Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot
Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - 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 3.0.1-SNAPSHOT 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
<Bundle xmlns="http://hl7.org/fhir">
<id value="bundle-compound-heterozygote"/>
<type value="transaction"/>
<entry>
<fullUrl value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"/>
<resource>
<Observation>
<id value="Inline-Instance-for-compound-heterozygote-1"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-compound-heterozygote-1"> </a><p><b>Generated Narrative: Observation</b><a name="Inline-Instance-for-compound-heterozygote-1"> </a><a name="hcInline-Instance-for-compound-heterozygote-1"> </a></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 Observation "Inline-Instance-for-compound-heterozygote-1" </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/5.3.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span>, Genetics <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html">diagnosticServiceSectionId</a>#GE)</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>subject</b>: See on this page: urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac</p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: Mar 5, 2019, 4:04:44 PM</p><p><b>performer</b>: See on this page: urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab</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>: DNA change (c.HGVS) <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48004-6)</span></p><p><b>value</b>: NM_022787.3:c.769G>A <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html">Human Genome Variation Society nomenclature</a>#NM_022787.3:c.769G>A)</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></div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</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://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48004-6"/>
<display value="DNA change (c.HGVS)"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NM_022787.3:c.769G>A"/>
<display value="NM_022787.3:c.769G>A"/>
</coding>
</valueCodeableConcept>
</component>
<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>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e"/>
<resource>
<Observation>
<id value="Inline-Instance-for-compound-heterozygote-2"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-compound-heterozygote-2"> </a><p><b>Generated Narrative: Observation</b><a name="Inline-Instance-for-compound-heterozygote-2"> </a><a name="hcInline-Instance-for-compound-heterozygote-2"> </a></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 Observation "Inline-Instance-for-compound-heterozygote-2" </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/5.3.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span>, Genetics <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html">diagnosticServiceSectionId</a>#GE)</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>subject</b>: See on this page: urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac</p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: Mar 5, 2019, 4:04:44 PM</p><p><b>performer</b>: See on this page: urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab</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>: DNA change (c.HGVS) <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48004-6)</span></p><p><b>value</b>: NM_022787.3:c.53A>G <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html">Human Genome Variation Society nomenclature</a>#NM_022787.3:c.53A>G)</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></div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</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://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48004-6"/>
<display value="DNA change (c.HGVS)"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NM_022787.3:c.53A>G"/>
<display value="NM_022787.3:c.53A>G"/>
</coding>
</valueCodeableConcept>
</component>
<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>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12a"/>
<resource>
<Observation>
<id value="Inline-Instance-for-compound-heterozygote-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-compound-heterozygote-3"> </a><p><b>Generated Narrative: Observation</b><a name="Inline-Instance-for-compound-heterozygote-3"> </a><a name="hcInline-Instance-for-compound-heterozygote-3"> </a></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 Observation "Inline-Instance-for-compound-heterozygote-3" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-genotype.html">Genotype</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/5.3.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span>, Genetics <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Genotype name Patient <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#84413-4)</span></p><p><b>subject</b>: See on this page: urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac</p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: Mar 5, 2019, 4:04:44 PM</p><p><b>performer</b>: See on this page: urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab</p><p><b>value</b>: NM_022787.3(NMNAT1):c.[53A>G];[769G>A] AND Cone-rod dystrophy <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-ClinVarV.html">ClinVar Variant ID</a>#RCV000664188.1)</span></p><p><b>hasMember</b>: </p><ul><li>See on this page: urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e: NM_022787.3:c.53A>G</li><li>See on this page: urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d: NM_022787.3:c.769G>A</li></ul></div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="84413-4"/>
</coding>
</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
value="NM_022787.3(NMNAT1):c.[53A>G];[769G>A] AND Cone-rod dystrophy"/>
</coding>
</valueCodeableConcept>
<hasMember>
<reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e"/>
<display value="NM_022787.3:c.53A>G"/>
</hasMember>
<hasMember>
<reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"/>
<display value="NM_022787.3:c.769G>A"/>
</hasMember>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</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><b>Generated Narrative: Organization</b><a name="performingLab"> </a><a name="hcperformingLab"> </a></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 Organization "performingLab" </p></div><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>
</resource>
<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><b>Generated Narrative: Patient</b><a name="patient"> </a><a name="hcpatient"> </a></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 Patient "patient" </p></div><p><b>name</b>: John Storm(Official), Johnny Storm(Nickname), The Human Torch(Nickname)</p><p><b>gender</b>: male</p><p><b>birthDate</b>: 1986-12-31</p></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#3.0.1-SNAPSHOT based on FHIR 4.0.1. Generated 2024-04-09
Links: Table of Contents |
QA Report
| Version History |
|
Propose a change