Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 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
{
"resourceType" : "Observation",
"id" : "MultipleRepeatExpansions",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text" : {
"status" : "extensions",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation MultipleRepeatExpansions</b></p><a name=\"MultipleRepeatExpansions\"> </a><a name=\"hcMultipleRepeatExpansions\"> </a><a name=\"MultipleRepeatExpansions-en-US\"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2023-06-01</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied ID</span></p><p><b>value</b>: <span title=\"Codes:{http://www.genenames.org HGNC:3775}\">FMR1</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48001-2}\">Cytogenetic (chromosome) location</span></p><p><b>value</b>: <span title=\"Codes:\">chrx</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51958-7}\">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_002024.5}\">NM_002024.5</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48004-6}\">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NM_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]}\">NM_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81254-5}\">Genomic allele start-end</span></p><p><b>value</b>: 3-?</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 1</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-motif}\">Repeat Expansion Motif</span></p><p><b>value</b>: GGC</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 1</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-number}\">Number of Repeat Expansions</span></p><p><b>value</b>: 10</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 2</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-motif}\">Repeat Expansion Motif</span></p><p><b>value</b>: GGA</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 2</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-number}\">Number of Repeat Expansions</span></p><p><b>value</b>: 1</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 3</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-motif}\">Repeat Expansion Motif</span></p><p><b>value</b>: GGC</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 3</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-number}\">Number of Repeat Expansions</span></p><p><b>value</b>: 9</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 4</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-motif}\">Repeat Expansion Motif</span></p><p><b>value</b>: GGA</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 4</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-number}\">Number of Repeat Expansions</span></p><p><b>value</b>: 1</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 5</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-motif}\">Repeat Expansion Motif</span></p><p><b>value</b>: GGC</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 5</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-number}\">Number of Repeat Expansions</span></p><p><b>value</b>: 10</p></blockquote></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
},
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69548-6",
"display" : "Genetic variant assessment"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2023-06-01",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6",
"display" : "Gene studied ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:3775",
"display" : "FMR1"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48001-2",
"display" : "Cytogenetic (chromosome) location"
}
]
},
"valueCodeableConcept" : {
"text" : "chrx"
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51958-7",
"display" : "Transcript reference sequence [ID]"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/refseq",
"code" : "NM_002024.5",
"display" : "NM_002024.5"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48004-6",
"display" : "DNA change (c.HGVS)"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"code" : "NM_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]",
"display" : "NM_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81254-5",
"display" : "Genomic allele start-end"
}
]
},
"valueRange" : {
"low" : {
"value" : 3
}
}
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order",
"valuePositiveInt" : 1
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "repeat-motif",
"display" : "Repeat Expansion Motif"
}
]
},
"valueString" : "GGC"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order",
"valuePositiveInt" : 1
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "repeat-number",
"display" : "Number of Repeat Expansions"
}
]
},
"valueQuantity" : {
"value" : 10
}
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order",
"valuePositiveInt" : 2
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "repeat-motif",
"display" : "Repeat Expansion Motif"
}
]
},
"valueString" : "GGA"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order",
"valuePositiveInt" : 2
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "repeat-number",
"display" : "Number of Repeat Expansions"
}
]
},
"valueQuantity" : {
"value" : 1
}
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order",
"valuePositiveInt" : 3
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "repeat-motif",
"display" : "Repeat Expansion Motif"
}
]
},
"valueString" : "GGC"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order",
"valuePositiveInt" : 3
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "repeat-number",
"display" : "Number of Repeat Expansions"
}
]
},
"valueQuantity" : {
"value" : 9
}
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order",
"valuePositiveInt" : 4
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "repeat-motif",
"display" : "Repeat Expansion Motif"
}
]
},
"valueString" : "GGA"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order",
"valuePositiveInt" : 4
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "repeat-number",
"display" : "Number of Repeat Expansions"
}
]
},
"valueQuantity" : {
"value" : 1
}
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order",
"valuePositiveInt" : 5
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "repeat-motif",
"display" : "Repeat Expansion Motif"
}
]
},
"valueString" : "GGC"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order",
"valuePositiveInt" : 5
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "repeat-number",
"display" : "Number of Repeat Expansions"
}
]
},
"valueQuantity" : {
"value" : 10
}
}
]
}
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-11-19
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