Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

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

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{
  "resourceType" : "Bundle",
  "id" : "bundle-sequence-phase-relation-CYP2C19",
  "type" : "transaction",
  "entry" : [
    {
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          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"dv-5c7e9e1ca8252\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource Observation &quot;dv-5c7e9e1ca8252&quot; </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-variant.html\">Variant</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69548-6)</span></p><p><b>subject</b>: <a href=\"#Patient_patient\">See above (urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac)</a></p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: Mar 5, 2019, 4:04:44 PM</p><p><b>performer</b>: <a href=\"#Organization_performingLab\">See above (urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab)</a></p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA9633-4)</span></p><blockquote><p><b>component</b></p><p><b>code</b>: Human reference sequence assembly version <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#62374-4)</span></p><p><b>value</b>: GRCh37 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA14029-5)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic reference sequence ID <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48013-7)</span></p><p><b>value</b>: NC_000010.10 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NC_000010.10)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic state <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#53034-5)</span></p><p><b>value</b>: heterozygous <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6706-1)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Ref nucleotide <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Alt allele <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69551-0)</span></p><p><b>value</b>: A</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic coord system <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#92822-6)</span></p><p><b>value</b>: 1-based character counting <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA30102-0)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic allele start-end <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81254-5)</span></p><p><b>value</b>: 96527334-?</p></blockquote></div>"
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        "code" : {
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              "code" : "69548-6",
              "display" : "Genetic variant assessment"
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        "issued" : "2019-03-05T16:04:44+00:00",
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        "component" : [
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            "valueCodeableConcept" : {
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          },
          {
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            "code" : {
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              ]
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            "valueCodeableConcept" : {
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          },
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                }
              ]
            },
            "valueString" : "A"
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                  "display" : "Genomic coord system"
                }
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      "resource" : {
        "resourceType" : "Observation",
        "id" : "dv-5c7e9e1ca82e4",
        "meta" : {
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            🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
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        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"dv-5c7e9e1ca82e4\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource Observation &quot;dv-5c7e9e1ca82e4&quot; </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-variant.html\">Variant</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69548-6)</span></p><p><b>subject</b>: <a href=\"#Patient_patient\">See above (urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac)</a></p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: Mar 5, 2019, 4:04:44 PM</p><p><b>performer</b>: <a href=\"#Organization_performingLab\">See above (urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab)</a></p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA9633-4)</span></p><blockquote><p><b>component</b></p><p><b>code</b>: Human reference sequence assembly version <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#62374-4)</span></p><p><b>value</b>: GRCh37 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA14029-5)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic reference sequence ID <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48013-7)</span></p><p><b>value</b>: NC_000010.10 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NC_000010.10)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic state <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#53034-5)</span></p><p><b>value</b>: heterozygous <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6706-1)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Ref nucleotide <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Alt allele <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69551-0)</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic coord system <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#92822-6)</span></p><p><b>value</b>: 1-based character counting <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA30102-0)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic allele start-end <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81254-5)</span></p><p><b>value</b>: 96527722-?</p></blockquote></div>"
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                "code" : "GE"
              }
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              "system" : "http://loinc.org",
              "code" : "69548-6",
              "display" : "Genetic variant assessment"
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        "component" : [
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            "code" : {
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            "valueCodeableConcept" : {
              "coding" : [
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          },
          {
            "code" : {
              "coding" : [
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      "resource" : {
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        "id" : "sid-5c7e9e1ca8a29",
        "meta" : {
          "profile" : [
            🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship"
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        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"sid-5c7e9e1ca8a29\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource Observation &quot;sid-5c7e9e1ca8a29&quot; </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-sequence-phase-relationship.html\">Sequence Phase Relationship</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Allelic phase <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82120-7)</span></p><p><b>subject</b>: <a href=\"#Patient_patient\">See above (urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac)</a></p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: Mar 5, 2019, 4:04:44 PM</p><p><b>performer</b>: <a href=\"#Organization_performingLab\">See above (urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab)</a></p><p><b>value</b>: Cis <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-sequence-phase-relationship-cs.html\">Sequence Phase Relationship Codes</a>#Cis)</span></p><p><b>derivedFrom</b>: </p><ul><li><a href=\"#Observation_dv-5c7e9e1ca8252\">See above (urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfe60)</a></li><li><a href=\"#Observation_dv-5c7e9e1ca82e4\">See above (urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe01)</a></li></ul></div>"
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              "system" : "http://loinc.org",
              "code" : "82120-7",
              "display" : "Allelic phase"
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    {
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      "resource" : {
        "resourceType" : "DiagnosticReport",
        "id" : "sequence-phase-relation-CYP2C19",
        "meta" : {
          "profile" : [
            🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"
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        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: DiagnosticReport</b><a name=\"sequence-phase-relation-CYP2C19\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource DiagnosticReport &quot;sequence-phase-relation-CYP2C19&quot; </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-genomic-report.html\">Genomic Report</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Genetic analysis report <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51969-4)</span></p><p><b>result</b>: </p><ul><li><a href=\"#Observation_dv-5c7e9e1ca8252\">See above (urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfe60)</a></li><li><a href=\"#Observation_dv-5c7e9e1ca82e4\">See above (urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe01)</a></li><li><a href=\"#Observation_sid-5c7e9e1ca8a29\">See above (urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe02)</a></li></ul></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\"><p><b>Generated Narrative: Organization</b><a name=\"performingLab\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource Organization &quot;performingLab&quot; </p></div><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\"><p><b>Generated Narrative: Patient</b><a name=\"patient\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource Patient &quot;patient&quot; </p></div><p><b>name</b>: John Storm(OFFICIAL), Johnny Storm(NICKNAME), The Human Torch(NICKNAME)</p><p><b>gender</b>: male</p><p><b>birthDate</b>: 1986-12-31</p></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"
      }
    }
  ]
}