Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build
Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild 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
| Page standards status: Informative |
@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <http://loinc.org/rdf#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
# - resource -------------------------------------------------------------------
<http://hl7.org/fhir/Procedure/analysisTumorNormalDNA> a fhir:Procedure ;
fhir:nodeRole fhir:treeRoot ;
fhir:Resource.id [ fhir:value "analysisTumorNormalDNA"] ;
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis" ;
fhir:index 0 ;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis>
]
] ;
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "extensions" ] ;
fhir:Narrative.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><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\"/><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-genomic-study-analysis.html\">Genomic Study Analysis</a></p></div><blockquote><p><b>Genomic Study Analysis Regions</b></p><ul><li>studied: <a href=\"DocumentReference-WES-FullSequencedRegion-GRCh38.html\">DocumentReference: identifier = http://example.org/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://example.org/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://example.org/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://example.org/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 (use: temp, period: 2021-01-01 --> (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://example.org/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 (use: temp, period: 2021-01-01 --> (ongoing)))</a></p><p><b>performed</b>: 2023-02-02 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>For technical reasons, BCR gene was deemed uncallable.</p>\n</div></blockquote></div>"
] ;
fhir:DomainResource.extension [
fhir:index 0 ;
fhir:Element.extension [
fhir:index 0 ;
fhir:Extension.url [ fhir:value "studied" ] ;
fhir:Extension.valueReference [
fhir:link <http://hl7.org/fhir/DocumentReference/WES-FullSequencedRegion-GRCh38> ;
fhir:Reference.reference [ fhir:value "DocumentReference/WES-FullSequencedRegion-GRCh38" ]
]
], [
fhir:index 1 ;
fhir:Extension.url [ fhir:value "studied" ] ;
fhir:Extension.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://www.genenames.org" ] ;
fhir:Coding.code [ fhir:value "HGNC:76" ] ;
fhir:Coding.display [ fhir:value "ABL1" ]
]
]
], [
fhir:index 2 ;
fhir:Extension.url [ fhir:value "studied" ] ;
fhir:Extension.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://www.genenames.org" ] ;
fhir:Coding.code [ fhir:value "HGNC:427" ] ;
fhir:Coding.display [ fhir:value "ALK" ]
]
]
], [
fhir:index 3 ;
fhir:Extension.url [ fhir:value "studied" ] ;
fhir:Extension.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://www.genenames.org" ] ;
fhir:Coding.code [ fhir:value "HGNC:583" ] ;
fhir:Coding.display [ fhir:value "APC" ]
]
]
], [
fhir:index 4 ;
fhir:Extension.url [ fhir:value "uncalled" ] ;
fhir:Extension.valueReference [
fhir:link <http://hl7.org/fhir/DocumentReference/WES-UncallableRegions-GRCh38> ;
fhir:Reference.reference [ fhir:value "DocumentReference/WES-UncallableRegions-GRCh38" ]
]
] ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions" ]
], [
fhir:index 1 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type" ] ;
fhir:Extension.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs" ] ;
fhir:Coding.code [ fhir:value "sequence-analysis-of-the-entire-coding-region" ] ;
fhir:Coding.display [ fhir:value "Sequence analysis of the entire coding region" ]
]
]
], [
fhir:index 2 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type" ] ;
fhir:Extension.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs" ] ;
fhir:Coding.code [ fhir:value "deletion-duplication-analysis" ] ;
fhir:Coding.display [ fhir:value "Deletion/duplication analysis" ]
]
]
], [
fhir:index 3 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type" ] ;
fhir:Extension.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://www.sequenceontology.org" ] ;
fhir:Coding.code [ fhir:value "SO:0001483" ] ;
fhir:Coding.display [ fhir:value "SNV" ]
]
]
], [
fhir:index 4 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type" ] ;
fhir:Extension.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://www.sequenceontology.org" ] ;
fhir:Coding.code [ fhir:value "SO:0002007" ] ;
fhir:Coding.display [ fhir:value "MNV" ]
]
]
], [
fhir:index 5 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type" ] ;
fhir:Extension.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://www.sequenceontology.org" ] ;
fhir:Coding.code [ fhir:value "SO:1000032" ] ;
fhir:Coding.display [ fhir:value "delins" ]
]
]
], [
fhir:index 6 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type" ] ;
fhir:Extension.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://www.sequenceontology.org" ] ;
fhir:Coding.code [ fhir:value "SO:0001019" ] ;
fhir:Coding.display [ fhir:value "CNV" ]
]
]
], [
fhir:index 7 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genome-build" ] ;
fhir:Extension.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:LA26806-2 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "LA26806-2" ] ;
fhir:Coding.display [ fhir:value "GRCh38" ]
]
]
], [
fhir:index 8 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen" ] ;
fhir:Extension.valueReference [
fhir:link <http://hl7.org/fhir/Specimen/tumorSpecimen> ;
fhir:Reference.reference [ fhir:value "Specimen/tumorSpecimen" ]
]
], [
fhir:index 9 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen" ] ;
fhir:Extension.valueReference [
fhir:link <http://hl7.org/fhir/Specimen/normalSpecimen> ;
fhir:Reference.reference [ fhir:value "Specimen/normalSpecimen" ]
]
], [
fhir:index 10 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus" ] ;
fhir:Extension.valueReference [
fhir:link <http://hl7.org/fhir/Patient/somaticPatient> ;
fhir:Reference.reference [ fhir:value "Patient/somaticPatient" ]
]
], [
fhir:index 11 ;
fhir:Element.extension [
fhir:index 0 ;
fhir:Extension.url [ fhir:value "type" ] ;
fhir:Extension.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs" ] ;
fhir:Coding.code [ fhir:value "vcf" ] ;
fhir:Coding.display [ fhir:value "VCF" ]
]
]
], [
fhir:index 1 ;
fhir:Extension.url [ fhir:value "file" ] ;
fhir:Extension.valueReference [
fhir:link <http://hl7.org/fhir/DocumentReference/somaticVCFfile> ;
fhir:Reference.reference [ fhir:value "DocumentReference/somaticVCFfile" ]
]
] ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output" ]
] ;
fhir:Procedure.status [ fhir:value "completed"] ;
fhir:Procedure.category [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/observation-category" ] ;
fhir:Coding.code [ fhir:value "laboratory" ]
]
] ;
fhir:Procedure.subject [
fhir:link <http://hl7.org/fhir/Patient/somaticPatient> ;
fhir:Reference.reference [ fhir:value "Patient/somaticPatient" ]
] ;
fhir:Procedure.performedDateTime [ fhir:value "2023-02-02T01:01:10-06:00"^^xsd:dateTime] ;
fhir:Procedure.note [
fhir:index 0 ;
fhir:Annotation.text [ fhir:value "For technical reasons, BCR gene was deemed uncallable." ]
] .
<http://hl7.org/fhir/DocumentReference/WES-FullSequencedRegion-GRCh38> a fhir:DocumentReference .
<http://hl7.org/fhir/DocumentReference/WES-UncallableRegions-GRCh38> a fhir:DocumentReference .
<http://hl7.org/fhir/Specimen/tumorSpecimen> a fhir:Specimen .
<http://hl7.org/fhir/Specimen/normalSpecimen> a fhir:Specimen .
<http://hl7.org/fhir/Patient/somaticPatient> a fhir:Patient .
<http://hl7.org/fhir/DocumentReference/somaticVCFfile> a fhir:DocumentReference .
# - ontology header ------------------------------------------------------------
<http://hl7.org/fhir/Procedure/analysisTumorNormalDNA.ttl> a owl:Ontology ;
owl:imports fhir:fhir.ttl ;
owl:versionIRI <http://build.fhir.org/Procedure/analysisTumorNormalDNA.ttl> .
IG © 2025+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#4.0.0-cibuild based on FHIR 4.0.1. Generated 2026-09-21
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