Genomics Reporting Implementation Guide
2.0.0 - trial-use
Genomics Reporting Implementation Guide
2.0.0 - trial-use
This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version. For a full list of available versions, see the Directory of published versions 
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<Observation>
<id value="dv-5c7e9e1ca8252"/>
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value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
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<div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><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">Resource "dv-5c7e9e1ca8252" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-variant.html">Variant</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69548-6)</span></p><p><b>issued</b>: Mar 5, 2019 4:04:44 PM</p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA9633-4)</span></p><blockquote><p><b>component</b></p><p><b>code</b>: Human reference sequence assembly version <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#62374-4)</span></p><p><b>value</b>: GRCh37 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA14029-5)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic reference sequence ID <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48013-7)</span></p><p><b>value</b>: NC_000010.10 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (nuccore#NC_000010.10)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic state <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#53034-5)</span></p><p><b>value</b>: heterozygous <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA6706-1)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Ref nucleotide <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69547-8)</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Alt allele <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69551-0)</span></p><p><b>value</b>: A</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic coord system <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#92822-6)</span></p><p><b>value</b>: 1-based character counting <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA30102-0)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic allele start-end <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81254-5)</span></p><p><b>value</b>: 96527334-?</p></blockquote></div>
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<code value="laboratory"/>
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<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
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<issued value="2019-03-05T16:04:44+00:00"/>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
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<coding>
<system value="http://loinc.org"/>
<code value="62374-4"/>
<display value="Human reference sequence assembly version"/>
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<code>
<coding>
<system value="http://loinc.org"/>
<code value="48013-7"/>
<display value="Genomic reference sequence ID"/>
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<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/nuccore"/>
<code value="NC_000010.10"/>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="53034-5"/>
<display value="Allelic state"/>
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<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6706-1"/>
<display value="heterozygous"/>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69547-8"/>
<display value="Ref nucleotide"/>
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<valueString value="C"/>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69551-0"/>
<display value="Alt allele"/>
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<valueString value="A"/>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="92822-6"/>
<display value="Genomic coord system"/>
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<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA30102-0"/>
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<system value="http://loinc.org"/>
<code value="81254-5"/>
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<entry>
<fullUrl value="urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe01"/>
<resource>
<Observation>
<id value="dv-5c7e9e1ca82e4"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
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<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><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">Resource "dv-5c7e9e1ca82e4" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-variant.html">Variant</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69548-6)</span></p><p><b>issued</b>: Mar 5, 2019 4:04:44 PM</p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA9633-4)</span></p><blockquote><p><b>component</b></p><p><b>code</b>: Human reference sequence assembly version <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#62374-4)</span></p><p><b>value</b>: GRCh37 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA14029-5)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic reference sequence ID <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48013-7)</span></p><p><b>value</b>: NC_000010.10 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (nuccore#NC_000010.10)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic state <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#53034-5)</span></p><p><b>value</b>: heterozygous <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA6706-1)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Ref nucleotide <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69547-8)</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Alt allele <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69551-0)</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic coord system <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#92822-6)</span></p><p><b>value</b>: 1-based character counting <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA30102-0)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic allele start-end <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81254-5)</span></p><p><b>value</b>: 96527722-?</p></blockquote></div>
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<status value="final"/>
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<code value="laboratory"/>
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<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
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<issued value="2019-03-05T16:04:44+00:00"/>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="62374-4"/>
<display value="Human reference sequence assembly version"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA14029-5"/>
<display value="GRCh37"/>
</coding>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48013-7"/>
<display value="Genomic reference sequence ID"/>
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<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/nuccore"/>
<code value="NC_000010.10"/>
</coding>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="53034-5"/>
<display value="Allelic state"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6706-1"/>
<display value="heterozygous"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69547-8"/>
<display value="Ref nucleotide"/>
</coding>
</code>
<valueString value="C"/>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69551-0"/>
<display value="Alt allele"/>
</coding>
</code>
<valueString value="G"/>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="92822-6"/>
<display value="Genomic coord system"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA30102-0"/>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81254-5"/>
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<valueRange>
<low>
<value value="96527722"/>
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<request>
<method value="POST"/>
<url value="Observation"/>
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</entry>
<entry>
<fullUrl value="urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe02"/>
<resource>
<Observation>
<id value="sid-5c7e9e1ca8a29"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><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">Resource "sid-5c7e9e1ca8a29" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-sequence-phase-relationship.html">Sequence Phase Relationship</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Allelic phase <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#82120-7)</span></p><p><b>issued</b>: Mar 5, 2019 4:04:44 PM</p><p><b>value</b>: Cis <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-sequence-phase-relationship-cs.html">Sequence Phase Relationship Codes</a>#Cis)</span></p><p><b>derivedFrom</b>: </p><ul><li><a href="#Observation_dv-5c7e9e1ca8252">See above (Observation/dv-5c7e9e1ca8252)</a></li><li><a href="#Observation_dv-5c7e9e1ca82e4">See above (Observation/dv-5c7e9e1ca82e4)</a></li></ul></div>
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<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="82120-7"/>
<display value="Allelic phase"/>
</coding>
</code>
<issued value="2019-03-05T16:04:44+00:00"/>
<valueCodeableConcept>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/sequence-phase-relationship-cs"/>
<code value="Cis"/>
<display value="Cis"/>
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<derivedFrom>
<reference value="Observation/dv-5c7e9e1ca8252"/>
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<derivedFrom>
<reference value="Observation/dv-5c7e9e1ca82e4"/>
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<request>
<method value="POST"/>
<url value="Observation"/>
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</entry>
<entry>
<fullUrl value="urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe03"/>
<resource>
<DiagnosticReport>
<id value="sequence-phase-relation-CYP2C19"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><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">Resource "sequence-phase-relation-CYP2C19" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-genomics-report.html">Genomics Report</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Genetics <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v2-0074.html">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Genetic analysis report <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81254-5)</span></p><p><b>result</b>: </p><ul><li><a href="#Observation_dv-5c7e9e1ca8252">See above (Observation/dv-5c7e9e1ca8252)</a></li><li><a href="#Observation_dv-5c7e9e1ca82e4">See above (Observation/dv-5c7e9e1ca82e4)</a></li><li><a href="#Observation_sid-5c7e9e1ca8a29">See above (Observation/sid-5c7e9e1ca8a29)</a></li></ul></div>
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<status value="final"/>
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<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
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<code>
<coding>
<system value="http://loinc.org"/>
<code value="81254-5"/>
</coding>
<text value="Genetic analysis report"/>
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<reference value="Observation/dv-5c7e9e1ca8252"/>
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<result>
<reference value="Observation/dv-5c7e9e1ca82e4"/>
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<result>
<reference value="Observation/sid-5c7e9e1ca8a29"/>
</result>
</DiagnosticReport>
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<request>
<method value="POST"/>
<url value="DiagnosticReport"/>
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</Bundle>
IG © 2022+ HL7 Clinical Genomics Working Group. Package hl7.fhir.uv.genomics-reporting#2.0.0 based on FHIR 4.0.1. Generated 2022-05-09
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