Genomics Reporting Implementation Guide
3.0.0 - STU3
Genomics Reporting Implementation Guide
3.0.0 - STU3
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
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<meta>
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value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
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<text>
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<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-complexVariant-nonHGVS-1"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-complexVariant-nonHGVS-1</b></p><a name="Inline-Instance-for-complexVariant-nonHGVS-1"> </a><a name="hcInline-Instance-for-complexVariant-nonHGVS-1"> </a><a name="Inline-Instance-for-complexVariant-nonHGVS-1-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="Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeac">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: 2019-03-05 16:04:44+0000</p><p><b>performer</b>: <a href="Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeab">Bundle: type = transaction</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 51958-7}">Transcript ref sequence ID</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_022787.3}">NM_022787.3</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>: 769-769</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>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69551-0}">Genomic alt allele [ID]</span></p><p><b>value</b>: A</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 53034-5}">Allelic state</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6706-1}">Heterozygous</span></p></blockquote></div>
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<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NM_022787.3"/>
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<component>
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<system value="http://loinc.org"/>
<code value="69547-8"/>
<display value="Genomic ref allele [ID]"/>
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<valueString value="G"/>
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<component>
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<system value="http://loinc.org"/>
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<display value="Genomic alt allele [ID]"/>
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<code value="LA6706-1"/>
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<Observation>
<id value="Inline-Instance-for-complexVariant-nonHGVS-2"/>
<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"><a name="Observation_Inline-Instance-for-complexVariant-nonHGVS-2"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-complexVariant-nonHGVS-2</b></p><a name="Inline-Instance-for-complexVariant-nonHGVS-2"> </a><a name="hcInline-Instance-for-complexVariant-nonHGVS-2"> </a><a name="Inline-Instance-for-complexVariant-nonHGVS-2-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="Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeac">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: 2019-03-05 16:04:44+0000</p><p><b>performer</b>: <a href="Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeab">Bundle: type = transaction</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 51958-7}">Transcript ref sequence ID</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_022787.3}">NM_022787.3</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>: 53-53</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>: A</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69551-0}">Genomic alt allele [ID]</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 53034-5}">Allelic state</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6706-1}">Heterozygous</span></p></blockquote></div>
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<code value="GE"/>
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<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
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<subject>
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<display value="Present"/>
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<system value="http://loinc.org"/>
<code value="51958-7"/>
<display value="Transcript ref sequence ID"/>
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<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NM_022787.3"/>
<display value="NM_022787.3"/>
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<component>
<code>
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<system value="http://loinc.org"/>
<code value="69547-8"/>
<display value="Genomic ref allele [ID]"/>
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<valueString value="A"/>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69551-0"/>
<display value="Genomic alt allele [ID]"/>
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<valueString value="G"/>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="53034-5"/>
<display value="Allelic state"/>
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</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6706-1"/>
<display value="Heterozygous"/>
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<request>
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<url value="Observation"/>
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</entry>
<entry>
<fullUrl value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12a"/>
<resource>
<Observation>
<id value="Inline-Instance-for-complexVariant-nonHGVS-3"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-complexVariant-nonHGVS-3"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-complexVariant-nonHGVS-3</b></p><a name="Inline-Instance-for-complexVariant-nonHGVS-3"> </a><a name="hcInline-Instance-for-complexVariant-nonHGVS-3"> </a><a name="Inline-Instance-for-complexVariant-nonHGVS-3-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 84413-4}">Genotype display name</span></p><p><b>subject</b>: <a href="Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeac">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: 2019-03-05 16:04:44+0000</p><p><b>performer</b>: <a href="Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeab">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/clinvar RCV000664188.1}">NM_022787.3(NMNAT1):c.[53A>G];[769G>A] AND Cone-rod dystrophy</span></p><p><b>hasMember</b>: </p><ul><li><a href="Bundle-bundle-complexVariant-nonHGVS.html#urn-uuid-16fdd5fc-e665-48af-99e4-48d603f3e12e">unpacked representation of NM_022787.3:c.53A>G</a></li><li><a href="Bundle-bundle-complexVariant-nonHGVS.html#urn-uuid-16fdd5fc-e665-48af-99e4-48d603f3e12d">unpacked representation of NM_022787.3:c.769G>A</a></li></ul></div>
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<status value="final"/>
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value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
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<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
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</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="84413-4"/>
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</code>
<subject>
<reference value="urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac"/>
</subject>
<effectiveDateTime value="2019-03-05"/>
<issued value="2019-03-05T16:04:44+00:00"/>
<performer>
<reference value="urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/clinvar"/>
<code value="RCV000664188.1"/>
<display
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<hasMember>
<reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e"/>
<display value="unpacked representation of NM_022787.3:c.53A>G"/>
</hasMember>
<hasMember>
<reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"/>
<display
value="unpacked representation of NM_022787.3:c.769G>A"/>
</hasMember>
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<request>
<method value="POST"/>
<url value="Observation"/>
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</entry>
<entry>
<fullUrl value="urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab"/>
<resource>
<Organization>
<id value="performingLab"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Organization_performingLab"> </a><p class="res-header-id"><b>Generated Narrative: Organization performingLab</b></p><a name="performingLab"> </a><a name="hcperformingLab"> </a><a name="performingLab-en-US"> </a><p><b>name</b>: aTypingLab Inc</p><p><b>alias</b>: aTL</p><p><b>telecom</b>: ph: 1-800-555-1234(Work)</p><p><b>address</b>: 123 Main St, Sometown, ND 99999(work)</p></div>
</text>
<name value="aTypingLab Inc"/>
<alias value="aTL"/>
<telecom>
<system value="phone"/>
<value value="1-800-555-1234"/>
<use value="work"/>
<rank value="1"/>
</telecom>
<address>
<use value="work"/>
<type value="both"/>
<text value="123 Main St, Sometown, ND 99999"/>
<line value="123 Main St"/>
<city value="Sometown"/>
<state value="ND"/>
<postalCode value="99999"/>
<country value="USA"/>
</address>
</Organization>
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<request>
<method value="POST"/>
<url value="Organization"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac"/>
<resource>
<Patient>
<id value="patient"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Patient_patient"> </a><p class="res-header-id"><b>Generated Narrative: Patient patient</b></p><a name="patient"> </a><a name="hcpatient"> </a><a name="patient-en-US"> </a><p style="border: 1px #661aff solid; background-color: #e6e6ff; padding: 10px;">John Storm(official) Male, DoB: 1986-12-31</p><hr/></div>
</text>
<name>
<use value="official"/>
<text value="John Storm"/>
<family value="Storm"/>
<given value="John"/>
</name>
<name>
<use value="nickname"/>
<text value="Johnny Storm"/>
<family value="Storm"/>
<given value="Johnny"/>
</name>
<name>
<use value="nickname"/>
<text value="The Human Torch"/>
</name>
<gender value="male"/>
<birthDate value="1986-12-31"/>
</Patient>
</resource>
<request>
<method value="POST"/>
<url value="Patient"/>
</request>
</entry>
</Bundle>
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-12-12
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