This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

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• XML
• JSON
• TTL

: Example - subset of CYP2C19 report from 1000 Genomes showing phase - JSON Representation

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{
  "resourceType" : "DiagnosticReport",
  "id" : "sequence-phase-relation-CYP2C19",
  "meta" : {
    "profile" : [
      "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report"
    ]
  },
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><h2><span title=\"Codes: {http://loinc.org 81247-9}\">Genetic analysis report</span> (<span title=\"Codes: {http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span>) </h2><table class=\"grid\"></table><p><b>Report Details</b></p><table class=\"grid\"><tr><td><b>Code</b></td><td><b>Value</b></td><td><b>Reported</b></td></tr><tr><td colspan=\"3\"><i>This Observation could not be resolved</i></td></tr><tr><td colspan=\"3\"><i>This Observation could not be resolved</i></td></tr><tr><td colspan=\"3\"><i>This Observation could not be resolved</i></td></tr></table></div>"
  },
  "contained" : [
    {
      "resourceType" : "Observation",
      "id" : "dv-5c7e9e1ca8252",
      "meta" : {
        "profile" : [
          "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
        ]
      },
      "status" : "final",
      "category" : [
        {
          "coding" : [
            {
              "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
              "code" : "laboratory"
            }
          ]
        }
      ],
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "69548-6",
            "display" : "Genetic variant assessment"
          }
        ]
      },
      "issued" : "2019-03-05T16:04:44+00:00",
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA9633-4",
            "display" : "Present"
          }
        ]
      },
      "component" : [
        {
          "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" : "48013-7",
                "display" : "Genomic reference sequence ID"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://www.ncbi.nlm.nih.gov/nuccore",
                "code" : "NC_000010.10"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "53034-5",
                "display" : "Allelic state"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "LA6706-1",
                "display" : "heterozygous"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "69547-8",
                "display" : "Ref nucleotide"
              }
            ]
          },
          "valueString" : "C"
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "69551-0",
                "display" : "Alt allele"
              }
            ]
          },
          "valueString" : "A"
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "92822-6",
                "display" : "Genomic coord system"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "LA30102-0"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes",
                "code" : "exact-start-end",
                "display" : "Variant exact start and end"
              }
            ]
          },
          "valueRange" : {
            "low" : {
              "value" : 96527334
            }
          }
        }
      ]
    },
    {
      "resourceType" : "Observation",
      "id" : "dv-5c7e9e1ca82e4",
      "meta" : {
        "profile" : [
          "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
        ]
      },
      "status" : "final",
      "category" : [
        {
          "coding" : [
            {
              "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
              "code" : "laboratory"
            }
          ]
        }
      ],
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "69548-6",
            "display" : "Genetic variant assessment"
          }
        ]
      },
      "issued" : "2019-03-05T16:04:44+00:00",
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA9633-4",
            "display" : "Present"
          }
        ]
      },
      "component" : [
        {
          "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" : "48013-7",
                "display" : "Genomic reference sequence ID"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://www.ncbi.nlm.nih.gov/nuccore",
                "code" : "NC_000010.10"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "53034-5",
                "display" : "Allelic state"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "LA6706-1",
                "display" : "heterozygous"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "69547-8",
                "display" : "Ref nucleotide"
              }
            ]
          },
          "valueString" : "C"
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "69551-0",
                "display" : "Alt allele"
              }
            ]
          },
          "valueString" : "G"
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "92822-6",
                "display" : "Genomic coord system"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "LA30102-0"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes",
                "code" : "exact-start-end",
                "display" : "Variant exact start and end"
              }
            ]
          },
          "valueRange" : {
            "low" : {
              "value" : 96527722
            }
          }
        }
      ]
    },
    {
      "resourceType" : "Observation",
      "id" : "sid-5c7e9e1ca8a29",
      "meta" : {
        "profile" : [
          "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship"
        ]
      },
      "status" : "final",
      "category" : [
        {
          "coding" : [
            {
              "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
              "code" : "laboratory"
            }
          ]
        }
      ],
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "82120-7",
            "display" : "Allelic phase"
          }
        ]
      },
      "issued" : "2019-03-05T16:04:44+00:00",
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/SequencePhaseRelationshipCS",
            "code" : "Cis",
            "display" : "Cis"
          }
        ]
      },
      "derivedFrom" : [
        {
          "reference" : "#dv-5c7e9e1ca8252"
        },
        {
          "reference" : "#dv-5c7e9e1ca82e4"
        }
      ]
    }
  ],
  "status" : "final",
  "category" : [
    {
      "coding" : [
        {
          "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
          "code" : "GE"
        }
      ]
    }
  ],
  "code" : {
    "coding" : [
      {
        "system" : "http://loinc.org",
        "code" : "81247-9"
      }
    ],
    "text" : "Genetic analysis report"
  },
  "result" : [
    {
      "reference" : "#dv-5c7e9e1ca8252"
    },
    {
      "reference" : "#dv-5c7e9e1ca82e4"
    },
    {
      "reference" : "#sid-5c7e9e1ca8a29"
    }
  ]
}