@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <https://loinc.org/rdf/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sct: <http://snomed.info/id/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

# - resource -------------------------------------------------------------------

<http://hl7.org/fhir/uv/cg-incubator/GenomicStudy/example-somaticStudy> a fhir:GenomicStudy ;
  fhir:resourceDefinition http://hl7.org/fhir/StructureDefinition/GenomicStudy|0.1.0-ci-build ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "example-somaticStudy"] ; # 
  fhir:language [ fhir:v "en"] ; # 
  fhir:text [
     fhir:status [ fhir:v "generated" ] ;
     fhir:div [ fhir:v "<div xmlns=\"http://www.w3.org/1999/xhtml\" xml:lang=\"en\" lang=\"en\"><p class=\"res-header-id\"><b>Generated Narrative: GenomicStudy example-somaticStudy</b></p><a name=\"example-somaticStudy\"> </a><a name=\"hcexample-somaticStudy\"> </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\">Language: en</p></div><p><b>identifier</b>: <code>http://example.org/identifiers/genomicstudies</code>/urn:uuid:somatic-study-0001 (use: temp, )</p><p><b>status</b>: Available</p><p><b>type</b>: <span title=\"Codes:\">My Test Cancer 700 Gene Panel</span></p><p><b>subject</b>: <a href=\"Patient-somaticPatient.html\">Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567 (use: temp, period: 2021-01-01 --&gt; (ongoing)))</a></p><p><b>startDate</b>: 2023-02-02</p><p><b>basedOn</b>: <a href=\"ServiceRequest-somaticServiceRequest.html\">ServiceRequest </a></p><p><b>interpreter</b>: <a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></p><h3>Reasons</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Concept</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://snomed.info/sct 424993006}\">Adenocarcinoma of lung, stage IV (disorder)</span></td></tr></table><p><b>note</b>: </p><blockquote><div><p>I. Assay Overview: The Genomic Cancer Testing Assay is a comprehensive molecular examination designed to detect and quantify specific DNA and RNA alterations associated with malignancies. The test incorporates Next Generation Sequencing (NGS) technology to profile tumor samples. II. Target Genes and Biomarkers: This assay evaluates an extensive panel of cancer-related genes. Sample Type: Formalin-fixed, paraffin-embedded (FFPE) tumor tissue. Sequencing Platform: Illumina-based NGS technology. Sensitivity: Detects variants with a mutant allele frequency (MAF) as low as 5%. Results are delivered within 10-14 working days from sample receipt.</p>\n</div></blockquote><p><b>description</b>: </p><div><p>Comprehensive somatic genomic profiling of lung adenocarcinoma (stage IV) using a 700-gene panel. Includes paired tumor/normal DNA sequencing for SNV, MNV, InDel and CNV detection, and RNA sequencing for gene fusion and transcript variant detection.</p>\n</div><blockquote><p><b>analysis</b></p><p><b>identifier</b>: <code>http://example.org/identifiers/genomicAnalyses</code>/urn:uuid:somatic-analysis-dna-0001 (use: temp, )</p><p><b>methodType</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype sequence-analysis-of-the-entire-coding-region}\">Sequence analysis of the entire coding region</span>, <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype deletion-duplication-analysis}\">Deletion/duplication analysis</span></p><p><b>changeType</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0001483}\">SNV</span>, <span title=\"Codes:{http://www.sequenceontology.org SO:0002007}\">MNV</span>, <span title=\"Codes:{http://www.sequenceontology.org SO:1000032}\">delins</span>, <span title=\"Codes:{http://www.sequenceontology.org SO:0001019}\">copy_number_variation</span></p><p><b>genomeBuild</b>: <span title=\"Codes:{http://loinc.org LA26806-2}\">GRCh38</span></p><p><b>genomicSourceClass</b>: <span title=\"Codes:{http://loinc.org LA6684-0}\">Somatic</span></p><p><b>title</b>: Tumor/Normal Paired DNA Sequencing - SNV, MNV, InDel, CNV</p><p><b>focus</b>: <a href=\"Patient-somaticPatient.html\">Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567 (use: temp, period: 2021-01-01 --&gt; (ongoing)))</a></p><p><b>specimen</b>: </p><ul><li><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 = FFPE tumor tissue. Tumor cellularity: 20%.</a></li><li><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; note = Matched normal blood specimen for tumor/normal paired sequencing.</a></li></ul><p><b>date</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><h3>Metrics</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>ReadDepth</b></td><td><b>SequencingCoverage</b></td><td><b>Description</b></td></tr><tr><td style=\"display: none\">*</td><td>500 x<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM  code1 = '1')</span></td><td>97 %<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM  code% = '%')</span></td><td>500x average tumor read depth, 97% target region coverage. Minimum allele frequency threshold 5%.</td></tr></table><blockquote><p><b>genomicRegion</b></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype studied}\">Studied</span></p><h3>Locus</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Reference</b></td></tr><tr><td style=\"display: none\">*</td><td><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.</a></td></tr></table></blockquote><blockquote><p><b>genomicRegion</b></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype called}\">Called</span></p><h3>Locus</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Reference</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"DocumentReference-somaticCalledRegions.html\">DocumentReference: identifier = http://example.org/identifiers/files#somatic-called-001; status = current; docStatus = preliminary; description = BED file describing regions that passed coverage and quality thresholds in the tumor/normal DNA analysis; securityLabel = Restricted</a></td></tr></table></blockquote><blockquote><p><b>genomicRegion</b></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype uncalled}\">Uncalled</span></p><h3>Locus</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Concept</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://www.genenames.org HGNC:1014}\">BCR</span></td></tr></table><p><b>description</b>: BCR was not callable due to low sequencing coverage in this tumor sample.</p></blockquote><h3>Outputs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>File</b></td><td><b>Type</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"DocumentReference-somaticVCFfile.html\">DocumentReference: identifier = http://example.org/identifiers/files#1134121; status = current; docStatus = preliminary; description = VCF file containing somatic variants identified from tumor/normal paired DNA sequencing; securityLabel = Restricted</a></td><td><span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat vcf}\">VCF</span></td></tr></table><h3>Performers</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Actor</b></td><td><b>Role</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></td><td><span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}\">Performer</span></td></tr></table><h3>Devices</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Device</b></td><td><b>Function</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Device-NGS-device.html\">Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)</a></td><td><span title=\"Codes:{http://loinc.org LA26398-0}\">Sequencing</span></td></tr></table></blockquote><blockquote><p><b>analysis</b></p><p><b>identifier</b>: <code>http://example.org/identifiers/genomicAnalyses</code>/urn:uuid:somatic-analysis-rna-0001 (use: temp, )</p><p><b>methodType</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype rna-analysis}\">RNA analysis</span></p><p><b>changeType</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0001565}\">gene_fusion</span>, <span title=\"Codes:{http://www.sequenceontology.org SO:0001576}\">transcript_variant</span></p><p><b>genomicSourceClass</b>: <span title=\"Codes:{http://loinc.org LA6684-0}\">Somatic</span></p><p><b>title</b>: Tumor RNA Sequencing - Gene Fusions and Transcript Variants</p><p><b>focus</b>: <a href=\"Patient-somaticPatient.html\">Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567 (use: temp, period: 2021-01-01 --&gt; (ongoing)))</a></p><p><b>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 = FFPE tumor tissue. Tumor cellularity: 20%.</a></p><p><b>date</b>: 2023-02-02 01:01:10-0600</p><blockquote><p><b>genomicRegion</b></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype studied}\">Studied</span></p><h3>Locus</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Reference</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"DocumentReference-somaticRNAstudiedRegions.html\">DocumentReference: identifier = http://example.org/identifiers/files#1076146520; status = current; docStatus = preliminary; description = BED file describing studied regions for RNA sequencing (fusion and transcript variant detection); securityLabel = Restricted</a></td></tr></table></blockquote><h3>Outputs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>File</b></td><td><b>Type</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"DocumentReference-somaticFusionFile.html\">DocumentReference: identifier = http://example.org/identifiers/files#somatic-fusion-001; status = current; docStatus = preliminary; description = VCF file containing gene fusions and transcript variants identified from tumor RNA sequencing; securityLabel = Restricted</a></td><td><span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat vcf}\">VCF</span></td></tr></table><h3>Performers</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Actor</b></td><td><b>Role</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></td><td><span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}\">Performer</span></td></tr></table><h3>Devices</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Device</b></td><td><b>Function</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Device-NGS-device.html\">Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)</a></td><td><span title=\"Codes:{http://loinc.org LA26398-0}\">Sequencing</span></td></tr></table></blockquote></div>"^^rdf:XMLLiteral ]
  ] ; # 
  fhir:identifier ( [
     fhir:use [ fhir:v "temp" ] ;
     fhir:system [
       fhir:v "http://example.org/identifiers/genomicstudies"^^xsd:anyURI ;
       fhir:l <http://example.org/identifiers/genomicstudies>
     ] ;
     fhir:value [ fhir:v "urn:uuid:somatic-study-0001" ]
  ] ) ; # 
#        Comprehensive somatic cancer 700-gene panel study.
#        Two analyses performed on the same tumor biopsy:
#          1. DNA panel (tumor + normal paired) - SNV, MNV, InDel, CNV, coding regions
#          2. RNA panel - gene fusions and transcript variants
#        Demonstrates: somatic genomicSourceClass, paired tumor/normal specimens,
#        mixed genomicRegion.studied (BED file + coded HGNC genes), genomicRegion.uncalled (coded HGNC gene with description),
#        RNA analysis with fusion change types, two distinct analyses within one study.
#    
  fhir:status [ fhir:v "available"] ; # 
  fhir:type ( [
     fhir:text [ fhir:v "My Test Cancer 700 Gene Panel" ]
  ] ) ; # 
  fhir:subject [
     fhir:l <http://hl7.org/fhir/uv/cg-incubator/Patient/somaticPatient> ;
     fhir:reference [ fhir:v "Patient/somaticPatient" ]
  ] ; # 
  fhir:startDate [ fhir:v "2023-02-02"^^xsd:date] ; # 
  fhir:basedOn ( [
     fhir:l <http://hl7.org/fhir/uv/cg-incubator/ServiceRequest/somaticServiceRequest> ;
     fhir:reference [ fhir:v "ServiceRequest/somaticServiceRequest" ]
  ] ) ; # 
  fhir:interpreter ( [
     fhir:l <http://hl7.org/fhir/uv/cg-incubator/Practitioner/practitioner02> ;
     fhir:reference [ fhir:v "Practitioner/practitioner02" ]
  ] ) ; # 
  fhir:reason ( [
     fhir:concept [
       fhir:coding ( [
         a sct:424993006 ;
         fhir:system [
           fhir:v "http://snomed.info/sct"^^xsd:anyURI ;
           fhir:l <http://snomed.info/sct>
         ] ;
         fhir:code [ fhir:v "424993006" ] ;
         fhir:display [ fhir:v "Adenocarcinoma of lung, stage IV (disorder)" ]
       ] )
     ]
  ] ) ; # 
  fhir:note ( [
     fhir:text [ fhir:v "I. Assay Overview: The Genomic Cancer Testing Assay is a comprehensive molecular examination designed to detect and quantify specific DNA and RNA alterations associated with malignancies. The test incorporates Next Generation Sequencing (NGS) technology to profile tumor samples. II. Target Genes and Biomarkers: This assay evaluates an extensive panel of cancer-related genes. Sample Type: Formalin-fixed, paraffin-embedded (FFPE) tumor tissue. Sequencing Platform: Illumina-based NGS technology. Sensitivity: Detects variants with a mutant allele frequency (MAF) as low as 5%. Results are delivered within 10-14 working days from sample receipt." ]
  ] ) ; # 
  fhir:description [ fhir:v "Comprehensive somatic genomic profiling of lung adenocarcinoma (stage IV) using a 700-gene panel. Includes paired tumor/normal DNA sequencing for SNV, MNV, InDel and CNV detection, and RNA sequencing for gene fusion and transcript variant detection."] ; # 
  fhir:analysis ( [
     fhir:identifier ( [
       fhir:use [ fhir:v "temp" ] ;
       fhir:system [
         fhir:v "http://example.org/identifiers/genomicAnalyses"^^xsd:anyURI ;
         fhir:l <http://example.org/identifiers/genomicAnalyses>
       ] ;
       fhir:value [ fhir:v "urn:uuid:somatic-analysis-dna-0001" ]
     ] ) ;
     fhir:methodType ( [
       fhir:coding ( [
         fhir:system [
           fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype"^^xsd:anyURI ;
           fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype>
         ] ;
         fhir:code [ fhir:v "sequence-analysis-of-the-entire-coding-region" ] ;
         fhir:display [ fhir:v "Sequence analysis of the entire coding region" ]
       ] )
     ] [
       fhir:coding ( [
         fhir:system [
           fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype"^^xsd:anyURI ;
           fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype>
         ] ;
         fhir:code [ fhir:v "deletion-duplication-analysis" ] ;
         fhir:display [ fhir:v "Deletion/duplication analysis" ]
       ] )
     ] ) ;
     fhir:changeType ( [
       fhir:coding ( [
         fhir:system [
           fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ;
           fhir:l <http://www.sequenceontology.org>
         ] ;
         fhir:code [ fhir:v "SO:0001483" ] ;
         fhir:display [ fhir:v "SNV" ]
       ] )
     ] [
       fhir:coding ( [
         fhir:system [
           fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ;
           fhir:l <http://www.sequenceontology.org>
         ] ;
         fhir:code [ fhir:v "SO:0002007" ] ;
         fhir:display [ fhir:v "MNV" ]
       ] )
     ] [
       fhir:coding ( [
         fhir:system [
           fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ;
           fhir:l <http://www.sequenceontology.org>
         ] ;
         fhir:code [ fhir:v "SO:1000032" ] ;
         fhir:display [ fhir:v "delins" ]
       ] )
     ] [
       fhir:coding ( [
         fhir:system [
           fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ;
           fhir:l <http://www.sequenceontology.org>
         ] ;
         fhir:code [ fhir:v "SO:0001019" ] ;
         fhir:display [ fhir:v "copy_number_variation" ]
       ] )
     ] ) ;
     fhir:genomeBuild [
       fhir:coding ( [
         a loinc:LA26806-2 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "LA26806-2" ] ;
         fhir:display [ fhir:v "GRCh38" ]
       ] )
     ] ;
     fhir:genomicSourceClass [
       fhir:coding ( [
         a loinc:LA6684-0 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "LA6684-0" ] ;
         fhir:display [ fhir:v "Somatic" ]
       ] )
     ] ;
     fhir:title [ fhir:v "Tumor/Normal Paired DNA Sequencing - SNV, MNV, InDel, CNV" ] ;
     fhir:focus ( [
       fhir:l <http://hl7.org/fhir/uv/cg-incubator/Patient/somaticPatient> ;
       fhir:reference [ fhir:v "Patient/somaticPatient" ]
     ] ) ; #  focus identifies the patient whose cancer is being profiled 
     fhir:specimen ( [
       fhir:l <http://hl7.org/fhir/uv/cg-incubator/Specimen/tumorSpecimen> ;
       fhir:reference [ fhir:v "Specimen/tumorSpecimen" ]
     ] [
       fhir:l <http://hl7.org/fhir/uv/cg-incubator/Specimen/normalSpecimen> ;
       fhir:reference [ fhir:v "Specimen/normalSpecimen" ]
     ] ) ; #  Two specimens: tumor biopsy (FFPE) and matched normal (blood) 
     fhir:date [ fhir:v "2023-02-02T01:01:10-06:00"^^xsd:dateTime ] ;
     fhir:note ( [
       fhir:text [ fhir:v "For technical reasons, BCR gene was deemed uncallable." ]
     ] ) ;
     fhir:metrics [
       fhir:readDepth [
         fhir:value [ fhir:v "500"^^xsd:decimal ] ;
         fhir:unit [ fhir:v "x" ] ;
         fhir:system [
           fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ;
           fhir:l <http://unitsofmeasure.org>
         ] ;
         fhir:code [ fhir:v "1" ]
       ] ;
       fhir:sequencingCoverage [
         fhir:value [ fhir:v "97"^^xsd:decimal ] ;
         fhir:unit [ fhir:v "%" ] ;
         fhir:system [
           fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ;
           fhir:l <http://unitsofmeasure.org>
         ] ;
         fhir:code [ fhir:v "%" ]
       ] ;
       fhir:description [ fhir:v "500x average tumor read depth, 97% target region coverage. Minimum allele frequency threshold 5%." ]
     ] ;
     fhir:genomicRegion ( [
       fhir:type [
         fhir:coding ( [
           fhir:system [
             fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"^^xsd:anyURI ;
             fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype>
           ] ;
           fhir:code [ fhir:v "studied" ] ;
           fhir:display [ fhir:v "Studied" ]
         ] )
       ] ;
       fhir:locus ( [
         fhir:reference [
           fhir:l <http://hl7.org/fhir/uv/cg-incubator/DocumentReference/WES-FullSequencedRegion-GRCh38> ;
           fhir:reference [ fhir:v "DocumentReference/WES-FullSequencedRegion-GRCh38" ]
         ]
       ] )
     ] [
       fhir:type [
         fhir:coding ( [
           fhir:system [
             fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"^^xsd:anyURI ;
             fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype>
           ] ;
           fhir:code [ fhir:v "called" ] ;
           fhir:display [ fhir:v "Called" ]
         ] )
       ] ;
       fhir:locus ( [
         fhir:reference [
           fhir:l <http://hl7.org/fhir/uv/cg-incubator/DocumentReference/somaticCalledRegions> ;
           fhir:reference [ fhir:v "DocumentReference/somaticCalledRegions" ]
         ]
       ] )
     ] [
       fhir:type [
         fhir:coding ( [
           fhir:system [
             fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"^^xsd:anyURI ;
             fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype>
           ] ;
           fhir:code [ fhir:v "uncalled" ] ;
           fhir:display [ fhir:v "Uncalled" ]
         ] )
       ] ;
       fhir:locus ( [
         fhir:concept [
           fhir:coding ( [
             fhir:system [
               fhir:v "http://www.genenames.org"^^xsd:anyURI ;
               fhir:l <http://www.genenames.org>
             ] ;
             fhir:code [ fhir:v "HGNC:1014" ] ;
             fhir:display [ fhir:v "BCR" ]
           ] )
         ]
       ] ) ;
       fhir:description [ fhir:v "BCR was not callable due to low sequencing coverage in this tumor sample." ]
     ] ) ; #  genomicRegion: studied = full 700-gene panel expressed as a BED file 
     fhir:output ( [
       fhir:file [
         fhir:l <http://hl7.org/fhir/uv/cg-incubator/DocumentReference/somaticVCFfile> ;
         fhir:reference [ fhir:v "DocumentReference/somaticVCFfile" ]
       ] ;
       fhir:type [
         fhir:coding ( [
           fhir:system [
             fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"^^xsd:anyURI ;
             fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat>
           ] ;
           fhir:code [ fhir:v "vcf" ] ;
           fhir:display [ fhir:v "VCF" ]
         ] )
       ]
     ] ) ;
     fhir:performer ( [
       fhir:actor [
         fhir:l <http://hl7.org/fhir/uv/cg-incubator/Practitioner/practitioner02> ;
         fhir:reference [ fhir:v "Practitioner/practitioner02" ]
       ] ;
       fhir:role [
         fhir:coding ( [
           fhir:system [
             fhir:v "http://terminology.hl7.org/CodeSystem/v3-ParticipationType"^^xsd:anyURI ;
             fhir:l <http://terminology.hl7.org/CodeSystem/v3-ParticipationType>
           ] ;
           fhir:code [ fhir:v "PRF" ] ;
           fhir:display [ fhir:v "Performer" ]
         ] )
       ]
     ] ) ;
     fhir:device ( [
       fhir:device [
         fhir:l <http://hl7.org/fhir/uv/cg-incubator/Device/NGS-device> ;
         fhir:reference [ fhir:v "Device/NGS-device" ]
       ] ;
       fhir:function [
         fhir:coding ( [
           a loinc:LA26398-0 ;
           fhir:system [
             fhir:v "http://loinc.org"^^xsd:anyURI ;
             fhir:l <http://loinc.org>
           ] ;
           fhir:code [ fhir:v "LA26398-0" ] ;
           fhir:display [ fhir:v "Sequencing" ]
         ] )
       ]
     ] )
  ] [
     fhir:identifier ( [
       fhir:use [ fhir:v "temp" ] ;
       fhir:system [
         fhir:v "http://example.org/identifiers/genomicAnalyses"^^xsd:anyURI ;
         fhir:l <http://example.org/identifiers/genomicAnalyses>
       ] ;
       fhir:value [ fhir:v "urn:uuid:somatic-analysis-rna-0001" ]
     ] ) ;
     fhir:methodType ( [
       fhir:coding ( [
         fhir:system [
           fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype"^^xsd:anyURI ;
           fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype>
         ] ;
         fhir:code [ fhir:v "rna-analysis" ] ;
         fhir:display [ fhir:v "RNA analysis" ]
       ] )
     ] ) ;
     fhir:changeType ( [
       fhir:coding ( [
         fhir:system [
           fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ;
           fhir:l <http://www.sequenceontology.org>
         ] ;
         fhir:code [ fhir:v "SO:0001565" ] ;
         fhir:display [ fhir:v "gene_fusion" ]
       ] )
     ] [
       fhir:coding ( [
         fhir:system [
           fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ;
           fhir:l <http://www.sequenceontology.org>
         ] ;
         fhir:code [ fhir:v "SO:0001576" ] ;
         fhir:display [ fhir:v "transcript_variant" ]
       ] )
     ] ) ;
     fhir:genomicSourceClass [
       fhir:coding ( [
         a loinc:LA6684-0 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "LA6684-0" ] ;
         fhir:display [ fhir:v "Somatic" ]
       ] )
     ] ;
     fhir:title [ fhir:v "Tumor RNA Sequencing - Gene Fusions and Transcript Variants" ] ;
     fhir:focus ( [
       fhir:l <http://hl7.org/fhir/uv/cg-incubator/Patient/somaticPatient> ;
       fhir:reference [ fhir:v "Patient/somaticPatient" ]
     ] ) ; #  RNA analysis uses tumor biopsy only (not matched normal) 
     fhir:specimen ( [
       fhir:l <http://hl7.org/fhir/uv/cg-incubator/Specimen/tumorSpecimen> ;
       fhir:reference [ fhir:v "Specimen/tumorSpecimen" ]
     ] ) ;
     fhir:date [ fhir:v "2023-02-02T01:01:10-06:00"^^xsd:dateTime ] ;
     fhir:genomicRegion ( [
       fhir:type [
         fhir:coding ( [
           fhir:system [
             fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"^^xsd:anyURI ;
             fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype>
           ] ;
           fhir:code [ fhir:v "studied" ] ;
           fhir:display [ fhir:v "Studied" ]
         ] )
       ] ;
       fhir:locus ( [
         fhir:reference [
           fhir:l <http://hl7.org/fhir/uv/cg-incubator/DocumentReference/somaticRNAstudiedRegions> ;
           fhir:reference [ fhir:v "DocumentReference/somaticRNAstudiedRegions" ]
         ]
       ] )
     ] ) ;
     fhir:output ( [
       fhir:file [
         fhir:l <http://hl7.org/fhir/uv/cg-incubator/DocumentReference/somaticFusionFile> ;
         fhir:reference [ fhir:v "DocumentReference/somaticFusionFile" ]
       ] ;
       fhir:type [
         fhir:coding ( [
           fhir:system [
             fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"^^xsd:anyURI ;
             fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat>
           ] ;
           fhir:code [ fhir:v "vcf" ] ;
           fhir:display [ fhir:v "VCF" ]
         ] )
       ]
     ] ) ;
     fhir:performer ( [
       fhir:actor [
         fhir:l <http://hl7.org/fhir/uv/cg-incubator/Practitioner/practitioner02> ;
         fhir:reference [ fhir:v "Practitioner/practitioner02" ]
       ] ;
       fhir:role [
         fhir:coding ( [
           fhir:system [
             fhir:v "http://terminology.hl7.org/CodeSystem/v3-ParticipationType"^^xsd:anyURI ;
             fhir:l <http://terminology.hl7.org/CodeSystem/v3-ParticipationType>
           ] ;
           fhir:code [ fhir:v "PRF" ] ;
           fhir:display [ fhir:v "Performer" ]
         ] )
       ]
     ] ) ;
     fhir:device ( [
       fhir:device [
         fhir:l <http://hl7.org/fhir/uv/cg-incubator/Device/NGS-device> ;
         fhir:reference [ fhir:v "Device/NGS-device" ]
       ] ;
       fhir:function [
         fhir:coding ( [
           a loinc:LA26398-0 ;
           fhir:system [
             fhir:v "http://loinc.org"^^xsd:anyURI ;
             fhir:l <http://loinc.org>
           ] ;
           fhir:code [ fhir:v "LA26398-0" ] ;
           fhir:display [ fhir:v "Sequencing" ]
         ] )
       ]
     ] )
  ] ) . #  Analysis 1: DNA Tumor/Normal Paired Sequencing 

<http://hl7.org/fhir/uv/cg-incubator/Patient/somaticPatient> a fhir:Uv .

<http://hl7.org/fhir/uv/cg-incubator/ServiceRequest/somaticServiceRequest> a fhir:Uv .

<http://hl7.org/fhir/uv/cg-incubator/Practitioner/practitioner02> a fhir:Uv .

<http://hl7.org/fhir/uv/cg-incubator/Specimen/tumorSpecimen> a fhir:Uv .

<http://hl7.org/fhir/uv/cg-incubator/Specimen/normalSpecimen> a fhir:Uv .

<http://hl7.org/fhir/uv/cg-incubator/DocumentReference/WES-FullSequencedRegion-GRCh38> a fhir:Uv .

<http://hl7.org/fhir/uv/cg-incubator/DocumentReference/somaticCalledRegions> a fhir:Uv .

<http://hl7.org/fhir/uv/cg-incubator/DocumentReference/somaticVCFfile> a fhir:Uv .

<http://hl7.org/fhir/uv/cg-incubator/Device/NGS-device> a fhir:Uv .

<http://hl7.org/fhir/uv/cg-incubator/DocumentReference/somaticRNAstudiedRegions> a fhir:Uv .

<http://hl7.org/fhir/uv/cg-incubator/DocumentReference/somaticFusionFile> a fhir:Uv .

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