Genomics Reporting Implementation Guide
2.0.0 - CI Build

Genomics Reporting Implementation Guide, published by HL7 International Clinical Genomics Work Group. This is not an authorized publication; it is the continuous build for version 2.0.0). This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

: Example - Genomics Reporting - JSON Representation

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{
  "resourceType" : "Bundle",
  "id" : "diagnosticreport-cgexample",
  "type" : "collection",
  "entry" : [
    {
      "fullUrl" : "http://example.org/fhir/DiagnosticReport/report",
      "resource" : {
        "resourceType" : "DiagnosticReport",
        "id" : "report",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "basedOn" : [
          {
            "reference" : "DiagnosticRequest/request"
          }
        ],
        "status" : "final",
        "code" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "81247-9"
            }
          ]
        },
        "subject" : {
          "reference" : "Patient/patient"
        },
        "effectiveDateTime" : "2016",
        "issued" : "2016-09-06T00:00:00-05:00",
        "performer" : [
          {
            "reference" : "Organization/lab"
          }
        ],
        "result" : [
          {
            "reference" : "Observation/overall-interp"
          },
          {
            "reference" : "Observation/discrete-variant"
          },
          {
            "reference" : "Observation/dis-path"
          },
          {
            "reference" : "Observation/complex-variant"
          },
          {
            "reference" : "Observation/complex-dis-path"
          },
          {
            "reference" : "Observation/pharmPanel"
          }
        ],
        "presentedForm" : [
          {
            "contentType" : "text/plain",
            "data" : "UHV0IHRoZSByZXBvcnQgdGV4dCBoZXJlIC0gbWltZS1lbmNvZGVk"
          }
        ]
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Patient/patient",
      "resource" : {
        "resourceType" : "Patient",
        "id" : "patient",
        "text" : {
          "status" : "additional",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">This would contain patient identifiers, demographics, etc.</div>"
        }
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Specimen/specimen",
      "resource" : {
        "resourceType" : "Specimen",
        "id" : "specimen",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/specimen"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "subject" : {
          "reference" : "Patient/patient"
        }
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Organization/lab",
      "resource" : {
        "resourceType" : "Organization",
        "id" : "lab",
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "name" : "Some lab"
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/DiagnosticRequest/request",
      "resource" : {
        "resourceType" : "ServiceRequest",
        "id" : "request",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/servicerequest"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "status" : "active",
        "intent" : "original-order",
        "code" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "81247-9"
            }
          ]
        },
        "subject" : {
          "reference" : "Patient/patient"
        },
        "reasonCode" : [
          {
            "text" : "Worried about family planning"
          }
        ]
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Observation/overall-interp",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "overall-interp",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/overall-interpretation"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "status" : "final",
        "category" : [
          {
            "coding" : [
              {
                "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
                "code" : "laboratory"
              }
            ]
          }
        ],
        "code" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "51968-6"
            }
          ]
        },
        "subject" : {
          "reference" : "Patient/patient"
        },
        "effectiveDateTime" : "2016",
        "issued" : "2016-09-06T00:00:00-05:00",
        "performer" : [
          {
            "reference" : "Organization/lab"
          }
        ],
        "valueCodeableConcept" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "LA6576-8",
              "display" : "Positive"
            },
            {
              "system" : "http://snomed.info/sct",
              "code" : "10828004",
              "display" : "Positive"
            }
          ]
        },
        "specimen" : {
          "reference" : "Specimen/specimen"
        }
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Observation/discrete-variant",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "discrete-variant",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "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"
            }
          ]
        },
        "subject" : {
          "reference" : "Patient/patient"
        },
        "effectiveDateTime" : "2016",
        "issued" : "2016-09-06T00:00:00-05:00",
        "performer" : [
          {
            "reference" : "Organization/lab"
          }
        ],
        "valueCodeableConcept" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "LA9633-4",
              "display" : "Present"
            }
          ]
        },
        "specimen" : {
          "reference" : "Specimen/specimen"
        },
        "component" : [
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "81252-9",
                  "display" : "Discrete genetic variant"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/clinvar",
                  "version" : "???",
                  "code" : "30880",
                  "display" : "NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys)"
                },
                {
                  "system" : "http://example.org/cigar",
                  "code" : "tbd"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48018-6"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/hgnc",
                  "code" : "21497",
                  "display" : "ACAD9"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "51958-7"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://www.ncbi.nlm.nih.gov/refseq",
                  "code" : "NM_014049.4"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48013-7"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://www.ncbi.nlm.nih.gov/refseq",
                  "code" : "NG_017064.1"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "81290-9"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/HGVS.g",
                  "version" : "15.11",
                  "code" : "NC_000003.11:g.128625063C>T"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "81255-2"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/dbsnp",
                  "version" : "137",
                  "code" : "rs368949613"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48004-6"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/HGVS.c",
                  "version" : "15.11",
                  "code" : "c.1249C>T"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48005-3"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/HGVS.p",
                  "version" : "15.11",
                  "code" : "p.Arg417Cys"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48019-4"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "LA6690-7",
                  "display" : "Substitution"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48006-1"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "LA6698-0",
                  "display" : "Missense"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "69547-8"
                }
              ]
            },
            "valueString" : "C"
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes",
                  "code" : "exact-start-end"
                }
              ]
            },
            "valueRange" : {
              "low" : {
                "value" : 31731
              },
              "high" : {
                "value" : 31731
              }
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "69551-0"
                }
              ]
            },
            "valueString" : "T"
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48001-2"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/Chrom-Loc",
                  "code" : "3q21"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48002-0"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "LA6683-2",
                  "display" : "Germline"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "53034-5"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "LA6706-1",
                  "display" : "Heterozygous"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "81258-6"
                }
              ]
            },
            "valueQuantity" : {
              "value" : 47,
              "system" : "http://unitsofmeasure.org",
              "code" : "%"
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "82121-5"
                }
              ]
            },
            "valueQuantity" : {
              "value" : 208,
              "system" : "http://unitsofmeasure.org",
              "code" : "1"
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "82155-3"
                }
              ]
            },
            "valueQuantity" : {
              "value" : 1,
              "system" : "http://unitsofmeasure.org",
              "code" : "1"
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "81299-0"
                }
              ]
            },
            "valueQuantity" : {
              "value" : 0.48
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "81300-6"
                }
              ]
            },
            "valueQuantity" : {
              "value" : 1396929,
              "system" : "http://unitsofmeasure.org",
              "code" : "1"
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "81301-4"
                }
              ]
            },
            "valueRange" : {
              "low" : {
                "value" : 13200589
              },
              "high" : {
                "value" : 15592000
              }
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "81302-2"
                }
              ]
            },
            "valueRange" : {
              "low" : {
                "value" : 14184616
              },
              "high" : {
                "value" : 15581544
              }
            }
          }
        ]
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Observation/dis-path",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "dis-path",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "status" : "final",
        "category" : [
          {
            "coding" : [
              {
                "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
                "code" : "laboratory"
              }
            ]
          }
        ],
        "code" : {
          "coding" : [
            {
              "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes",
              "code" : "diagnostic-implication"
            }
          ]
        },
        "subject" : {
          "reference" : "Patient/patient"
        },
        "effectiveDateTime" : "2016",
        "issued" : "2016-09-06T00:00:00-05:00",
        "performer" : [
          {
            "reference" : "Organization/lab"
          }
        ],
        "derivedFrom" : [
          {
            "reference" : "Observation/discrete-variant"
          }
        ],
        "component" : [
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "53037-8"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "LA6668-3",
                  "display" : "Pathogenic"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "81259-4"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/MedGen-Dis",
                  "code" : "C1970173",
                  "display" : "Acyl-CoA dehydrogenase family, member 9, deficiency of"
                }
              ]
            }
          }
        ]
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Observation/complex-variant",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "complex-variant",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "status" : "final",
        "category" : [
          {
            "coding" : [
              {
                "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
                "code" : "laboratory"
              }
            ]
          }
        ],
        "code" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "69548-6"
            }
          ]
        },
        "subject" : {
          "reference" : "Patient/patient"
        },
        "effectiveDateTime" : "2016",
        "issued" : "2016-09-06T00:00:00-05:00",
        "performer" : [
          {
            "reference" : "Organization/lab"
          }
        ],
        "valueCodeableConcept" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "LA9633-4",
              "display" : "Present"
            }
          ]
        },
        "specimen" : {
          "reference" : "Specimen/specimen"
        },
        "hasMember" : [
          {
            "reference" : "Observation/complex-component-D"
          },
          {
            "reference" : "Observation/complex-component-E"
          }
        ],
        "component" : [
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "81263-6"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "LA26218-0",
                  "display" : "Haplotype"
                }
              ]
            }
          }
        ]
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Observation/complex-dis-path",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "complex-dis-path",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "status" : "final",
        "category" : [
          {
            "coding" : [
              {
                "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
                "code" : "laboratory"
              }
            ]
          }
        ],
        "code" : {
          "coding" : [
            {
              "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes",
              "code" : "diagnostic-implication"
            }
          ]
        },
        "subject" : {
          "reference" : "Patient/patient"
        },
        "effectiveDateTime" : "2016",
        "issued" : "2016-09-06T00:00:00-05:00",
        "performer" : [
          {
            "reference" : "Organization/lab"
          }
        ],
        "derivedFrom" : [
          {
            "reference" : "Observation/complex-variant"
          }
        ],
        "component" : [
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "53037-8"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "LA6668-3",
                  "display" : "Pathogenic"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "81259-4"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://snomed.info/sct",
                  "code" : "293498008",
                  "display" : "Debrisoquine adverse reaction (disorder)"
                }
              ]
            }
          }
        ]
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Observation/complex-component-D",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "complex-component-D",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "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"
            }
          ]
        },
        "subject" : {
          "reference" : "Patient/patient"
        },
        "effectiveDateTime" : "2016",
        "issued" : "2016-09-06T00:00:00-05:00",
        "performer" : [
          {
            "reference" : "Organization/lab"
          }
        ],
        "valueCodeableConcept" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "LA9633-4",
              "display" : "Present"
            }
          ]
        },
        "specimen" : {
          "reference" : "Specimen/specimen"
        },
        "component" : [
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "81252-9",
                  "display" : "Discrete genetic variant"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/clinvar",
                  "version" : "???",
                  "code" : "31934",
                  "display" : "NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys)"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "51958-7"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/RefSeq-T",
                  "code" : "NM_000106.5"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48004-6"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/HGVS.c",
                  "version" : "15.11",
                  "code" : "c.886C>T"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48005-3"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/HGVS.p",
                  "version" : "15.11",
                  "code" : "p.Arg296Cys"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48019-4"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "LA6690-7",
                  "display" : "Substitution"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48006-1"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "LA6698-0",
                  "display" : "Missense"
                }
              ]
            }
          }
        ]
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Observation/complex-component-E",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "complex-component-E",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "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"
            }
          ]
        },
        "subject" : {
          "reference" : "Patient/patient"
        },
        "effectiveDateTime" : "2016",
        "issued" : "2016-09-06T00:00:00-05:00",
        "performer" : [
          {
            "reference" : "Organization/lab"
          }
        ],
        "valueCodeableConcept" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "LA9633-4",
              "display" : "Present"
            }
          ]
        },
        "specimen" : {
          "reference" : "Specimen/specimen"
        },
        "component" : [
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "81252-9",
                  "display" : "Discrete genetic variant"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/clinvar",
                  "version" : "???",
                  "code" : "38486",
                  "display" : "NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr)"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "51958-7"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/RefSeq-T",
                  "code" : "NM_000106.5"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48004-6"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/HGVS.c",
                  "version" : "15.11",
                  "code" : "c.1457G>C"
                }
              ]
            }
          }
        ]
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Observation/pharmPanel",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "pharmPanel",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/grouper"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "extension" : [
          {
            "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/RecommendedAction",
            "valueReference" : {
              "reference" : "Task/usage"
            }
          }
        ],
        "status" : "final",
        "category" : [
          {
            "coding" : [
              {
                "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
                "code" : "laboratory"
              }
            ]
          }
        ],
        "code" : {
          "coding" : [
            {
              "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes",
              "code" : "grouper"
            }
          ]
        },
        "subject" : {
          "reference" : "Patient/patient"
        },
        "effectiveDateTime" : "2016",
        "issued" : "2016-09-06T00:00:00-05:00",
        "performer" : [
          {
            "reference" : "Organization/lab"
          }
        ],
        "hasMember" : [
          {
            "reference" : "Observation/haplotype"
          },
          {
            "reference" : "Observation/genotype"
          },
          {
            "reference" : "Observation/metab"
          },
          {
            "reference" : "Observation/efficacy"
          }
        ]
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Observation/haplotype",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "haplotype",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "status" : "final",
        "category" : [
          {
            "coding" : [
              {
                "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
                "code" : "laboratory"
              }
            ]
          }
        ],
        "code" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "84414-2"
            }
          ]
        },
        "subject" : {
          "reference" : "Patient/patient"
        },
        "effectiveDateTime" : "2016",
        "issued" : "2016-09-06T00:00:00-05:00",
        "performer" : [
          {
            "reference" : "Organization/lab"
          }
        ],
        "valueCodeableConcept" : {
          "coding" : [
            {
              "system" : "http://example.org/???",
              "code" : "*2"
            }
          ]
        },
        "specimen" : {
          "reference" : "Specimen/specimen"
        },
        "derivedFrom" : [
          {
            "reference" : "Observation/discrete-variant"
          }
        ]
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Observation/genotype",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "genotype",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "status" : "final",
        "category" : [
          {
            "coding" : [
              {
                "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
                "code" : "laboratory"
              }
            ]
          }
        ],
        "code" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "84413-4"
            }
          ]
        },
        "subject" : {
          "reference" : "Patient/patient"
        },
        "effectiveDateTime" : "2016",
        "issued" : "2016-09-06T00:00:00-05:00",
        "performer" : [
          {
            "reference" : "Organization/lab"
          }
        ],
        "valueCodeableConcept" : {
          "coding" : [
            {
              "system" : "http://www.pharmvar.org",
              "code" : "CYP2C9 *2/*5",
              "display" : "CYP2C9 *2/*5"
            }
          ]
        },
        "specimen" : {
          "reference" : "Specimen/specimen"
        },
        "derivedFrom" : [
          {
            "reference" : "Observation/haplotype"
          }
        ],
        "component" : [
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48018-6"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/hgnc",
                  "code" : "2623",
                  "display" : "CYP2C9"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48018-6"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://example.org/hgnc",
                  "code" : "23663",
                  "display" : "VKORC1"
                }
              ]
            }
          }
        ]
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Observation/metab",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "metab",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "status" : "final",
        "category" : [
          {
            "coding" : [
              {
                "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
                "code" : "laboratory"
              }
            ]
          }
        ],
        "code" : {
          "coding" : [
            {
              "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes",
              "code" : "therapeutic-implication"
            }
          ]
        },
        "subject" : {
          "reference" : "Patient/patient"
        },
        "effectiveDateTime" : "2016",
        "issued" : "2016-09-06T00:00:00-05:00",
        "performer" : [
          {
            "reference" : "Organization/lab"
          }
        ],
        "derivedFrom" : [
          {
            "reference" : "Observation/genotype"
          }
        ],
        "component" : [
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "51963-7"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://www.nlm.nih.gov/research/umls/rxnorm",
                  "code" : "11289",
                  "display" : "Warfarin"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "53040-2"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "LA25390-8",
                  "display" : "Rapid metabolizer"
                }
              ]
            }
          }
        ]
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Observation/efficacy",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "efficacy",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "status" : "final",
        "category" : [
          {
            "coding" : [
              {
                "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
                "code" : "laboratory"
              }
            ]
          }
        ],
        "code" : {
          "coding" : [
            {
              "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes",
              "code" : "therapeutic-implication"
            }
          ]
        },
        "subject" : {
          "reference" : "Patient/patient"
        },
        "effectiveDateTime" : "2016",
        "issued" : "2016-09-06T00:00:00-05:00",
        "performer" : [
          {
            "reference" : "Organization/lab"
          }
        ],
        "derivedFrom" : [
          {
            "reference" : "Observation/genotype"
          }
        ],
        "component" : [
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "51961-1"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "LA6676-6",
                  "display" : "Resistant"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "51963-7"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://www.nlm.nih.gov/research/umls/rxnorm",
                  "code" : "11289",
                  "display" : "Warfarin"
                }
              ]
            }
          }
        ]
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Observation/highrisk",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "highrisk",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "status" : "final",
        "category" : [
          {
            "coding" : [
              {
                "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
                "code" : "laboratory"
              }
            ]
          }
        ],
        "code" : {
          "coding" : [
            {
              "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes",
              "code" : "therapeutic-implication"
            }
          ]
        },
        "subject" : {
          "reference" : "Patient/patient"
        },
        "effectiveDateTime" : "2016",
        "issued" : "2016-09-06T00:00:00-05:00",
        "performer" : [
          {
            "reference" : "Organization/lab"
          }
        ],
        "derivedFrom" : [
          {
            "reference" : "Observation/genotype"
          }
        ],
        "component" : [
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "83009-1"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "LA19542-2",
                  "display" : "Low risk"
                }
              ]
            }
          },
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "51963-7"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://www.nlm.nih.gov/research/umls/rxnorm",
                  "code" : "11289",
                  "display" : "Warfarin"
                }
              ]
            }
          }
        ]
      }
    },
    {
      "fullUrl" : "http://example.org/fhir/Task/usage",
      "resource" : {
        "resourceType" : "Task",
        "id" : "usage",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/task-med-chg"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
        },
        "contained" : [
          {
            "resourceType" : "MedicationStatement",
            "id" : "med",
            "status" : "unknown",
            "medicationCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://www.nlm.nih.gov/research/umls/rxnorm",
                  "code" : "11289",
                  "display" : "Warfarin"
                }
              ]
            },
            "subject" : {
              "reference" : "Patient/patient"
            }
          }
        ],
        "status" : "requested",
        "intent" : "proposal",
        "code" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "LA26423-6",
              "display" : "Increase dose"
            }
          ],
          "text" : "May need higher dosage than usual."
        },
        "focus" : {
          "reference" : "#med"
        },
        "for" : {
          "reference" : "Patient/patient"
        },
        "requester" : {
          "reference" : "Organization/lab"
        },
        "reasonReference" : {
          "reference" : "Observation/metab"
        }
      }
    }
  ]
}