Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot
Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot
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-ballot 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
| Page standards status: Informative |
{
"resourceType" : "GenomicStudy",
"id" : "genomicstudy-trio2",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: GenomicStudy genomicstudy-trio2</b></p><a name=\"genomicstudy-trio2\"> </a><a name=\"hcgenomicstudy-trio2\"> </a><p><b>identifier</b>: <code>http://example.org/identifiers/genomicstudies</code>/urn:uuid:1111-1111-1111-1113\u00a0(use:\u00a0temp,\u00a0)</p><p><b>status</b>: Available</p><p><b>type</b>: <span title=\"Codes:\">Trio Analysis</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>startDate</b>: 2023-10-01</p><p><b>interpreter</b>: <a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></p><p><b>note</b>: </p><blockquote><div><p>De novo mutation study of the patient. The Prenatal Trio Whole Exome Sequencing (Prenatal Trio WES) test is ordered by a physician and must be accompanied with a consent form and detailed clinical information. In general, the test is used when prenatal imaging detects an anomaly that strongly suggests that there is an underlying genetic etiology. Prenatal Trio WES is often considered only after fetal chromosome microarray analysis has been non-diagnostic.</p>\n</div></blockquote><blockquote><p><b>analysis</b></p><p><b>genomeBuild</b>: <span title=\"Codes:{http://loinc.org LA26806-2}\">GRCh38</span></p><p><b>instantiatesUri</b>: <a href=\"https://pubmed.ncbi.nlm.nih.gov/33927380/\">https://pubmed.ncbi.nlm.nih.gov/33927380/</a></p><p><b>title</b>: Parental Sequence Variation Detection Using Next Generation Sequencing</p><p><b>focus</b>: </p><ul><li><a href=\"Patient-denovoFather.html\">Father Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 6789-11111\u00a0(use:\u00a0temp,\u00a0))</a></li><li><a href=\"Patient-denovoMother.html\">Mother Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 0987-11111\u00a0(use:\u00a0temp,\u00a0))</a></li></ul><p><b>date</b>: 2023-10-01</p><p><b>protocolPerformed</b>: <a href=\"Procedure-SequencingProcedure.html\">Procedure Sequencing of entire coding region of gene (procedure)</a></p><blockquote><p><b>input</b></p><p><b>file</b>: <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></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/genomicstudy-dataformat bam}\">BAM</span></p></blockquote><blockquote><p><b>input</b></p><p><b>file</b>: <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></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/genomicstudy-dataformat bam}\">BAM</span></p></blockquote><blockquote><p><b>input</b></p><p><b>file</b>: <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></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/genomicstudy-dataformat bam}\">BAM</span></p></blockquote><h3>Outputs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>File</b></td><td><b>Type</b></td></tr><tr><td style=\"display: none\">*</td><td><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></td><td><span title=\"Codes:{http://hl7.org/fhir/genomicstudy-dataformat vcf}\">VCF</span></td></tr></table></blockquote></div>"
},
"identifier" : [
{
"use" : "temp",
"system" : "http://example.org/identifiers/genomicstudies",
"value" : "urn:uuid:1111-1111-1111-1113"
}
],
"status" : "available",
"type" : [
{
"text" : "Trio Analysis"
}
],
"subject" : {
🔗 "reference" : "Patient/denovoChild"
},
"startDate" : "2023-10-01",
"interpreter" : [
{
🔗 "reference" : "Practitioner/practitioner02"
}
],
"note" : [
{
"text" : "De novo mutation study of the patient. The Prenatal Trio Whole Exome Sequencing (Prenatal Trio WES) test is ordered by a physician and must be accompanied with a consent form and detailed clinical information. In general, the test is used when prenatal imaging detects an anomaly that strongly suggests that there is an underlying genetic etiology. Prenatal Trio WES is often considered only after fetal chromosome microarray analysis has been non-diagnostic."
}
],
"analysis" : [
{
"genomeBuild" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26806-2",
"display" : "GRCh38"
}
]
},
"instantiatesUri" : "https://pubmed.ncbi.nlm.nih.gov/33927380/",
"title" : "Parental Sequence Variation Detection Using Next Generation Sequencing",
"focus" : [
{
🔗 "reference" : "Patient/denovoFather"
},
{
🔗 "reference" : "Patient/denovoMother"
}
],
"date" : "2023-10-01",
"protocolPerformed" : {
🔗 "reference" : "Procedure/SequencingProcedure"
},
"input" : [
{
"file" : {
🔗 "reference" : "DocumentReference/genomicFileProbandBAM"
},
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/genomicstudy-dataformat",
"code" : "bam",
"display" : "BAM"
}
]
}
},
{
"file" : {
🔗 "reference" : "DocumentReference/genomicFileMotherBAM"
},
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/genomicstudy-dataformat",
"code" : "bam",
"display" : "BAM"
}
]
}
},
{
"file" : {
🔗 "reference" : "DocumentReference/genomicFileFatherBAM"
},
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/genomicstudy-dataformat",
"code" : "bam",
"display" : "BAM"
}
]
}
}
],
"output" : [
{
"file" : {
🔗 "reference" : "DocumentReference/genomicFileProbandVCF"
},
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/genomicstudy-dataformat",
"code" : "vcf",
"display" : "VCF"
}
]
}
}
]
}
]
}
IG © 2025+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#4.0.0-ballot based on FHIR 6.0.0-ballot3. Generated 2025-10-16
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