Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT 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

: HER2byImmuneStainExample - JSON Representation

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{
  "resourceType" : "Observation",
  "id" : "HER2byImmuneStainExample",
  "meta" : {
    "profile" : [
      🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker"
    ]
  },
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"HER2byImmuneStainExample\"> </a><a name=\"hcHER2byImmuneStainExample\"> </a></p><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\">Resource Observation &quot;HER2byImmuneStainExample&quot; </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-molecular-biomarker.html\">Molecular Biomarker</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, A characterization of a given biomarker observation. <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#biomarker-category)</span></p><p><b>code</b>: HER2 Ag [Presence] in Tissue by Immune stain <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#18474-7)</span></p><p><b>subject</b>: <a href=\"Patient-CGPatientExample01.html\">Patient/CGPatientExample01</a> &quot; EVERYMAN&quot;</p><p><b>effective</b>: 2019-04-01</p><p><b>performer</b>: <a href=\"Organization-ExampleOrg.html\">Organization/ExampleOrg</a> &quot;some lab&quot;</p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA9633-4)</span></p><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></p><p><b>value</b>: ERBB2 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgnc.html\">HUGO Gene Nomenclature Committee Genes</a>#HGNC:3430)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: A characterization of a given biomarker observation. <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#biomarker-category)</span></p><p><b>value</b>: immune stain category <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-molecular-biomarker-ontology-cs.html\">Molecular Biomarker Ontology Codes</a>#immuneStain)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: A characterization of a given biomarker observation. <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#biomarker-category)</span></p><p><b>value</b>: cell receptor category <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-molecular-biomarker-ontology-cs.html\">Molecular Biomarker Ontology Codes</a>#cellReceptor)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: A characterization of a given biomarker observation. <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#biomarker-category)</span></p><p><b>value</b>: protein category <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-molecular-biomarker-ontology-cs.html\">Molecular Biomarker Ontology Codes</a>#protein)</span></p></blockquote></div>"
  },
  "status" : "final",
  "category" : [
    {
      "coding" : [
        {
          "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
          "code" : "laboratory"
        }
      ]
    },
    {
      "coding" : [
        {
          "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
          "code" : "biomarker-category"
        }
      ]
    }
  ],
  "code" : {
    "coding" : [
      {
        "system" : "http://loinc.org",
        "code" : "18474-7",
        "display" : "HER2 Ag [Presence] in Tissue by Immune stain"
      }
    ]
  },
  "subject" : {
    🔗 "reference" : "Patient/CGPatientExample01"
  },
  "effectiveDateTime" : "2019-04-01",
  "performer" : [
    {
      🔗 "reference" : "Organization/ExampleOrg"
    }
  ],
  "valueCodeableConcept" : {
    "coding" : [
      {
        "system" : "http://loinc.org",
        "code" : "LA9633-4",
        "display" : "Present"
      }
    ]
  },
  "component" : [
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48018-6",
            "display" : "Gene studied [ID]"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://www.genenames.org",
            "code" : "HGNC:3430",
            "display" : "ERBB2"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
            "code" : "biomarker-category"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs",
            "code" : "immuneStain",
            "display" : "immune stain category"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
            "code" : "biomarker-category"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs",
            "code" : "cellReceptor",
            "display" : "cell receptor category"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
            "code" : "biomarker-category"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs",
            "code" : "protein",
            "display" : "protein category"
          }
        ]
      }
    }
  ]
}