{
  "resourceType" : "Procedure",
  "id" : "lungMass-analysis2",
  "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 lungMass-analysis2</b></p><a name=\"lungMass-analysis2\"> </a><a name=\"hclungMass-analysis2\"> </a><div style=\"display: inline-block; background-color: #fbffeb; 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><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 Source Class</b>: <span title=\"Codes:{http://loinc.org LA6684-0}\">Somatic</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-genomicSpecimen.html\">Specimen: identifier = http://example.org/identifiers/specimens#4; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2019-03-01 01:01:01+0000</a></p><p><b>Genomic Study Analysis Focus</b>: <a href=\"Patient-genomicPatient.html\">John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --&gt; (ongoing)))</a></p><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>called: <a href=\"DocumentReference-CNVAnalysis-called.html\">DocumentReference: identifier = http://example.org/identifiers/files#11120; status = current; docStatus = preliminary; description = CNVAnalysis_called: 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></ul></blockquote><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-genomicVCFfile-cnv.html\">DocumentReference: identifier = http://example.org/identifiers/files#11121; status = current; docStatus = preliminary; description = genomicVCFfile_cnv: A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li></ul></blockquote><p><b>instantiatesUri</b>: <a href=\"https://pubmed.ncbi.nlm.nih.gov/33927380/\">https://pubmed.ncbi.nlm.nih.gov/33927380/</a></p><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-genomicPatient.html\">John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --&gt; (ongoing)))</a></p><p><b>performed</b>: 2019-03-01 01:01:10-0600</p><h3>Performers</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Function</b></td><td><b>Actor</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}\">Performer</span></td><td><a href=\"Practitioner-practitioner02.html\">Jane Doel (Provider number: 11116\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --&gt; (ongoing)))</a></td></tr></table><p><b>note</b>: </p><blockquote><div><p>For technical reasons, PIK3CB was deemed uncallable using this method.</p>\n</div></blockquote></div>"
  },
  "extension" : [{
    "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-genomic-source-class",
    "valueCodeableConcept" : {
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "LA6684-0",
        "display" : "Somatic"
      }]
    }
  },
  {
    "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/genomicSpecimen"
    }
  },
  {
    "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus",
    "valueReference" : {
      "reference" : "Patient/genomicPatient"
    }
  },
  {
    "extension" : [{
      "url" : "studied",
      "valueReference" : {
        "reference" : "DocumentReference/WES-FullSequencedRegion-GRCh38"
      }
    },
    {
      "url" : "called",
      "valueReference" : {
        "reference" : "DocumentReference/CNVAnalysis-called"
      }
    }],
    "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions"
  },
  {
    "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/genomicVCFfile-cnv"
      }
    }],
    "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output"
  }],
  "instantiatesUri" : ["https://pubmed.ncbi.nlm.nih.gov/33927380/"],
  "status" : "completed",
  "category" : {
    "coding" : [{
      "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
      "code" : "laboratory"
    }]
  },
  "subject" : {
    "reference" : "Patient/genomicPatient"
  },
  "performedDateTime" : "2019-03-01T01:01:10-06:00",
  "performer" : [{
    "function" : {
      "coding" : [{
        "system" : "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
        "code" : "PRF",
        "display" : "Performer"
      }]
    },
    "actor" : {
      "reference" : "Practitioner/practitioner02"
    }
  }],
  "note" : [{
    "text" : "For technical reasons, PIK3CB was deemed uncallable using this method."
  }]
}