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

## : SNVexample - JSON Representation

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    {
      "resourceType" : "Observation",
      "id" : "SNVexample",
      "meta" : {
        "profile" : [
          🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
        ]
      },
      "text" : {
        "status" : "generated",
        "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation SNVexample</b></p><a name=\"SNVexample\"> </a><a name=\"hcSNVexample\"> </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-variant.html\">Variant</a></p></div><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2023-06-01</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>method</b>: <span title=\"Codes:{http://loinc.org LA26398-0}\">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://slk-kliniken.de/fhir/namingSystem/tissueID</code>/16-123456-23</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied ID</span></p><p><b>value</b>: <span title=\"Codes:{http://www.genenames.org HGNC:644}\">AR</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48001-2}\">Cytogenetic (chromosome) location</span></p><p><b>value</b>: <span title=\"Codes:\">chrX</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 62374-4}\">Human reference sequence assembly version</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA14029-5}\">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48002-0}\">Genomic source class</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6684-0}\">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48004-6}\">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NM_000044.6:c.7G&gt;A}\">NM_000044.6:c.7G&gt;A</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48005-3}\">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NP_000035.2:p.Val3Met}\">NP_000035.2:p.Val3Met</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51958-7}\">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_000044.3}\">NM_000044.6</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81258-6}\">Sample VAF</span></p><p><b>value</b>: 0.44 decimal</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 82121-5}\">Allelic read depth</span></p><p><b>value</b>: 120 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM  code1 = '1')</span></p></blockquote></div>"
      },
      "status" : "final",
      "category" : [
        {
          "coding" : [
            {
              "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
              "code" : "laboratory"
            }
          ]
        },
        {
          "coding" : [
            {
              "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
              "code" : "GE"
            }
          ]
        }
      ],
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "69548-6",
            "display" : "Genetic variant assessment"
          }
        ]
      },
      "subject" : {
        🔗 "reference" : "Patient/ExamplePatient"
      },
      "effectiveDateTime" : "2023-06-01",
      "performer" : [
        {
          🔗 "reference" : "Organization/ExampleLab"
        }
      ],
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA9633-4",
            "display" : "Present"
          }
        ]
      },
      "method" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA26398-0",
            "display" : "Sequencing"
          }
        ]
      },
      "specimen" : {
        "identifier" : {
          "system" : "http://slk-kliniken.de/fhir/namingSystem/tissueID",
          "value" : "16-123456-23"
        }
      },
      "component" : [
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "48018-6",
                "display" : "Gene studied ID"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://www.genenames.org",
                "code" : "HGNC:644",
                "display" : "AR"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "48001-2",
                "display" : "Cytogenetic (chromosome) location"
              }
            ]
          },
          "valueCodeableConcept" : {
            "text" : "chrX"
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "62374-4",
                "display" : "Human reference sequence assembly version"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "LA14029-5",
                "display" : "GRCh37"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "48002-0",
                "display" : "Genomic source class"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "LA6684-0",
                "display" : "Somatic"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "48004-6",
                "display" : "DNA change (c.HGVS)"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://varnomen.hgvs.org",
                "code" : "NM_000044.6:c.7G>A"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "48005-3",
                "display" : "Amino acid change (pHGVS)"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://varnomen.hgvs.org",
                "code" : "NP_000035.2:p.Val3Met",
                "display" : "NP_000035.2:p.Val3Met"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "51958-7",
                "display" : "Transcript reference sequence [ID]"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://www.ncbi.nlm.nih.gov/refseq",
                "code" : "NM_000044.3",
                "display" : "NM_000044.6"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "81258-6",
                "display" : "Sample VAF"
              }
            ]
          },
          "valueQuantity" : {
            "value" : 0.44,
            "unit" : "decimal",
            "system" : "http://unitsofmeasure.org"
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "82121-5",
                "display" : "Allelic read depth"
              }
            ]
          },
          "valueQuantity" : {
            "value" : 120,
            "unit" : "reads per base pair",
            "system" : "http://unitsofmeasure.org",
            "code" : "1"
          }
        }
      ]
    }