Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build
Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild 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-prequel-prenatal-trisomy13"/>
<type value="transaction"/>
<entry>
<fullUrl value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"/>
<resource>
<Patient>
<id value="prequel-patient-jane-miller"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Patient_prequel-patient-jane-miller"> </a><p class="res-header-id"><b>Generated Narrative: Patient prequel-patient-jane-miller</b></p><a name="prequel-patient-jane-miller"> </a><a name="hcprequel-patient-jane-miller"> </a><p style="border: 1px #661aff solid; background-color: #e6e6ff; padding: 10px;">Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)</p><hr/></div>
</text>
<identifier>
<system value="http://example.org/mrn"/>
<value value="FAKERQIHPT13S"/>
</identifier>
<name>
<family value="Miller"/>
<given value="Jane"/>
</name>
<gender value="female"/>
<birthDate value="1997-11-11"/>
</Patient>
</resource>
<request>
<method value="POST"/>
<url value="Patient"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000002"/>
<resource>
<Practitioner>
<id value="prequel-practitioner-paul-smith"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Practitioner_prequel-practitioner-paul-smith"> </a><p class="res-header-id"><b>Generated Narrative: Practitioner prequel-practitioner-paul-smith</b></p><a name="prequel-practitioner-paul-smith"> </a><a name="hcprequel-practitioner-paul-smith"> </a><p><b>identifier</b>: <a href="http://terminology.hl7.org/7.1.0/NamingSystem-npi.html" title="National Provider Identifier">United States National Provider Identifier</a>/4253506008</p><p><b>name</b>: Paul Smith </p></div>
</text>
<identifier>
<system value="http://hl7.org/fhir/sid/us-npi"/>
<value value="4253506008"/>
</identifier>
<name>
<family value="Smith"/>
<given value="Paul"/>
<prefix value="Dr."/>
</name>
</Practitioner>
</resource>
<request>
<method value="POST"/>
<url value="Practitioner"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000003"/>
<resource>
<Organization>
<id value="prequel-org-umc"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Organization_prequel-org-umc"> </a><p class="res-header-id"><b>Generated Narrative: Organization prequel-org-umc</b></p><a name="prequel-org-umc"> </a><a name="hcprequel-org-umc"> </a><p><b>name</b>: University Medical Center</p><h3>Contacts</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Telecom</b></td><td><b>Address</b></td></tr><tr><td style="display: none">*</td><td>ph: (800) 555-1212, fax: (800) 555-1212</td><td>123 Main Street City CA 10231 </td></tr></table></div>
</text>
<name value="University Medical Center"/>
<contact>
<telecom>
<system value="phone"/>
<value value="(800) 555-1212"/>
</telecom>
<telecom>
<system value="fax"/>
<value value="(800) 555-1212"/>
</telecom>
<address>
<line value="123 Main Street"/>
<city value="City"/>
<state value="CA"/>
<postalCode value="10231"/>
</address>
</contact>
</Organization>
</resource>
<request>
<method value="POST"/>
<url value="Organization"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000004"/>
<resource>
<Organization>
<id value="prequel-org-myriad"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Organization_prequel-org-myriad"> </a><p class="res-header-id"><b>Generated Narrative: Organization prequel-org-myriad</b></p><a name="prequel-org-myriad"> </a><a name="hcprequel-org-myriad"> </a><p><b>identifier</b>: <a href="http://terminology.hl7.org/7.1.0/NamingSystem-CLIA.html" title=""The Centers for Medicare & Medicaid Services (CMS) regulates all laboratory testing (except research) performed on humans in the U.S. through the Clinical Laboratory Improvement Amendments (CLIA). In total, CLIA covers approximately 330,000 laboratory entities. The Division of Clinical Laboratory Improvement & Quality, within the Quality, Safety & Oversight Group, under the Center for Clinical Standards and Quality (CCSQ) has the responsibility for implementing the CLIA Program.
The objective of the CLIA program is to ensure quality laboratory testing. Although all clinical laboratories must be properly certified to receive Medicare or Medicaid payments, CLIA has no direct Medicare or Medicaid program responsibilities."
CMS CLIA certified laboratories will be assigned a10-digit alphanumeric CLIA identification number, with the "D" in the third position identifying the provider/supplier as a laboratory certified under CLIA."
CLIA is maintained by CMS. It is in the public domain and free to use without restriction.
See http://cms.gov/regulations-and-guidance/legislation/clia.">Clinical Laboratory Improvement Amendments</a>/05D1102604</p><p><b>name</b>: Myriad Women's Health, Inc.</p><h3>Contacts</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Telecom</b></td><td><b>Address</b></td></tr><tr><td style="display: none">*</td><td>ph: (888) 268-6795, <a href="http://www.myriadwomenshealth.com">http://www.myriadwomenshealth.com</a></td><td>180 Kimball Way South San Francisco CA 94080 </td></tr></table></div>
</text>
<identifier>
<system value="urn:oid:2.16.840.1.113883.4.7"/>
<value value="05D1102604"/>
</identifier>
<name value="Myriad Women's Health, Inc."/>
<contact>
<telecom>
<system value="phone"/>
<value value="(888) 268-6795"/>
</telecom>
<telecom>
<system value="url"/>
<value value="http://www.myriadwomenshealth.com"/>
</telecom>
<address>
<line value="180 Kimball Way"/>
<city value="South San Francisco"/>
<state value="CA"/>
<postalCode value="94080"/>
</address>
</contact>
</Organization>
</resource>
<request>
<method value="POST"/>
<url value="Organization"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000005"/>
<resource>
<ServiceRequest>
<id value="prequel-service-request"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="ServiceRequest_prequel-service-request"> </a><p class="res-header-id"><b>Generated Narrative: ServiceRequest prequel-service-request</b></p><a name="prequel-service-request"> </a><a name="hcprequel-service-request"> </a><p><b>status</b>: Completed</p><p><b>intent</b>: Order</p><h3>Codes</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Concept</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://loinc.org 24364-2}">Myriad Prequel Prenatal Screen with AMPLIFY technology — Chromosomes 13, 18, 21 aneuploidy screening (NIPS v4.0)</span></td></tr></table><p><b>subject</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000001">Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)</a></p><p><b>authoredOn</b>: 2024-06-06</p><p><b>requester</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000002">Practitioner Paul Smith </a></p><p><b>performer</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000004">Organization Myriad Women's Health, Inc.</a></p><p><b>specimen</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000006">Specimen: identifier = http://example.org/barcode#31200020477415; status = available; type = Blood venous; receivedTime = 2024-06-09</a></p><p><b>note</b>: </p><blockquote><div><p>Singleton pregnancy; gestational age 8 weeks 0 days; ovum donor: N/A; patient height 5ft 6in; patient weight 120lbs; NT 1mm (ultrasound 2024-06-06); CRL 10cm; expected due date 2025-01-16</p>
</div></blockquote></div>
</text>
<status value="completed"/>
<intent value="order"/>
<code>
<concept>
<coding>
<system value="http://loinc.org"/>
<code value="24364-2"/>
<display value="Obstetric 1996 panel - Serum and Blood"/>
</coding>
<text
value="Myriad Prequel Prenatal Screen with AMPLIFY technology — Chromosomes 13, 18, 21 aneuploidy screening (NIPS v4.0)"/>
</concept>
</code>
<subject>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"/>
</subject>
<authoredOn value="2024-06-06"/>
<requester>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000002"/>
</requester>
<performer>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000004"/>
</performer>
<specimen>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000006"/>
</specimen>
<note>
<text
value="Singleton pregnancy; gestational age 8 weeks 0 days; ovum donor: N/A; patient height 5ft 6in; patient weight 120lbs; NT 1mm (ultrasound 2024-06-06); CRL 10cm; expected due date 2025-01-16"/>
</note>
</ServiceRequest>
</resource>
<request>
<method value="POST"/>
<url value="ServiceRequest"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000006"/>
<resource>
<Specimen>
<id value="prequel-specimen-cfdna"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Specimen_prequel-specimen-cfdna"> </a><p class="res-header-id"><b>Generated Narrative: Specimen prequel-specimen-cfdna</b></p><a name="prequel-specimen-cfdna"> </a><a name="hcprequel-specimen-cfdna"> </a><p><b>identifier</b>: <code>http://example.org/barcode</code>/31200020477415</p><p><b>status</b>: Available</p><p><b>type</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0487 BLDV}">Streck Cell-Free DNA Blood Tube (cell-free DNA)</span></p><p><b>subject</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000001">Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)</a></p><p><b>receivedTime</b>: 2024-06-09</p><h3>Collections</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Collector</b></td><td><b>Collected[x]</b></td></tr><tr><td style="display: none">*</td><td><a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000002">Practitioner Paul Smith </a></td><td>2024-06-06</td></tr></table></div>
</text>
<identifier>
<system value="http://example.org/barcode"/>
<value value="31200020477415"/>
</identifier>
<status value="available"/>
<type>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0487"/>
<code value="BLDV"/>
<display value="Blood venous"/>
</coding>
<text value="Streck Cell-Free DNA Blood Tube (cell-free DNA)"/>
</type>
<subject>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"/>
</subject>
<receivedTime value="2024-06-09"/>
<collection>
<collector>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000002"/>
</collector>
<collectedDateTime value="2024-06-06"/>
</collection>
</Specimen>
</resource>
<request>
<method value="POST"/>
<url value="Specimen"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000007"/>
<resource>
<Observation>
<id value="prequel-biomarker-fetal-fraction"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_prequel-biomarker-fetal-fraction"> </a><p class="res-header-id"><b>Generated Narrative: Observation prequel-biomarker-fetal-fraction</b></p><a name="prequel-biomarker-fetal-fraction"> </a><a name="hcprequel-biomarker-fetal-fraction"> </a><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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-molecular-biomarker.html">Molecular Biomarker</a></p></div><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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs biomarker-category}">Biomarker Category</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 75605-6}">Cell-free DNA.fetal/Cell-free DNA.total in Plasma cell-free DNA by Dosage of chromosome-specific cfDNA</span></p><p><b>subject</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000001">Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)</a></p><p><b>effective</b>: 2024-06-16</p><p><b>performer</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000004">Organization Myriad Women's Health, Inc.</a></p><p><b>value</b>: 25 %<span style="background: LightGoldenRodYellow"> (Details: UCUM code% = '%')</span></p><p><b>note</b>: </p><blockquote><div><p>Fetal fraction is one component of the algorithm used and is combined with other quality metrics to determine the aneuploidy screening result.</p>
</div></blockquote><p><b>specimen</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000006">Specimen: identifier = http://example.org/barcode#31200020477415; status = available; type = Blood venous; receivedTime = 2024-06-09</a></p><h3>Components</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs biomarker-category}">Biomarker Category</span></td><td><span title="Codes:">Cell-free fetal DNA fraction</span></td></tr></table></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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="biomarker-category"/>
</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="75605-6"/>
<display
value="Cell-free DNA.fetal/Cell-free DNA.total in Plasma cell-free DNA by Dosage of chromosome-specific cfDNA"/>
</coding>
</code>
<subject>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"/>
</subject>
<effectiveDateTime value="2024-06-16"/>
<performer>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000004"/>
</performer>
<valueQuantity>
<value value="25"/>
<unit value="%"/>
<system value="http://unitsofmeasure.org"/>
<code value="%"/>
</valueQuantity>
<note>
<text
value="Fetal fraction is one component of the algorithm used and is combined with other quality metrics to determine the aneuploidy screening result."/>
</note>
<specimen>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000006"/>
</specimen>
<component>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="biomarker-category"/>
</coding>
</code>
<valueCodeableConcept>
<text value="Cell-free fetal DNA fraction"/>
</valueCodeableConcept>
</component>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000008"/>
<resource>
<Observation>
<id value="prequel-variant-chr13-trisomy"/>
<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_prequel-variant-chr13-trisomy"> </a><p class="res-header-id"><b>Generated Narrative: Observation prequel-variant-chr13-trisomy</b></p><a name="prequel-variant-chr13-trisomy"> </a><a name="hcprequel-variant-chr13-trisomy"> </a><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"/><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>: <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-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000001">Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)</a></p><p><b>effective</b>: 2024-06-16</p><p><b>performer</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000004">Organization Myriad Women's Health, Inc.</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 with fetal chromosome analysis (NIPS v4.0); Genome Reference Consortium Human Build 37 (GRCh37)/hg19</span></p><p><b>specimen</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000006">Specimen: identifier = http://example.org/barcode#31200020477415; status = available; type = Blood venous; receivedTime = 2024-06-09</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48000-4}">Chromosome [Identifier] in Blood or Tissue by Molecular genetics method</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA21266-4}">Chromosome 13</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></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 LA10429-1}">Fetal</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 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:0001742}">copy_number_gain</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs conclusion-string}">Conclusion Text</span></p><p><b>value</b>: Results suggestive of trisomy for chromosome 13. Positive predictive value (PPV): 34.07% (34.07 in 100). Test performance: Sensitivity 99.0% (95% CI: 65.8-100.0); Specificity 99.96% (95% CI: 99.93-99.98).</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"/>
</coding>
</code>
<subject>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"/>
</subject>
<effectiveDateTime value="2024-06-16"/>
<performer>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000004"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<method>
<coding>
<system value="http://loinc.org"/>
<code value="LA26398-0"/>
<display value="Sequencing"/>
</coding>
<text
value="Sequencing with fetal chromosome analysis (NIPS v4.0); Genome Reference Consortium Human Build 37 (GRCh37)/hg19"/>
</method>
<specimen>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000006"/>
</specimen>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48000-4"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA21266-4"/>
<display value="Chromosome 13"/>
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<system value="http://loinc.org"/>
<code value="LA14029-5"/>
<display value="GRCh37"/>
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<system value="http://loinc.org"/>
<code value="48002-0"/>
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<system value="http://loinc.org"/>
<code value="LA10429-1"/>
<display value="Fetal"/>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="82155-3"/>
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<valueQuantity>
<value value="3"/>
<system value="http://unitsofmeasure.org"/>
<code value="1"/>
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<system value="http://loinc.org"/>
<code value="48019-4"/>
</coding>
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<valueCodeableConcept>
<coding>
<system value="http://www.sequenceontology.org"/>
<code value="SO:0001742"/>
<display value="copy_number_gain"/>
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<component>
<code>
<coding>
<system
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<valueString
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<method value="POST"/>
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<entry>
<fullUrl value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000009"/>
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<Observation>
<id value="prequel-variant-chr18-negative"/>
<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_prequel-variant-chr18-negative"> </a><p class="res-header-id"><b>Generated Narrative: Observation prequel-variant-chr18-negative</b></p><a name="prequel-variant-chr18-negative"> </a><a name="hcprequel-variant-chr18-negative"> </a><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"/><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>: <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-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000001">Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)</a></p><p><b>effective</b>: 2024-06-16</p><p><b>performer</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000004">Organization Myriad Women's Health, Inc.</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9634-2}">Absent</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing with fetal chromosome analysis (NIPS v4.0); GRCh37/hg19</span></p><p><b>specimen</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000006">Specimen: identifier = http://example.org/barcode#31200020477415; status = available; type = Blood venous; receivedTime = 2024-06-09</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48000-4}">Chromosome [Identifier] in Blood or Tissue by Molecular genetics method</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA21271-4}">Chromosome 18</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></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 LA10429-1}">Fetal</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>: 2 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs conclusion-string}">Conclusion Text</span></p><p><b>value</b>: Results consistent with two copies of chromosome 18. Residual risk < 0.01% (1 in 10,000). Test performance: Sensitivity 97.9% (95% CI: 94.9-99.1); Specificity 99.96% (95% CI: 99.93-99.97).</p></blockquote></div>
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<code value="GE"/>
</coding>
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<system value="http://loinc.org"/>
<code value="69548-6"/>
</coding>
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<subject>
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<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000004"/>
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<code value="LA9634-2"/>
<display value="Absent"/>
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<system value="http://loinc.org"/>
<code value="LA26398-0"/>
<display value="Sequencing"/>
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<text
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<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000006"/>
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<code value="48000-4"/>
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<valueCodeableConcept>
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<code value="LA21271-4"/>
<display value="Chromosome 18"/>
</coding>
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<coding>
<system value="http://loinc.org"/>
<code value="62374-4"/>
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<valueCodeableConcept>
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<system value="http://loinc.org"/>
<code value="LA14029-5"/>
<display value="GRCh37"/>
</coding>
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<coding>
<system value="http://loinc.org"/>
<code value="48002-0"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA10429-1"/>
<display value="Fetal"/>
</coding>
</valueCodeableConcept>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="82155-3"/>
</coding>
</code>
<valueQuantity>
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<system value="http://unitsofmeasure.org"/>
<code value="1"/>
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<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="conclusion-string"/>
</coding>
</code>
<valueString
value="Results consistent with two copies of chromosome 18. Residual risk < 0.01% (1 in 10,000). Test performance: Sensitivity 97.9% (95% CI: 94.9-99.1); Specificity 99.96% (95% CI: 99.93-99.97)."/>
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<entry>
<fullUrl value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000010"/>
<resource>
<Observation>
<id value="prequel-variant-chr21-negative"/>
<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_prequel-variant-chr21-negative"> </a><p class="res-header-id"><b>Generated Narrative: Observation prequel-variant-chr21-negative</b></p><a name="prequel-variant-chr21-negative"> </a><a name="hcprequel-variant-chr21-negative"> </a><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"/><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>: <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-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000001">Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)</a></p><p><b>effective</b>: 2024-06-16</p><p><b>performer</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000004">Organization Myriad Women's Health, Inc.</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9634-2}">Absent</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing with fetal chromosome analysis (NIPS v4.0); GRCh37/hg19</span></p><p><b>specimen</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000006">Specimen: identifier = http://example.org/barcode#31200020477415; status = available; type = Blood venous; receivedTime = 2024-06-09</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48000-4}">Chromosome [Identifier] in Blood or Tissue by Molecular genetics method</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA21274-8}">Chromosome 21</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></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 LA10429-1}">Fetal</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>: 2 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs conclusion-string}">Conclusion Text</span></p><p><b>value</b>: Results consistent with two copies of chromosome 21. Residual risk < 0.01% (1 in 10,000). Test performance: Sensitivity 99.7% (95% CI: 99.1-99.9); Specificity 99.96% (95% CI: 99.93-99.98).</p></blockquote></div>
</text>
<status value="final"/>
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<code value="laboratory"/>
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<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"/>
</coding>
</code>
<subject>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"/>
</subject>
<effectiveDateTime value="2024-06-16"/>
<performer>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000004"/>
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<code value="LA9634-2"/>
<display value="Absent"/>
</coding>
</valueCodeableConcept>
<method>
<coding>
<system value="http://loinc.org"/>
<code value="LA26398-0"/>
<display value="Sequencing"/>
</coding>
<text
value="Sequencing with fetal chromosome analysis (NIPS v4.0); GRCh37/hg19"/>
</method>
<specimen>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000006"/>
</specimen>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48000-4"/>
</coding>
</code>
<valueCodeableConcept>
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<system value="http://loinc.org"/>
<code value="LA21274-8"/>
<display value="Chromosome 21"/>
</coding>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="62374-4"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA14029-5"/>
<display value="GRCh37"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48002-0"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA10429-1"/>
<display value="Fetal"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="82155-3"/>
</coding>
</code>
<valueQuantity>
<value value="2"/>
<system value="http://unitsofmeasure.org"/>
<code value="1"/>
</valueQuantity>
</component>
<component>
<code>
<coding>
<system
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<code value="conclusion-string"/>
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<valueString
value="Results consistent with two copies of chromosome 21. Residual risk < 0.01% (1 in 10,000). Test performance: Sensitivity 99.7% (95% CI: 99.1-99.9); Specificity 99.96% (95% CI: 99.93-99.98)."/>
</component>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000011"/>
<resource>
<Observation>
<id value="prequel-dx-implication-patau"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_prequel-dx-implication-patau"> </a><p class="res-header-id"><b>Generated Narrative: Observation prequel-dx-implication-patau</b></p><a name="prequel-dx-implication-patau"> </a><a name="hcprequel-dx-implication-patau"> </a><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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-diagnostic-implication.html">Diagnostic Implication</a></p></div><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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}">Diagnostic Implication</span></p><p><b>subject</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000001">Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)</a></p><p><b>effective</b>: 2024-06-16</p><p><b>performer</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000004">Organization Myriad Women's Health, Inc.</a></p><p><b>derivedFrom</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000008">Observation Genetic variant assessment</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 53037-8}">Genetic variation clinical significance [Imp]</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6668-3}">Pathogenic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81259-4}">Associated phenotype</span></p><p><b>value</b>: <span title="Codes:{http://purl.obolibrary.org/obo/mondo.owl MONDO:0009141}">Trisomy 13 (Patau Syndrome)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs condition-inheritance}">Condition Inheritance</span></p><p><b>value</b>: <span title="Codes:{http://purl.obolibrary.org/obo/hp.owl HP:0001466}">Contiguous gene syndrome (chromosomal aneuploidy; typically sporadic)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs conclusion-string}">Conclusion Text</span></p><p><b>value</b>: POSITIVE: Aneuploidy suspected (borderline value). Results suggestive of trisomy for chromosome 13. Positive predictive value (PPV): 34.07% (34.07 in 100). Trisomy 13 (Patau syndrome) is a life-limiting condition caused by an extra copy of chromosome 13. Common features include heart defects, brain and spine abnormalities, polydactyly, micropthalmia, hypotonia, kidney problems, and cleft lip/palate. Most infants die within the first few weeks of life. This is a screening test — false positives can occur. Definitive diagnosis requires CVS or amniocentesis.</p></blockquote></div>
</text>
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<system
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<code value="laboratory"/>
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<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
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<code>
<coding>
<system
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<code value="diagnostic-implication"/>
</coding>
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<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"/>
</subject>
<effectiveDateTime value="2024-06-16"/>
<performer>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000004"/>
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<derivedFrom>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000008"/>
</derivedFrom>
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<system value="http://loinc.org"/>
<code value="53037-8"/>
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<system value="http://loinc.org"/>
<code value="LA6668-3"/>
<display value="Pathogenic"/>
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<coding>
<system value="http://loinc.org"/>
<code value="81259-4"/>
</coding>
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<coding>
<system value="http://purl.obolibrary.org/obo/mondo.owl"/>
<code value="MONDO:0009141"/>
<display value="trisomy 13"/>
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<text value="Trisomy 13 (Patau Syndrome)"/>
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<code>
<coding>
<system
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<coding>
<system value="http://purl.obolibrary.org/obo/hp.owl"/>
<code value="HP:0001466"/>
</coding>
<text
value="Contiguous gene syndrome (chromosomal aneuploidy; typically sporadic)"/>
</valueCodeableConcept>
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<component>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="conclusion-string"/>
</coding>
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<valueString
value="POSITIVE: Aneuploidy suspected (borderline value). Results suggestive of trisomy for chromosome 13. Positive predictive value (PPV): 34.07% (34.07 in 100). Trisomy 13 (Patau syndrome) is a life-limiting condition caused by an extra copy of chromosome 13. Common features include heart defects, brain and spine abnormalities, polydactyly, micropthalmia, hypotonia, kidney problems, and cleft lip/palate. Most infants die within the first few weeks of life. This is a screening test — false positives can occur. Definitive diagnosis requires CVS or amniocentesis."/>
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<url value="Observation"/>
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<entry>
<fullUrl value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000014"/>
<resource>
<Observation>
<id value="prequel-dx-implication-edwards-negative"/>
<meta>
<profile
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<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_prequel-dx-implication-edwards-negative"> </a><p class="res-header-id"><b>Generated Narrative: Observation prequel-dx-implication-edwards-negative</b></p><a name="prequel-dx-implication-edwards-negative"> </a><a name="hcprequel-dx-implication-edwards-negative"> </a><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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-diagnostic-implication.html">Diagnostic Implication</a></p></div><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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}">Diagnostic Implication</span></p><p><b>subject</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000001">Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)</a></p><p><b>effective</b>: 2024-06-16</p><p><b>performer</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000004">Organization Myriad Women's Health, Inc.</a></p><p><b>derivedFrom</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000009">Observation Genetic variant assessment</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 53037-8}">Genetic variation clinical significance [Imp]</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA26334-5}">Likely benign</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81259-4}">Associated phenotype</span></p><p><b>value</b>: <span title="Codes:{http://purl.obolibrary.org/obo/mondo.owl MONDO:0009869}">Trisomy 18 (Edwards Syndrome)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs conclusion-string}">Conclusion Text</span></p><p><b>value</b>: NEGATIVE: Results consistent with two copies of chromosome 18. Residual risk < 0.01% (1 in 10,000). Test performance: Sensitivity 97.9% (95% CI: 94.9-99.1); Specificity 99.96% (95% CI: 99.93-99.97).</p></blockquote></div>
</text>
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<category>
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<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
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<code>
<coding>
<system
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<code value="diagnostic-implication"/>
</coding>
</code>
<subject>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"/>
</subject>
<effectiveDateTime value="2024-06-16"/>
<performer>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000004"/>
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<derivedFrom>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000009"/>
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<component>
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<system value="http://loinc.org"/>
<code value="53037-8"/>
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<coding>
<system value="http://loinc.org"/>
<code value="LA26334-5"/>
<display value="Likely benign"/>
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<component>
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<coding>
<system value="http://loinc.org"/>
<code value="81259-4"/>
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<valueCodeableConcept>
<coding>
<system value="http://purl.obolibrary.org/obo/mondo.owl"/>
<code value="MONDO:0009869"/>
<display value="trisomy 18"/>
</coding>
<text value="Trisomy 18 (Edwards Syndrome)"/>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system
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<code value="conclusion-string"/>
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<valueString
value="NEGATIVE: Results consistent with two copies of chromosome 18. Residual risk < 0.01% (1 in 10,000). Test performance: Sensitivity 97.9% (95% CI: 94.9-99.1); Specificity 99.96% (95% CI: 99.93-99.97)."/>
</component>
</Observation>
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<request>
<method value="POST"/>
<url value="Observation"/>
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<entry>
<fullUrl value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000015"/>
<resource>
<Observation>
<id value="prequel-dx-implication-down-negative"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_prequel-dx-implication-down-negative"> </a><p class="res-header-id"><b>Generated Narrative: Observation prequel-dx-implication-down-negative</b></p><a name="prequel-dx-implication-down-negative"> </a><a name="hcprequel-dx-implication-down-negative"> </a><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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-diagnostic-implication.html">Diagnostic Implication</a></p></div><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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}">Diagnostic Implication</span></p><p><b>subject</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000001">Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)</a></p><p><b>effective</b>: 2024-06-16</p><p><b>performer</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000004">Organization Myriad Women's Health, Inc.</a></p><p><b>derivedFrom</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000010">Observation Genetic variant assessment</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 53037-8}">Genetic variation clinical significance [Imp]</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA26334-5}">Likely benign</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81259-4}">Associated phenotype</span></p><p><b>value</b>: <span title="Codes:{http://purl.obolibrary.org/obo/mondo.owl MONDO:0008608}">Trisomy 21 (Down Syndrome)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs conclusion-string}">Conclusion Text</span></p><p><b>value</b>: NEGATIVE: Results consistent with two copies of chromosome 21. Residual risk < 0.01% (1 in 10,000). Test performance: Sensitivity 99.7% (95% CI: 99.1-99.9); Specificity 99.96% (95% CI: 99.93-99.98).</p></blockquote></div>
</text>
<status value="final"/>
<category>
<coding>
<system
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<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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="diagnostic-implication"/>
</coding>
</code>
<subject>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"/>
</subject>
<effectiveDateTime value="2024-06-16"/>
<performer>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000004"/>
</performer>
<derivedFrom>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000010"/>
</derivedFrom>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="53037-8"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA26334-5"/>
<display value="Likely benign"/>
</coding>
</valueCodeableConcept>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81259-4"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://purl.obolibrary.org/obo/mondo.owl"/>
<code value="MONDO:0008608"/>
<display value="trisomy 21"/>
</coding>
<text value="Trisomy 21 (Down Syndrome)"/>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="conclusion-string"/>
</coding>
</code>
<valueString
value="NEGATIVE: Results consistent with two copies of chromosome 21. Residual risk < 0.01% (1 in 10,000). Test performance: Sensitivity 99.7% (95% CI: 99.1-99.9); Specificity 99.96% (95% CI: 99.93-99.98)."/>
</component>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000012"/>
<resource>
<Task>
<id value="prequel-task-genetic-counseling"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Task_prequel-task-genetic-counseling"> </a><p class="res-header-id"><b>Generated Narrative: Task prequel-task-genetic-counseling</b></p><a name="prequel-task-genetic-counseling"> </a><a name="hcprequel-task-genetic-counseling"> </a><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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-followup-recommendation.html">Followup Recommendation</a></p></div><p><b>status</b>: Requested</p><p><b>intent</b>: proposal</p><p><b>code</b>: <span title="Codes:{http://loinc.org LA14020-4}">Genetic counseling recommended</span></p><p><b>description</b>: </p><div><p>Genetic counseling is recommended in view of a positive NIPS result for Trisomy 13 (PPV 34.07%). No irreversible decision should be made based on this screening result alone. If definitive diagnosis is desired, chorionic villus sampling (CVS) or amniocentesis is necessary. Clinical correlation with ultrasound findings and history is indicated.</p>
</div><p><b>for</b>: <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000001">Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)</a></p><h3>Reasons</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Reference</b></td></tr><tr><td style="display: none">*</td><td><a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000011">Observation Diagnostic Implication</a></td></tr></table></div>
</text>
<status value="requested"/>
<intent value="proposal"/>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="LA14020-4"/>
<display value="Genetic counseling recommended"/>
</coding>
</code>
<description
value="Genetic counseling is recommended in view of a positive NIPS result for Trisomy 13 (PPV 34.07%). No irreversible decision should be made based on this screening result alone. If definitive diagnosis is desired, chorionic villus sampling (CVS) or amniocentesis is necessary. Clinical correlation with ultrasound findings and history is indicated."/>
<for>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"/>
</for>
<reason>
<reference>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000011"/>
</reference>
</reason>
</Task>
</resource>
<request>
<method value="POST"/>
<url value="Task"/>
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</entry>
<entry>
<fullUrl value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000013"/>
<resource>
<DiagnosticReport>
<id value="prequel-genomic-report"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="DiagnosticReport_prequel-genomic-report"> </a><p class="res-header-id"><b>Generated Narrative: DiagnosticReport prequel-genomic-report</b></p><a name="prequel-genomic-report"> </a><a name="hcprequel-genomic-report"> </a><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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-genomic-report.html">Genomic Report</a></p></div><h2><span title="Codes:{http://loinc.org 51969-4}">Genetic analysis report</span> (<span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span>) </h2><table class="grid"><tr><td>Subject</td><td>Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)</td></tr><tr><td>When For</td><td>2024-06-17</td></tr><tr><td>Reported</td><td>2024-06-17 00:00:00+0000</td></tr><tr><td>Performer</td><td> <a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000004">Organization Myriad Women's Health, Inc.</a></td></tr></table><p><b>Report Details</b></p><table class="grid"><tr><td><b>Code</b></td><td><b>Value</b></td><td><b>Flags</b></td><td><b>Note</b></td><td><b>When For</b></td></tr><tr><td><a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000007"><span title="Codes:{http://loinc.org 75605-6}">Cell-free DNA.fetal/Cell-free DNA.total in Plasma cell-free DNA by Dosage of chromosome-specific cfDNA</span></a></td><td>25 %<span style="background: LightGoldenRodYellow"> (Details: UCUM code% = '%')</span></td><td>Final</td><td><blockquote><div><p>Fetal fraction is one component of the algorithm used and is combined with other quality metrics to determine the aneuploidy screening result.</p>
</div></blockquote></td><td>2024-06-16</td></tr><tr><td><a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000008"><span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></a></td><td><span title="Codes:{http://loinc.org LA9633-4}">Present</span></td><td>Final</td><td/><td>2024-06-16</td></tr><tr><td><a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000009"><span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></a></td><td><span title="Codes:{http://loinc.org LA9634-2}">Absent</span></td><td>Final</td><td/><td>2024-06-16</td></tr><tr><td><a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000010"><span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></a></td><td><span title="Codes:{http://loinc.org LA9634-2}">Absent</span></td><td>Final</td><td/><td>2024-06-16</td></tr><tr><td><a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000011"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2024-06-16</td></tr><tr><td><a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000014"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2024-06-16</td></tr><tr><td><a href="Bundle-bundle-prequel-prenatal-trisomy13.html#urn-uuid-2c9e6be3-1b0e-4e3a-9d9e-000000000015"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2024-06-16</td></tr></table><div><p>POSITIVE: PREGNANCY AT INCREASED RISK. Chromosome 13 aneuploidy detected — results suggestive of Trisomy 13 (Patau Syndrome). Positive predictive value (PPV): 34.07% (34.07 in 100). Chromosomes 18 (Edwards Syndrome) and 21 (Down Syndrome) are NEGATIVE with residual risk < 0.01% (1 in 10,000) each. Fetal fraction: 25.0%. Method: sequencing with fetal chromosome analysis (NIPS v4.0; GRCh37/hg19). This is a screening test — false positive and false negative results can occur. Genetic counseling is recommended. If definitive diagnosis is desired, chorionic villus sampling or amniocentesis is necessary.</p>
</div><p><b>Coded Conclusions:</b></p><ul><li><span title="Codes:{http://snomed.info/sct 10828004}">POSITIVE: Pregnancy at Increased Risk for Trisomy 13 (Patau Syndrome)</span></li></ul></div>
</text>
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<result>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000014"/>
</result>
<result>
<reference value="urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000015"/>
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<conclusion
value="POSITIVE: PREGNANCY AT INCREASED RISK. Chromosome 13 aneuploidy detected — results suggestive of Trisomy 13 (Patau Syndrome). Positive predictive value (PPV): 34.07% (34.07 in 100). Chromosomes 18 (Edwards Syndrome) and 21 (Down Syndrome) are NEGATIVE with residual risk < 0.01% (1 in 10,000) each. Fetal fraction: 25.0%. Method: sequencing with fetal chromosome analysis (NIPS v4.0; GRCh37/hg19). This is a screening test — false positive and false negative results can occur. Genetic counseling is recommended. If definitive diagnosis is desired, chorionic villus sampling or amniocentesis is necessary."/>
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<title
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<creation value="2024-06-17"/>
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IG © 2025+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#4.0.0-cibuild based on FHIR 6.0.0-ballot3. Generated 2026-03-31
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