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" : "ExampleGermlineCNV",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation ExampleGermlineCNV</b></p><a name=\"ExampleGermlineCNV\"> </a><a name=\"hcExampleGermlineCNV\"> </a><a name=\"ExampleGermlineCNV-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-CGPatientExample01.html\">Adam B. Everyman Male, DoB: 1951-01-20 ( Medical Record Number: m123\u00a0(use:\u00a0usual,\u00a0))</a></p><p><b>effective</b>: 2019-04-01</p><p><b>performer</b>: <a href=\"Organization-ExampleOrg.html\">Organization some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>method</b>: <span title=\"Codes:{http://loinc.org LA26398-0}\">Sequencing</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48019-4}\">DNA change type</span></p><p><b>value</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0001019}\">copy_number_variation</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69547-8}\">Genomic ref allele [ID]</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48002-0}\">Genomic source class [Type]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6683-2}\">Germline</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48013-7}\">Genomic reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NC_000022.10}\">NC_000022.10</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 82155-3}\">Genomic structural variant copy number</span></p><p><b>value</b>: 3 1<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 92822-6}\">Genomic coordinate system [Type]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA30102-0}\">1-based character counting</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81302-2}\">Structural variant inner start and end</span></p><p><b>value</b>: 42523949-42533891</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 94186-4}\">Origin of germline genetic variant [Type]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA26320-4}\">Maternal</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 82309-6}\">Basis for allelic phase [Type]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA26426-9}\">Directly measured</span></p></blockquote></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
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"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"
}
]
},
"subject" : {
🔗 "reference" : "Patient/CGPatientExample01"
},
"effectiveDateTime" : "2019-04-01",
"performer" : [
{
🔗 "reference" : "Organization/ExampleOrg"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
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]
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"method" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26398-0",
"display" : "Sequencing"
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"component" : [
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"code" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "48019-4"
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"valueCodeableConcept" : {
"coding" : [
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"system" : "http://www.sequenceontology.org",
"code" : "SO:0001019",
"display" : "copy_number_variation"
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"code" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "69547-8"
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"valueString" : "T"
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{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48002-0"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6683-2",
"display" : "Germline"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48013-7"
}
]
},
"valueCodeableConcept" : {
"coding" : [
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"system" : "http://www.ncbi.nlm.nih.gov/refseq",
"code" : "NC_000022.10"
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{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "82155-3"
}
]
},
"valueQuantity" : {
"value" : 3,
"system" : "http://unitsofmeasure.org",
"code" : "1"
}
},
{
"code" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "92822-6"
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"valueCodeableConcept" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "LA30102-0",
"display" : "1-based character counting"
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{
"code" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "81302-2"
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"valueRange" : {
"low" : {
"value" : 42523949
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"high" : {
"value" : 42533891
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},
{
"code" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "94186-4"
}
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"valueCodeableConcept" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "LA26320-4",
"display" : "Maternal"
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"code" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "82309-6"
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"valueCodeableConcept" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "LA26426-9",
"display" : "Directly measured"
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