Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild 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

Page standards status: Informative

Raw json | Download

    {
      "resourceType" : "Procedure",
      "id" : "lungMass-analysis1",
      "meta" : {
        "profile" : [
          🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis"
        ]
      },
      "text" : {
        "status" : "extensions",
        "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><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\"/><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-genomic-study-analysis.html\">Genomic Study Analysis</a></p></div><p><b>Genomic Study Analysis Method Type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs sequence-analysis-of-the-entire-coding-region}\">Sequence analysis of the entire coding region</span></p><p><b>Genomic Study Analysis Source Class</b>: <span title=\"Codes:{http://loinc.org LA6684-0}\">Somatic</span></p><p><b>Genomic Study Analysis Change Type</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0001483}\">SNV</span></p><p><b>Genomic Study Analysis Change Type</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0002007}\">MNV</span></p><p><b>Genomic Study Analysis Change Type</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:1000032}\">delins</span></p><p><b>Genomic Study Analysis Genome Build</b>: <span title=\"Codes:{http://loinc.org LA26806-2}\">GRCh38</span></p><p><b>Genomic Study Analysis Specimen</b>: <a href=\"Specimen-genomicSpecimen.html\">Specimen: identifier = http://example.org/identifiers/specimens#4; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2019-03-01 01:01:01+0000</a></p><p><b>Genomic Study Analysis Focus</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><blockquote><p><b>Genomic Study Analysis Device</b></p><ul><li>device: <a href=\"Device-triodenovo-software.html\">Device: identifier = http://example.org/identifiers/devices#11112; status = active; manufacturer = Vanderbilt Genetics Institute; type = Software (physical object)</a></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Regions</b></p><ul><li>studied: <a href=\"DocumentReference-WES-FullSequencedRegion-GRCh38.html\">DocumentReference: identifier = http://example.org/identifiers/files#11117; status = current; docStatus = preliminary; description = WES_FullSequencedRegion_GRCh38: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li><li>uncalled: <a href=\"DocumentReference-UncallableRegions.html\">DocumentReference: identifier = http://example.org/identifiers/files#11125; status = current; docStatus = preliminary; description = Representing a BED file that represents uncallable regions; securityLabel = Restricted</a></li><li>called: <a href=\"DocumentReference-SimpleVariantAnalysis-called.html\">DocumentReference: identifier = http://example.org/identifiers/files#11118; status = current; docStatus = preliminary; description = SimpleVariantAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Output</b></p><ul><li>type: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs vcf}\">VCF</span></li><li>file: <a href=\"DocumentReference-genomicVCFfile-simple.html\">DocumentReference: identifier = http://example.org/identifiers/files#11119; status = current; docStatus = preliminary; description = genomicVCFfile_simple: A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li></ul></blockquote><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>: </p><blockquote><div><p>For technical reasons, PIK3CB was deemed uncallable using this method.</p>\n</div></blockquote></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://www.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://www.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://www.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."
        }
      ]
    }