Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

: bundle-complexVariant-nonHGVS - JSON Representation

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{
  "resourceType" : "Bundle",
  "id" : "bundle-complexVariant-nonHGVS",
  "type" : "transaction",
  "entry" : [
    {
      "fullUrl" : "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "Inline-Instance-for-complexVariant-nonHGVS-1",
        "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_Inline-Instance-for-complexVariant-nonHGVS-1\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation Inline-Instance-for-complexVariant-nonHGVS-1</b></p><a name=\"Inline-Instance-for-complexVariant-nonHGVS-1\"> </a><a name=\"hcInline-Instance-for-complexVariant-nonHGVS-1\"> </a><a name=\"Inline-Instance-for-complexVariant-nonHGVS-1-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 51958-7}\">Transcript ref sequence ID</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_022787.3}\">NM_022787.3</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>: 769-769</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69547-8}\">Genomic ref allele [ID]</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 69551-0}\">Genomic alt allele [ID]</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 53034-5}\">Allelic state</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6706-1}\">Heterozygous</span></p></blockquote></div>"
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            "valueString" : "G"
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    },
    {
      "fullUrl" : "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "Inline-Instance-for-complexVariant-nonHGVS-2",
        "meta" : {
          "profile" : [
            🔗 "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\"><a name=\"Observation_Inline-Instance-for-complexVariant-nonHGVS-2\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation Inline-Instance-for-complexVariant-nonHGVS-2</b></p><a name=\"Inline-Instance-for-complexVariant-nonHGVS-2\"> </a><a name=\"hcInline-Instance-for-complexVariant-nonHGVS-2\"> </a><a name=\"Inline-Instance-for-complexVariant-nonHGVS-2-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 51958-7}\">Transcript ref sequence ID</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_022787.3}\">NM_022787.3</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>: 53-53</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69547-8}\">Genomic ref allele [ID]</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 69551-0}\">Genomic alt allele [ID]</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 53034-5}\">Allelic state</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6706-1}\">Heterozygous</span></p></blockquote></div>"
        },
        "status" : "final",
        "category" : [
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            "coding" : [
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                "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
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              "code" : "69548-6",
              "display" : "Genetic variant assessment"
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        },
        "effectiveDateTime" : "2019-03-05",
        "issued" : "2019-03-05T16:04:44+00:00",
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            "reference" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab"
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        "component" : [
          {
            "code" : {
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                {
                  "system" : "http://loinc.org",
                  "code" : "51958-7",
                  "display" : "Transcript ref sequence ID"
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            "valueCodeableConcept" : {
              "coding" : [
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                  "system" : "http://www.ncbi.nlm.nih.gov/refseq",
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                }
              ]
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                  "code" : "69547-8",
                  "display" : "Genomic ref allele [ID]"
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            "valueString" : "A"
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            "code" : {
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                {
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                  "code" : "69551-0",
                  "display" : "Genomic alt allele [ID]"
                }
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            "valueString" : "G"
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            "valueCodeableConcept" : {
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          }
        ]
      },
      "request" : {
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        "url" : "Observation"
      }
    },
    {
      "fullUrl" : "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12a",
      "resource" : {
        "resourceType" : "Observation",
        "id" : "Inline-Instance-for-complexVariant-nonHGVS-3",
        "meta" : {
          "profile" : [
            🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_Inline-Instance-for-complexVariant-nonHGVS-3\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation Inline-Instance-for-complexVariant-nonHGVS-3</b></p><a name=\"Inline-Instance-for-complexVariant-nonHGVS-3\"> </a><a name=\"hcInline-Instance-for-complexVariant-nonHGVS-3\"> </a><a name=\"Inline-Instance-for-complexVariant-nonHGVS-3-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 84413-4}\">Genotype display name</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://www.ncbi.nlm.nih.gov/clinvar RCV000664188.1}\">NM_022787.3(NMNAT1):c.[53A&gt;G];[769G&gt;A] AND Cone-rod dystrophy</span></p><p><b>hasMember</b>: </p><ul><li><a href=\"Bundle-bundle-complexVariant-nonHGVS.html#urn-uuid-16fdd5fc-e665-48af-99e4-48d603f3e12e\">unpacked representation of NM_022787.3:c.53A&gt;G</a></li><li><a href=\"Bundle-bundle-complexVariant-nonHGVS.html#urn-uuid-16fdd5fc-e665-48af-99e4-48d603f3e12d\">unpacked representation of NM_022787.3:c.769G&gt;A</a></li></ul></div>"
        },
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                "code" : "laboratory"
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          {
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                "code" : "GE"
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            ]
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        "code" : {
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        "issued" : "2019-03-05T16:04:44+00:00",
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          {
            "reference" : "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d",
            "display" : "unpacked representation of NM_022787.3:c.769G>A"
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    {
      "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"
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        "telecom" : [
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            "use" : "work",
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            "text" : "123 Main St, Sometown, ND 99999",
            "line" : [
              "123 Main St"
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            "city" : "Sometown",
            "state" : "ND",
            "postalCode" : "99999",
            "country" : "USA"
          }
        ]
      },
      "request" : {
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        "url" : "Organization"
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    },
    {
      "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"
      },
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        "url" : "Patient"
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}