"type": [
{
"coding": [
{
"system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-type",
"code": "trio",
"display": "Trio analysis"
}
]
}
],
"subject": {
"reference": "Patient/proband"
},
"encounter": {
"reference": "Encounter/denovoEncounter"
},
"startDate": "2022-05-01",
"basedOn": [
{
"reference": "ServiceRequest/genomicSRProband"
},
{
"reference": "ServiceRequest/genomicSRMother"
},
{
"reference": "ServiceRequest/genomicSRFather"
}
],
"referrer": {
"reference": "Practitioner/practitioner01"
},
"interpreter": [
{
"reference": "Practitioner/practitioner02"
}
],
"reason": [
{
"concept": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "67799006",
"display": "Cystic fibrosis, prenatal detection (procedure)"
}
]
}
}
],
"note": [
{
"text": "This de novo mutation is urgent and important for establishing the treatment plan."
}
],
"description": "De novo mutation study of the patient. The Prenatal Trio Whole Exome Sequencing (Prenatal Trio WES) test is ordered by a physician and must be accompanied with a consent form and detailed clinical information. In general, the test is used when prenatal imaging detects an anomaly that strongly suggests that there is an underlying genetic etiology. Prenatal Trio WES is often considered only after fetal chromosome microarray analysis has been non-diagnostic.",
"analysis": [
{
"identifier": [
{
"use": "temp",
"system": "http://example.org/identifiers/genomicAnalyses",
"value": "urn:uuid:1111-1111-1111-1112"
}
],
"genomicSourceClass": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA6683-2",
"display": "Germline"
}
]
},
"title": "Maternal Sequence Variation Detection Using Next Generation Sequencing",
"focus": [
{
"reference": "Patient/mother"
}
],
"specimen": [
{
"reference": "Specimen/specimenMother"
}
],
"date": "2022-07-01T01:01:10-06:00",
"note": [
{
"text": "This is a next generation sequencing analysis of a mother of a proband."
}
],
"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"
}
}
]
},
{
"identifier": [
{
"use": "temp",
"system": "http://example.org/identifiers/genomicAnalyses",
"value": "urn:uuid:1111-1111-1111-1113"
}
],
"genomicSourceClass": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA6683-2",
"display": "Germline"
}
]
},
"title": "Paternal Sequence Variation Detection Using Next Generation Sequencing",
"focus": [
{
"reference": "Patient/father"
}
],
"specimen": [
{
"reference": "Specimen/specimenFather"
}
],
"date": "2022-07-01T01:01:10-06:00",
"note": [
{
"text": "This is a next generation sequencing analysis of a father of a proband."
}
],
"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"
}
}
]
},
{
"identifier": [
{
"use": "temp",
"system": "http://example.org/identifiers/genomicAnalyses",
"value": "urn:uuid:1111-1111-1111-1114"
}
],
"title": "De Novo Mutation Detection and Interpretation",
"focus": [
{
"reference": "Patient/denovoChild"
},
{
"reference": "RelatedPerson/relatedPersonDenovoFather"
},
{
"reference": "RelatedPerson/relatedPersonDenovoMother"
}
],
"date": "2022-07-01T03:01:10-06:00",
"note": [
{
"text": "This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences."
}
],
"input": [
{
"file": {
"reference": "DocumentReference/genomicFileProband"
},
"type": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
"code": "bam",
"display": "BAM"
}
]
}
},
{
"file": {
"reference": "DocumentReference/genomicFileMother"
},
"type": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
"code": "bam",
"display": "BAM"
}
]
}
},
{
"file": {
"reference": "DocumentReference/genomicFileFather"
},
"type": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
"code": "bam",
"display": "BAM"
}
]
}
}
],
"output": [
{
"file": {
"reference": "DocumentReference/genomicFileGroupAsSubject"
},
"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/Triodenovo-SW"
}
}
]
}
]
}