PROTECT-CHILD Pediatric Transplant Data Implementation Guide, published by Protect Child. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/hl7-eu/protect-child/ and changes regularly. See the Directory of published versions

• Narrative Content
• XML
• JSON
• TTL

: Example Genomic Test - JSON Representation

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{
  "resourceType" : "Basic",
  "id" : "genomic-test-example-1",
  "meta" : {
    "profile" : [
      🔗 "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test"
    ]
  },
  "text" : {
    "status" : "extensions",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Basic genomic-test-example-1</b></p><a name=\"genomic-test-example-1\"> </a><a name=\"hcgenomic-test-example-1\"> </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-test.html\">Genomic Test</a></p></div><p><b>Reference Genome ID relationship</b>: <a href=\"Basic-reference-genome-grch38.html\">Basic GRCh38</a></p><p><b>Genomic Test Name</b>: ExomeSeq v1</p><p><b>Genomic Test Version</b>: 1.2.3</p><p><b>Sequencing device</b>: Illumina NovaSeq 6000</p><p><b>Target capture</b>: Exome capture kit XYZ v5</p><p><b>Read type</b>: Paired-end</p><p><b>Read length</b>: 150</p><p><b>Mean target coverage</b>: 120.5</p><p><b>Per target base cover x100</b>: 95.3</p><p><b>Alignment tools</b>: BWA-MEM 0.7.17</p><p><b>Variant calling tools</b>: GATK HaplotypeCaller 4.2.0</p><p><b>Chromosome coordinate</b>: GRCh38 (1-based, inclusive)</p><p><b>Annotation tools</b>: VEP 104</p><p><b>Annotation databases</b>: gnomAD v3.1, ClinVar 2025-01, dbNSFP 4.3</p><p><b>identifier</b>: <code>https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/genomic-test-id</code>/GT0001</p><p><b>code</b>: <span title=\"Codes:{https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/CodeSystem/genomic-test-type exome}\">Exome sequencing</span></p></div>"
  },
  "extension" : [
    {
      "url" : "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-reference-genome",
      "valueReference" : {
        🔗 "reference" : "Basic/reference-genome-grch38"
      }
    },
    {
      "url" : "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-name",
      "valueString" : "ExomeSeq v1"
    },
    {
      "url" : "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-version",
      "valueString" : "1.2.3"
    },
    {
      "url" : "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-sequencing-device",
      "valueString" : "Illumina NovaSeq 6000"
    },
    {
      "url" : "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-target-capture",
      "valueString" : "Exome capture kit XYZ v5"
    },
    {
      "url" : "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-read-type",
      "valueString" : "Paired-end"
    },
    {
      "url" : "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-read-length",
      "valueInteger" : 150
    },
    {
      "url" : "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-mean-target-coverage",
      "valueDecimal" : 120.5
    },
    {
      "url" : "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-per-target-base-cover-100x",
      "valueDecimal" : 95.3
    },
    {
      "url" : "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-alignment-tools",
      "valueString" : "BWA-MEM 0.7.17"
    },
    {
      "url" : "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-variant-calling-tools",
      "valueString" : "GATK HaplotypeCaller 4.2.0"
    },
    {
      "url" : "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-chromosome-corrdinate",
      "valueString" : "GRCh38 (1-based, inclusive)"
    },
    {
      "url" : "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-annotation-tools",
      "valueString" : "VEP 104"
    },
    {
      "url" : "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-annotation-databases",
      "valueString" : "gnomAD v3.1, ClinVar 2025-01, dbNSFP 4.3"
    }
  ],
  "identifier" : [
    {
      "system" : "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/genomic-test-id",
      "value" : "GT0001"
    }
  ],
  "code" : {
    "coding" : [
      {
        "system" : "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/CodeSystem/genomic-test-type",
        "code" : "exome",
        "display" : "Exome sequencing"
      }
    ]
  }
}