GenomeX Data Exchange FHIR IG
0.2.0 - draft

GenomeX Data Exchange FHIR IG, published by MITRE. This guide is not an authorized publication; it is the continuous build for version 0.2.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/CodeX-HL7-FHIR-Accelerator/GenomeX-DataExchange/ and changes regularly. See the Directory of published versions

: PrenatalVariant2FragileXSyndromePatientFemale - JSON Representation

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{
  "resourceType" : "Observation",
  "id" : "PrenatalVariant2FragileXSyndromePatientFemale",
  "meta" : {
    "versionId" : "1",
    "lastUpdated" : "2024-09-25T00:02:13.030+00:00",
    "source" : "#mzuK1EHcvMPipAda",
    "profile" : [
      🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
    ]
  },
  "text" : {
    "status" : "extensions",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation PrenatalVariant2FragileXSyndromePatientFemale</b></p><a name=\"PrenatalVariant2FragileXSyndromePatientFemale\"> </a><a name=\"hcPrenatalVariant2FragileXSyndromePatientFemale\"> </a><a name=\"PrenatalVariant2FragileXSyndromePatientFemale-en-US\"> </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\">version: 1; Last updated: 2024-09-25 00:02:13+0000; </p><p style=\"margin-bottom: 0px\">Information Source: #mzuK1EHcvMPipAda</p><p style=\"margin-bottom: 0px\">Profile: <a href=\"http://hl7.org/fhir/uv/genomics-reporting/2024Jan/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-PatientFemale.html\">Jenny M (official) Female, DoB: 1988-02-12 ( Patient ID: 7fb905f171204b94b8ee33d33cb624e6\u00a0(use:\u00a0official,\u00a0))</a></p><p><b>effective</b>: 2024-06-26</p><p><b>performer</b>: <a href=\"Practitioner-PractitionerLabDirector.html\">Practitioner PractitionerJane Smith </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><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 53037-8}\">Genetic variation clinical significance [Imp]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org 66876-4}\">FMR1 gene premutation/premutation+full mutation in Blood by Molecular genetics method</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48002-0}\">Genomic source class [Type]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6683-2}\">Germline</span></p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 1</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-motif}\">Repeat Expansion Motif</span></p><p><b>value</b>: GGC</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 1</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-number}\">Number of Repeat Expansions</span></p><p><b>value</b>: 92</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 53034-5}\">Allelic state</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org LA6706-1}\">Heterozygous</span></p></blockquote><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:3775}\">FMR1</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/PatientFemale"
  },
  "effectiveDateTime" : "2024-06-26",
  "performer" : [
    {
      🔗 "reference" : "Practitioner/PractitionerLabDirector"
    }
  ],
  "valueCodeableConcept" : {
    "coding" : [
      {
        "system" : "http://loinc.org",
        "code" : "LA9633-4",
        "display" : "Present"
      }
    ]
  },
  "method" : {
    "coding" : [
      {
        "system" : "http://loinc.org",
        "code" : "LA26398-0",
        "display" : "Sequencing"
      }
    ]
  },
  "component" : [
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "53037-8",
            "display" : "Genetic variation clinical significance [Imp]"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "66876-4",
            "display" : "FMR1 gene premutation/premutation+full mutation in Blood by Molecular genetics method"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48002-0",
            "display" : "Genomic source class [Type]"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA6683-2",
            "display" : "Germline"
          }
        ]
      }
    },
    {
      "extension" : [
        {
          "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order",
          "valuePositiveInt" : 1
        }
      ],
      "code" : {
        "coding" : [
          {
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
            "code" : "repeat-motif",
            "display" : "Repeat Expansion Motif"
          }
        ]
      },
      "valueString" : "GGC"
    },
    {
      "extension" : [
        {
          "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order",
          "valuePositiveInt" : 1
        }
      ],
      "code" : {
        "coding" : [
          {
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
            "code" : "repeat-number",
            "display" : "Number of Repeat Expansions"
          }
        ]
      },
      "valueQuantity" : {
        "value" : 92
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "53034-5",
            "display" : "Allelic state"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://varnomen.hgvs.org",
            "code" : "LA6706-1",
            "display" : "Heterozygous"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48018-6",
            "display" : "Gene studied [ID]"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://www.genenames.org",
            "code" : "HGNC:3775",
            "display" : "FMR1"
          }
        ]
      }
    }
  ]
}