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

: analysisTumorNormalDNA - JSON Representation

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{
  "resourceType" : "Procedure",
  "id" : "analysisTumorNormalDNA",
  "meta" : {
    "profile" : [
      🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis"
    ]
  },
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Procedure analysisTumorNormalDNA</b></p><a name=\"analysisTumorNormalDNA\"> </a><a name=\"hcanalysisTumorNormalDNA\"> </a><a name=\"analysisTumorNormalDNA-en-US\"> </a><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-somaticPatient.html\">Substance Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --&gt; (ongoing)))</a></p><p><b>performed</b>: 2023-02-02 01:01:10-0600</p><p><b>note</b>: For technical reasons, BCR gene was deemed uncallable.</p></div>"
  },
  "extension" : [
    {
      "extension" : [
        {
          "url" : "studied",
          "valueReference" : {
            🔗 "reference" : "DocumentReference/WES-FullSequencedRegion-GRCh38"
          }
        },
        {
          "url" : "studied",
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://www.genenames.org",
                "code" : "HGNC:76",
                "display" : "ABL1"
              }
            ]
          }
        },
        {
          "url" : "studied",
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://www.genenames.org",
                "code" : "HGNC:427",
                "display" : "ALK"
              }
            ]
          }
        },
        {
          "url" : "studied",
          "valueCodeableConcept" : {
            "coding" : [
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                "system" : "http://www.genenames.org",
                "code" : "HGNC:583",
                "display" : "APC"
              }
            ]
          }
        },
        {
          "url" : "uncalled",
          "valueReference" : {
            🔗 "reference" : "DocumentReference/WES-UncallableRegions-GRCh38"
          }
        }
      ],
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions"
    },
    {
      "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" : "sequence-analysis-of-the-entire-coding-region",
            "display" : "Sequence analysis of the entire coding region"
          }
        ]
      }
    },
    {
      "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-change-type",
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://sequenceontology.org",
            "code" : "SO:0001483",
            "display" : "SNV"
          }
        ]
      }
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://sequenceontology.org",
            "code" : "SO:0002007",
            "display" : "MNV"
          }
        ]
      }
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://sequenceontology.org",
            "code" : "SO:1000032",
            "display" : "delins"
          }
        ]
      }
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://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/tumorSpecimen"
      }
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen",
      "valueReference" : {
        🔗 "reference" : "Specimen/normalSpecimen"
      }
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus",
      "valueReference" : {
        🔗 "reference" : "Patient/somaticPatient"
      }
    },
    {
      "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/somaticVCFfile"
          }
        }
      ],
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output"
    }
  ],
  "status" : "completed",
  "category" : {
    "coding" : [
      {
        "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
        "code" : "laboratory"
      }
    ]
  },
  "subject" : {
    🔗 "reference" : "Patient/somaticPatient"
  },
  "performedDateTime" : "2023-02-02T01:01:10-06:00",
  "note" : [
    {
      "text" : "For technical reasons, BCR gene was deemed uncallable."
    }
  ]
}