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

## : analysisTumorNormalDNA - JSON Representation

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    {
      "resourceType" : "Procedure",
      "id" : "analysisTumorNormalDNA",
      "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 analysisTumorNormalDNA</b></p><a name=\"analysisTumorNormalDNA\"> </a><a name=\"hcanalysisTumorNormalDNA\"> </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><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>studied: <span title=\"Codes:{http://www.genenames.org HGNC:76}\">ABL1</span></li><li>studied: <span title=\"Codes:{http://www.genenames.org HGNC:427}\">ALK</span></li><li>studied: <span title=\"Codes:{http://www.genenames.org HGNC:583}\">APC</span></li><li>uncalled: <a href=\"DocumentReference-WES-UncallableRegions-GRCh38.html\">DocumentReference: identifier = http://example.org/identifiers/files#11146520; status = current; docStatus = preliminary; description = Regions deemed uncallable (generally due to low coverage).; securityLabel = Restricted</a></li></ul></blockquote><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 Method Type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs deletion-duplication-analysis}\">Deletion/duplication analysis</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 Change Type</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0001019}\">CNV</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-tumorSpecimen.html\">Specimen: identifier = http://example.org/identifiers/specimens#222333; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2023-01-23 01:01:01+0000; note = Tumor: 20%</a></p><p><b>Genomic Study Analysis Specimen</b>: <a href=\"Specimen-normalSpecimen.html\">Specimen: identifier = http://example.org/identifiers/specimens#444555; status = available; type = Blood specimen (specimen); receivedTime = 2023-01-23 01:01:01+0000</a></p><p><b>Genomic Study Analysis Focus</b>: <a href=\"Patient-somaticPatient.html\">Substance Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --&gt; (ongoing)))</a></p><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-somaticVCFfile.html\">DocumentReference: identifier = http://example.org/identifiers/files#1134121; status = current; docStatus = preliminary; description = VCF file containing identified variants; securityLabel = Restricted</a></li></ul></blockquote><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-somaticPatient.html\">Substance Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --&gt; (ongoing)))</a></p><p><b>performed</b>: 2023-02-02 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>For technical reasons, BCR gene was deemed uncallable.</p>\n</div></blockquote></div>"
      },
      "extension" : [
        {
          "extension" : [
            {
              "url" : "studied",
              "valueReference" : {
                🔗 "reference" : "DocumentReference/WES-FullSequencedRegion-GRCh38"
              }
            },
            {
              "url" : "studied",
              "valueCodeableConcept" : {
                "coding" : [
                  {
                    "system" : "http://www.genenames.org",
                    "code" : "HGNC:76",
                    "display" : "ABL1"
                  }
                ]
              }
            },
            {
              "url" : "studied",
              "valueCodeableConcept" : {
                "coding" : [
                  {
                    "system" : "http://www.genenames.org",
                    "code" : "HGNC:427",
                    "display" : "ALK"
                  }
                ]
              }
            },
            {
              "url" : "studied",
              "valueCodeableConcept" : {
                "coding" : [
                  {
                    "system" : "http://www.genenames.org",
                    "code" : "HGNC:583",
                    "display" : "APC"
                  }
                ]
              }
            },
            {
              "url" : "uncalled",
              "valueReference" : {
                🔗 "reference" : "DocumentReference/WES-UncallableRegions-GRCh38"
              }
            }
          ],
          "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions"
        },
        {
          "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-method-type",
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs",
                "code" : "deletion-duplication-analysis",
                "display" : "Deletion/duplication analysis"
              }
            ]
          }
        },
        {
          "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-change-type",
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://www.sequenceontology.org",
                "code" : "SO:0001019",
                "display" : "CNV"
              }
            ]
          }
        },
        {
          "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/tumorSpecimen"
          }
        },
        {
          "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen",
          "valueReference" : {
            🔗 "reference" : "Specimen/normalSpecimen"
          }
        },
        {
          "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus",
          "valueReference" : {
            🔗 "reference" : "Patient/somaticPatient"
          }
        },
        {
          "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/somaticVCFfile"
              }
            }
          ],
          "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output"
        }
      ],
      "status" : "completed",
      "category" : {
        "coding" : [
          {
            "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
            "code" : "laboratory"
          }
        ]
      },
      "subject" : {
        🔗 "reference" : "Patient/somaticPatient"
      },
      "performedDateTime" : "2023-02-02T01:01:10-06:00",
      "note" : [
        {
          "text" : "For technical reasons, BCR gene was deemed uncallable."
        }
      ]
    }