Genomics Reporting Implementation Guide
3.0.0 - STU3 International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0: STU3) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

: bundle-sequence-phase-relation-CYP2C19 - JSON Representation

Raw json | Download

{
  "resourceType" : "Bundle",
  "id" : "bundle-sequence-phase-relation-CYP2C19",
  "type" : "transaction",
  "entry" : [
    {
      "fullUrl" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfe60",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "dv-5c7e9e1ca8252",
        "meta" : {
          "profile" : [
            🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_dv-5c7e9e1ca8252\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation dv-5c7e9e1ca8252</b></p><a name=\"dv-5c7e9e1ca8252\"> </a><a name=\"hcdv-5c7e9e1ca8252\"> </a><a name=\"dv-5c7e9e1ca8252-en-US\"> </a><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=\"Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeac\">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: 2019-03-05 16:04:44+0000</p><p><b>performer</b>: <a href=\"Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeab\">Bundle: type = transaction</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 62374-4}\">Human reference sequence assembly version</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA14029-5}\">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48013-7}\">Genomic reference sequence ID</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NC_000010.10}\">NC_000010.10</span></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://loinc.org LA6706-1}\">heterozygous</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69547-8}\">Ref nucleotide</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69551-0}\">Alt allele</span></p><p><b>value</b>: A</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 92822-6}\">Genomic coord system</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA30102-0}\">1-based character counting</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81254-5}\">Genomic allele start-end</span></p><p><b>value</b>: 96527334-?</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" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac"
        },
        "effectiveDateTime" : "2019-03-05",
        "issued" : "2019-03-05T16:04:44+00:00",
        "performer" : [
          {
            "reference" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab"
          }
        ],
        "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/refseq",
                  "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://loinc.org",
                  "code" : "81254-5"
                }
              ]
            },
            "valueRange" : {
              "low" : {
                "value" : 96527334
              }
            }
          }
        ]
      },
      "request" : {
        "method" : "POST",
        "url" : "Observation"
      }
    },
    {
      "fullUrl" : "urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe01",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "dv-5c7e9e1ca82e4",
        "meta" : {
          "profile" : [
            🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_dv-5c7e9e1ca82e4\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation dv-5c7e9e1ca82e4</b></p><a name=\"dv-5c7e9e1ca82e4\"> </a><a name=\"hcdv-5c7e9e1ca82e4\"> </a><a name=\"dv-5c7e9e1ca82e4-en-US\"> </a><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=\"Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeac\">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: 2019-03-05 16:04:44+0000</p><p><b>performer</b>: <a href=\"Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeab\">Bundle: type = transaction</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 62374-4}\">Human reference sequence assembly version</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA14029-5}\">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48013-7}\">Genomic reference sequence ID</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NC_000010.10}\">NC_000010.10</span></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://loinc.org LA6706-1}\">heterozygous</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69547-8}\">Ref nucleotide</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69551-0}\">Alt allele</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 92822-6}\">Genomic coord system</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA30102-0}\">1-based character counting</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81254-5}\">Genomic allele start-end</span></p><p><b>value</b>: 96527722-?</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" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac"
        },
        "effectiveDateTime" : "2019-03-05",
        "issued" : "2019-03-05T16:04:44+00:00",
        "performer" : [
          {
            "reference" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab"
          }
        ],
        "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/refseq",
                  "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://loinc.org",
                  "code" : "81254-5"
                }
              ]
            },
            "valueRange" : {
              "low" : {
                "value" : 96527722
              }
            }
          }
        ]
      },
      "request" : {
        "method" : "POST",
        "url" : "Observation"
      }
    },
    {
      "fullUrl" : "urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe02",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "sid-5c7e9e1ca8a29",
        "meta" : {
          "profile" : [
            🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_sid-5c7e9e1ca8a29\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation sid-5c7e9e1ca8a29</b></p><a name=\"sid-5c7e9e1ca8a29\"> </a><a name=\"hcsid-5c7e9e1ca8a29\"> </a><a name=\"sid-5c7e9e1ca8a29-en-US\"> </a><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 82120-7}\">Allelic phase</span></p><p><b>subject</b>: <a href=\"Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeac\">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: 2019-03-05 16:04:44+0000</p><p><b>performer</b>: <a href=\"Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeab\">Bundle: type = transaction</a></p><p><b>value</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/sequence-phase-relationship-cs Cis}\">Cis</span></p><p><b>derivedFrom</b>: </p><ul><li><a href=\"Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfe60\">Bundle: type = transaction</a></li><li><a href=\"Bundle-bundle-CYP2C19.html#urn-uuid-20ac0aeb-6bd4-4e92-a891-d44a807bfe01\">Bundle: type = transaction</a></li></ul></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" : "82120-7",
              "display" : "Allelic phase"
            }
          ]
        },
        "subject" : {
          "reference" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac"
        },
        "effectiveDateTime" : "2019-03-05",
        "issued" : "2019-03-05T16:04:44+00:00",
        "performer" : [
          {
            "reference" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab"
          }
        ],
        "valueCodeableConcept" : {
          "coding" : [
            {
              "system" : "http://terminology.hl7.org/CodeSystem/sequence-phase-relationship-cs",
              "code" : "Cis",
              "display" : "Cis"
            }
          ]
        },
        "derivedFrom" : [
          {
            "reference" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfe60"
          },
          {
            "reference" : "urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe01"
          }
        ]
      },
      "request" : {
        "method" : "POST",
        "url" : "Observation"
      }
    },
    {
      "fullUrl" : "urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe03",
      "resource" : {
        "resourceType" : "DiagnosticReport",
        "id" : "sequence-phase-relation-CYP2C19",
        "meta" : {
          "profile" : [
            🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"DiagnosticReport_sequence-phase-relation-CYP2C19\"> </a><p class=\"res-header-id\"><b>Generated Narrative: DiagnosticReport sequence-phase-relation-CYP2C19</b></p><a name=\"sequence-phase-relation-CYP2C19\"> </a><a name=\"hcsequence-phase-relation-CYP2C19\"> </a><a name=\"sequence-phase-relation-CYP2C19-en-US\"> </a><h2><span title=\"Codes:{http://loinc.org 51969-4}\">Genetic analysis report</span> (<span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span>) </h2><table class=\"grid\"/><p><b>Report Details</b></p><table class=\"grid\"><tr><td><b>Code</b></td><td><b>Value</b></td></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr></table></div>"
        },
        "status" : "final",
        "category" : [
          {
            "coding" : [
              {
                "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
                "code" : "GE"
              }
            ]
          }
        ],
        "code" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "51969-4"
            }
          ]
        },
        "result" : [
          {
            "reference" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfe60"
          },
          {
            "reference" : "urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe01"
          },
          {
            "reference" : "urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe02"
          }
        ]
      },
      "request" : {
        "method" : "POST",
        "url" : "DiagnosticReport"
      }
    },
    {
      "fullUrl" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab",
      "resource" : {
        "resourceType" : "Organization",
        "id" : "performingLab",
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Organization_performingLab\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Organization performingLab</b></p><a name=\"performingLab\"> </a><a name=\"hcperformingLab\"> </a><a name=\"performingLab-en-US\"> </a><p><b>name</b>: aTypingLab Inc</p><p><b>alias</b>: aTL</p><p><b>telecom</b>: ph: 1-800-555-1234(Work)</p><p><b>address</b>: 123 Main St, Sometown, ND 99999(work)</p></div>"
        },
        "name" : "aTypingLab Inc",
        "alias" : [
          "aTL"
        ],
        "telecom" : [
          {
            "system" : "phone",
            "value" : "1-800-555-1234",
            "use" : "work",
            "rank" : 1
          }
        ],
        "address" : [
          {
            "use" : "work",
            "type" : "both",
            "text" : "123 Main St, Sometown, ND 99999",
            "line" : [
              "123 Main St"
            ],
            "city" : "Sometown",
            "state" : "ND",
            "postalCode" : "99999",
            "country" : "USA"
          }
        ]
      },
      "request" : {
        "method" : "POST",
        "url" : "Organization"
      }
    },
    {
      "fullUrl" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac",
      "resource" : {
        "resourceType" : "Patient",
        "id" : "patient",
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Patient_patient\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Patient patient</b></p><a name=\"patient\"> </a><a name=\"hcpatient\"> </a><a name=\"patient-en-US\"> </a><p style=\"border: 1px #661aff solid; background-color: #e6e6ff; padding: 10px;\">John Storm(official) Male, DoB: 1986-12-31</p><hr/></div>"
        },
        "name" : [
          {
            "use" : "official",
            "text" : "John Storm",
            "family" : "Storm",
            "given" : [
              "John"
            ]
          },
          {
            "use" : "nickname",
            "text" : "Johnny Storm",
            "family" : "Storm",
            "given" : [
              "Johnny"
            ]
          },
          {
            "use" : "nickname",
            "text" : "The Human Torch"
          }
        ],
        "gender" : "male",
        "birthDate" : "1986-12-31"
      },
      "request" : {
        "method" : "POST",
        "url" : "Patient"
      }
    }
  ]
}