genomics-reporting-viewer

Genetic Variants

Example

Rendered

Molecular Report

Code

  <genetic-variants genetic-observations='
    [{
      "resourceType":"Observation",
      "id":"354",
      "meta":
        {  
          "versionId":"1",
          "lastUpdated":"2020-05-25T20:58:56.935+02:00",
          "source":"#2eVInoNVLgo7AOBm",
          "profile":["http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"]
        },
        "extension":
          [{
            "url":"http://hl7.org/fhir/StructureDefinition/workflow-episodeOfCare",
            "valueReference":
              {
              "reference":"https://fhir.molit.eu/EpisodeOfCare/123"
              }
          }],
        "basedOn":
          [{
            "reference":"https://fhir.molit.eu/ServiceRequest/789"
          }],
        "status":"final",
        "category":
          [{
            "coding":
              [{
                "system":"http://terminology.hl7.org/CodeSystem/observation-category",
                  "code":"laboratory",
                  "display":"Laboratory"
              }]
          }],
        "code":
          {
            "coding":
              [{
                "system":"http://loinc.org",
                "code":"69548-6",
                "display":"Genetic variant assessment"
              }]
          },
        "subject":
          {
            "reference":"https://fhir.molit.eu/Patient/456"},
            "valueCodeableConcept":
              {
                "coding":
                  [{
                    "system":"http://loinc.org",
                    "code":"LA9633-4",
                    "display":"Present"
                  }]
              },
            "specimen":
              {
                "reference":"https://fhir.molit.eu/Specimen/123"
              },
            "component":
              [{
               "code":
                  {
                    "coding":
                      [{
                        "system":"http://loinc.org",
                        "code":"48019-4",
                        "display":"DNA change type"
                      }]
                  },
                "valueCodeableConcept":
                  {
                    "coding":
                      [{
                        "system":"http://sequenceontology.org",
                        "code":"SO:0001019",
                        "display":"copy_number_variation"
                      },
                      {
                        "system":"http://sequenceontology.org",
                        "code":"amp",
                         "display":"amp"
                      }]
                  }
              },{
                "code":
                  {
                    "coding":
                      [{
                        "system:""http://loinc.org",
                        "code":"62374-4",
                        "display":"Human reference sequence assembly version"
                      }]
                  },
                "valueCodeableConcept":
                  {
                    "coding":
                      [{
                        "system":"http://molit.eu/fhir/vitu-tbd-codes",
                        "code":"hg19",
                        "display":"hg19"
                      }]
                  }
              },{
                "code":
                  {
                    "coding":
                      [{
                        "system":"http://molit.eu/fhir/vitu-tbd-codes",
                        "code":"cnv-size",
                        "display":"cnv-size"
                      }]
                  },
                "valueCodeableConcept":
                  {
                    "coding":
                      [{
                        "system":"http://molite.eu/fhir/cnv-size",
                        "code":"non-focal",
                        "display":"non-focal"
                      }]
                  }
              },{
                "code":
                  {
                    "coding":
                      [{
                        "system":"http://loinc.org",
                        "code":"82155-3",
                        "display":"Genomic structural variant copy number"
                      }]
                  },
                "valueQuantity":
                  {
                    "value":5
                  }
              },{
                "code":
                  {
                    "coding":
                      [{
                        "system":"http://loinc.org",
                        "code":"48018-6",
                        "display":"Gene studied ID"
                      }]
                  },
                "valueCodeableConcept":
                  {
                    "coding":
                      [{
                        "system":"http://www.genenames.org/geneId",
                        "code":"MUC1",
                        "display":"MUC1"
                      }]
                  }
              },{
                "code":
                  {
                    "coding":
                      [{
                        "system":"http://loinc.org",
                        "code":"48018-6",
                        "display":"Gene studied ID"
                      }]
                  },
                "valueCodeableConcept":
                  {
                    "coding":
                      [{
                        "system":"http://www.genenames.org/geneId",
                        "code":"MUC2",
                        "display":"MUC2"
                      }]
                  }
              },{  
                "code":
                  {
                    "coding":
                      [{
                        "system":"http://molit.eu/fhir/vitu-tbd-codes",
                        "code":"exons",
                        "display":"Exons"
                      }]
                  },
                "valueRange":
                  {
                    "low":{"value":0},
                    "high":{"value":0}
                  }
              },{
                "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_002456.5",
                        "display":"NM_002456.5"
                      }]
                  }
              },{
                "code":
                  {
                    "coding":
                      [{
                        "system":"http://loinc.org",
                        "code":"48001-2",
                        "display":"Cytogenetic (chromosome) location"
                      }]
                  },
                "valueCodeableConcept":
                  {
                    "coding":
                      [{
                        "system":"https://ghr.nlm.nih.gov/primer/howgeneswork/genelocation",
                        "code":"chr1",
                        "display":"chr1"
                      }]
                  }
              },{
                "code":
                  {
                    "coding":
                      [{
                        "system":"http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes",
                        "code":"exact-start-end",
                        "display":"Variant exact start and end"
                      }]
                  },
                "valueRange":
                  {
                    "low":{"value":155158300},
                    "high":{"value":155162706}
                  }
              },{
                "code":
                  {
                    "coding":
                      [{
                        "system":"http://loinc.org",
                        "code":"48002-0",
                        "display":"Genomic source class [Type]"
                      }]
                  },
                "valueCodeableConcept":
                  {
                    "coding":
                      [{
                        "system":"http://loinc.org",
                        "code":"LA6684-0",
                        "display":"Somatic"
                      }]
                  }
              }]
          }
      }]
  }]' 
  type="sv" gv-title="SVs"></genetic-variants>