{
  "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: #fbffeb; 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))</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))</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))</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"
}