Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions
{
"resourceType" : "Procedure",
"id" : "analysisTumorNormalDNA",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis"
]
},
"text" : {
"status" : "extensions",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Procedure analysisTumorNormalDNA</b></p><a name=\"analysisTumorNormalDNA\"> </a><a name=\"hcanalysisTumorNormalDNA\"> </a><a name=\"analysisTumorNormalDNA-en-US\"> </a><blockquote><p><b>Genomic Study Analysis Regions</b></p><ul><li>studied: <a href=\"DocumentReference-WES-FullSequencedRegion-GRCh38.html\">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</a></li><li>studied: <span title=\"Codes:{http://www.genenames.org HGNC:76}\">ABL1</span></li><li>studied: <span title=\"Codes:{http://www.genenames.org HGNC:427}\">ALK</span></li><li>studied: <span title=\"Codes:{http://www.genenames.org HGNC:583}\">APC</span></li><li>uncalled: <a href=\"DocumentReference-WES-UncallableRegions-GRCh38.html\">DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11146520; status = current; docStatus = preliminary; description = Regions deemed uncallable (generally due to low coverage).; securityLabel = Restricted</a></li></ul></blockquote><p><b>Genomic Study Analysis Method Type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs sequence-analysis-of-the-entire-coding-region}\">Sequence analysis of the entire coding region</span></p><p><b>Genomic Study Analysis Method Type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs deletion-duplication-analysis}\">Deletion/duplication analysis</span></p><p><b>Genomic Study Analysis Change Type</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0001483}\">SNV</span></p><p><b>Genomic Study Analysis Change Type</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0002007}\">MNV</span></p><p><b>Genomic Study Analysis Change Type</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:1000032}\">delins</span></p><p><b>Genomic Study Analysis Change Type</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0001019}\">CNV</span></p><p><b>Genomic Study Analysis Genome Build</b>: <span title=\"Codes:{http://loinc.org LA26806-2}\">GRCh38</span></p><p><b>Genomic Study Analysis Specimen</b>: <a href=\"Specimen-tumorSpecimen.html\">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%</a></p><p><b>Genomic Study Analysis Specimen</b>: <a href=\"Specimen-normalSpecimen.html\">Specimen: identifier = http://www.somesystemabc.net/identifiers/specimens#444555; status = available; type = Blood specimen (specimen); receivedTime = 2023-01-23 01:01:01+0000</a></p><p><b>Genomic Study Analysis Focus</b>: <a href=\"Patient-somaticPatient.html\">Substance Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --> (ongoing)))</a></p><blockquote><p><b>Genomic Study Analysis Output</b></p><ul><li>type: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs vcf}\">VCF</span></li><li>file: <a href=\"DocumentReference-somaticVCFfile.html\">DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#1134121; status = current; docStatus = preliminary; description = VCF file containing identified variants; securityLabel = Restricted</a></li></ul></blockquote><p><b>status</b>: Completed</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span></p><p><b>subject</b>: <a href=\"Patient-somaticPatient.html\">Substance Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --> (ongoing)))</a></p><p><b>performed</b>: 2023-02-02 01:01:10-0600</p><p><b>note</b>: For technical reasons, BCR gene was deemed uncallable.</p></div>"
},
"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" : [
{
"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."
}
]
}
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-11-19
Links: Table of Contents |
QA Report
| Version History |
|
Propose a change