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

: lungMass-analysis1 - JSON Representation

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{
  "resourceType" : "Procedure",
  "id" : "lungMass-analysis1",
  "meta" : {
    "profile" : [
      🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis"
    ]
  },
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Procedure lungMass-analysis1</b></p><a name=\"lungMass-analysis1\"> </a><a name=\"hclungMass-analysis1\"> </a><a name=\"lungMass-analysis1-en-US\"> </a><p><b>instantiatesUri</b>: <a href=\"https://pubmed.ncbi.nlm.nih.gov/33927380/\">https://pubmed.ncbi.nlm.nih.gov/33927380/</a></p><p><b>status</b>: Completed</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span></p><p><b>subject</b>: <a href=\"Patient-genomicPatient.html\">John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --&gt; (ongoing)))</a></p><p><b>performed</b>: 2019-03-01 01:01:10-0600</p><h3>Performers</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Function</b></td><td><b>Actor</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}\">Performer</span></td><td><a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></td></tr></table><p><b>note</b>: For technical reasons, PIK3CB was deemed uncallable using this method.</p></div>"
  },
  "extension" : [
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type",
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs",
            "code" : "sequence-analysis-of-the-entire-coding-region",
            "display" : "Sequence analysis of the entire coding region"
          }
        ]
      }
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genomic-source-class",
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA6684-0",
            "display" : "Somatic"
          }
        ]
      }
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://sequenceontology.org",
            "code" : "SO:0001483",
            "display" : "SNV"
          }
        ]
      }
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://sequenceontology.org",
            "code" : "SO:0002007",
            "display" : "MNV"
          }
        ]
      }
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://sequenceontology.org",
            "code" : "SO:1000032",
            "display" : "delins"
          }
        ]
      }
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genome-build",
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA26806-2",
            "display" : "GRCh38"
          }
        ]
      }
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen",
      "valueReference" : {
        🔗 "reference" : "Specimen/genomicSpecimen"
      }
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus",
      "valueReference" : {
        🔗 "reference" : "Patient/genomicPatient"
      }
    },
    {
      "extension" : [
        {
          "url" : "device",
          "valueReference" : {
            🔗 "reference" : "Device/triodenovo-software"
          }
        }
      ],
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device"
    },
    {
      "extension" : [
        {
          "url" : "studied",
          "valueReference" : {
            🔗 "reference" : "DocumentReference/WES-FullSequencedRegion-GRCh38"
          }
        },
        {
          "url" : "uncalled",
          "valueReference" : {
            🔗 "reference" : "DocumentReference/UncallableRegions"
          }
        },
        {
          "url" : "called",
          "valueReference" : {
            🔗 "reference" : "DocumentReference/SimpleVariantAnalysis-called"
          }
        }
      ],
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions"
    },
    {
      "extension" : [
        {
          "url" : "type",
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs",
                "code" : "vcf",
                "display" : "VCF"
              }
            ]
          }
        },
        {
          "url" : "file",
          "valueReference" : {
            🔗 "reference" : "DocumentReference/genomicVCFfile-simple"
          }
        }
      ],
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output"
    }
  ],
  "instantiatesUri" : [
    "https://pubmed.ncbi.nlm.nih.gov/33927380/"
  ],
  "status" : "completed",
  "category" : {
    "coding" : [
      {
        "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
        "code" : "laboratory"
      }
    ]
  },
  "subject" : {
    🔗 "reference" : "Patient/genomicPatient"
  },
  "performedDateTime" : "2019-03-01T01:01:10-06:00",
  "performer" : [
    {
      "function" : {
        "coding" : [
          {
            "system" : "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
            "code" : "PRF",
            "display" : "Performer"
          }
        ]
      },
      "actor" : {
        🔗 "reference" : "Practitioner/practitioner02"
      }
    }
  ],
  "note" : [
    {
      "text" : "For technical reasons, PIK3CB was deemed uncallable using this method."
    }
  ]
}