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

## : genomicstudyanalysis-trio2 - JSON Representation

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    {
      "resourceType" : "Procedure",
      "id" : "genomicstudyanalysis-trio2",
      "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 genomicstudyanalysis-trio2</b></p><a name=\"genomicstudyanalysis-trio2\"> </a><a name=\"hcgenomicstudyanalysis-trio2\"> </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 Genome Build</b>: <span title=\"Codes:{http://loinc.org LA26806-2}\">GRCh38</span></p><p><b>Genomic Study Analysis Focus</b>: <a href=\"Patient-denovoFather.html\">Father Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 6789-11111\u00a0(use:\u00a0temp,\u00a0))</a></p><p><b>Genomic Study Analysis Focus</b>: <a href=\"Patient-denovoMother.html\">Mother Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 0987-11111\u00a0(use:\u00a0temp,\u00a0))</a></p><p><b>Genomic Study Analysis Title</b>: Parental Sequence Variation Detection Using Next Generation Sequencing</p><p><b>Genomic Study Analysis Protocol Performed</b>: <a href=\"Procedure-SequencingProcedure.html\">Procedure Sequencing of entire coding region of gene (procedure)</a></p><blockquote><p><b>Genomic Study Analysis Input</b></p><ul><li>file: <a href=\"DocumentReference-genomicFileProbandBAM.html\">DocumentReference: identifier = http://example.org/identifiers/files#11118; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li><li>type: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs bam}\">BAM</span></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Input</b></p><ul><li>file: <a href=\"DocumentReference-genomicFileMotherBAM.html\">DocumentReference: identifier = http://example.org/identifiers/files#11125; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li><li>type: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs bam}\">BAM</span></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Input</b></p><ul><li>file: <a href=\"DocumentReference-genomicFileFatherBAM.html\">DocumentReference: identifier = http://example.org/identifiers/files#11132; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li><li>type: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs bam}\">BAM</span></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Output</b></p><ul><li>file: <a href=\"DocumentReference-genomicFileProbandVCF.html\">DocumentReference: identifier = http://example.org/identifiers/files#11150; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li><li>type: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs vcf}\">VCF</span></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-denovoChild.html\">Child Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 1234-11111\u00a0(use:\u00a0temp,\u00a0))</a></p><p><b>performed</b>: 2023-10-01</p></div>"
      },
      "extension" : [
        {
          "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-focus",
          "valueReference" : {
            🔗 "reference" : "Patient/denovoFather"
          }
        },
        {
          "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus",
          "valueReference" : {
            🔗 "reference" : "Patient/denovoMother"
          }
        },
        {
          "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-title",
          "valueString" : "Parental Sequence Variation Detection Using Next Generation Sequencing"
        },
        {
          "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-protocol-performed",
          "valueReference" : {
            🔗 "reference" : "Procedure/SequencingProcedure"
          }
        },
        {
          "extension" : [
            {
              "url" : "file",
              "valueReference" : {
                🔗 "reference" : "DocumentReference/genomicFileProbandBAM"
              }
            },
            {
              "url" : "type",
              "valueCodeableConcept" : {
                "coding" : [
                  {
                    "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs",
                    "code" : "bam",
                    "display" : "BAM"
                  }
                ]
              }
            }
          ],
          "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input"
        },
        {
          "extension" : [
            {
              "url" : "file",
              "valueReference" : {
                🔗 "reference" : "DocumentReference/genomicFileMotherBAM"
              }
            },
            {
              "url" : "type",
              "valueCodeableConcept" : {
                "coding" : [
                  {
                    "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs",
                    "code" : "bam",
                    "display" : "BAM"
                  }
                ]
              }
            }
          ],
          "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input"
        },
        {
          "extension" : [
            {
              "url" : "file",
              "valueReference" : {
                🔗 "reference" : "DocumentReference/genomicFileFatherBAM"
              }
            },
            {
              "url" : "type",
              "valueCodeableConcept" : {
                "coding" : [
                  {
                    "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs",
                    "code" : "bam",
                    "display" : "BAM"
                  }
                ]
              }
            }
          ],
          "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input"
        },
        {
          "extension" : [
            {
              "url" : "file",
              "valueReference" : {
                🔗 "reference" : "DocumentReference/genomicFileProbandVCF"
              }
            },
            {
              "url" : "type",
              "valueCodeableConcept" : {
                "coding" : [
                  {
                    "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs",
                    "code" : "vcf",
                    "display" : "VCF"
                  }
                ]
              }
            }
          ],
          "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/denovoChild"
      },
      "performedDateTime" : "2023-10-01"
    }