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
{
"resourceType" : "Bundle",
"id" : "bundle-prequel-prenatal-trisomy13",
"type" : "transaction",
"entry" : [
{
"fullUrl" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001",
"resource" : {
"resourceType" : "Patient",
"id" : "prequel-patient-jane-miller",
"text" : {
"status" : "generated",
"div" : "<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>"
},
"identifier" : [
{
"system" : "http://example.org/mrn",
"value" : "FAKERQIHPT13S"
}
],
"name" : [
{
"family" : "Miller",
"given" : [
"Jane"
]
}
],
"gender" : "female",
"birthDate" : "1997-11-11"
},
"request" : {
"method" : "POST",
"url" : "Patient"
}
},
{
"fullUrl" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000002",
"resource" : {
"resourceType" : "Practitioner",
"id" : "prequel-practitioner-paul-smith",
"text" : {
"status" : "generated",
"div" : "<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>"
},
"identifier" : [
{
"system" : "http://hl7.org/fhir/sid/us-npi",
"value" : "4253506008"
}
],
"name" : [
{
"family" : "Smith",
"given" : [
"Paul"
],
"prefix" : [
"Dr."
]
}
]
},
"request" : {
"method" : "POST",
"url" : "Practitioner"
}
},
{
"fullUrl" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000003",
"resource" : {
"resourceType" : "Organization",
"id" : "prequel-org-umc",
"text" : {
"status" : "generated",
"div" : "<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>"
},
"name" : "University Medical Center",
"contact" : [
{
"telecom" : [
{
"system" : "phone",
"value" : "(800) 555-1212"
},
{
"system" : "fax",
"value" : "(800) 555-1212"
}
],
"address" : {
"line" : [
"123 Main Street"
],
"city" : "City",
"state" : "CA",
"postalCode" : "10231"
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Organization"
}
},
{
"fullUrl" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000004",
"resource" : {
"resourceType" : "Organization",
"id" : "prequel-org-myriad",
"text" : {
"status" : "generated",
"div" : "<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.\r\n\r\nThe 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."\r\n\r\nCMS 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."\r\n\r\nCLIA is maintained by CMS. It is in the public domain and free to use without restriction.\r\n\r\nSee 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>"
},
"identifier" : [
{
"system" : "urn:oid:2.16.840.1.113883.4.7",
"value" : "05D1102604"
}
],
"name" : "Myriad Women's Health, Inc.",
"contact" : [
{
"telecom" : [
{
"system" : "phone",
"value" : "(888) 268-6795"
},
{
"system" : "url",
"value" : "http://www.myriadwomenshealth.com"
}
],
"address" : {
"line" : [
"180 Kimball Way"
],
"city" : "South San Francisco",
"state" : "CA",
"postalCode" : "94080"
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Organization"
}
},
{
"fullUrl" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000005",
"resource" : {
"resourceType" : "ServiceRequest",
"id" : "prequel-service-request",
"text" : {
"status" : "generated",
"div" : "<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>\n</div></blockquote></div>"
},
"status" : "completed",
"intent" : "order",
"code" : {
"concept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "24364-2",
"display" : "Obstetric 1996 panel - Serum and Blood"
}
],
"text" : "Myriad Prequel Prenatal Screen with AMPLIFY technology — Chromosomes 13, 18, 21 aneuploidy screening (NIPS v4.0)"
}
},
"subject" : {
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"
},
"authoredOn" : "2024-06-06",
"requester" : {
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000002"
},
"performer" : [
{
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000004"
}
],
"specimen" : [
{
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000006"
}
],
"note" : [
{
"text" : "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"
}
]
},
"request" : {
"method" : "POST",
"url" : "ServiceRequest"
}
},
{
"fullUrl" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000006",
"resource" : {
"resourceType" : "Specimen",
"id" : "prequel-specimen-cfdna",
"text" : {
"status" : "generated",
"div" : "<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>"
},
"identifier" : [
{
"system" : "http://example.org/barcode",
"value" : "31200020477415"
}
],
"status" : "available",
"type" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0487",
"code" : "BLDV",
"display" : "Blood venous"
}
],
"text" : "Streck Cell-Free DNA Blood Tube (cell-free DNA)"
},
"subject" : {
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"
},
"receivedTime" : "2024-06-09",
"collection" : {
"collector" : {
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000002"
},
"collectedDateTime" : "2024-06-06"
}
},
"request" : {
"method" : "POST",
"url" : "Specimen"
}
},
{
"fullUrl" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000007",
"resource" : {
"resourceType" : "Observation",
"id" : "prequel-biomarker-fetal-fraction",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker"
]
},
"text" : {
"status" : "generated",
"div" : "<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>\n</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>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
},
{
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "biomarker-category"
}
]
},
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "75605-6",
"display" : "Cell-free DNA.fetal/Cell-free DNA.total in Plasma cell-free DNA by Dosage of chromosome-specific cfDNA"
}
]
},
"subject" : {
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"
},
"effectiveDateTime" : "2024-06-16",
"performer" : [
{
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000004"
}
],
"valueQuantity" : {
"value" : 25,
"unit" : "%",
"system" : "http://unitsofmeasure.org",
"code" : "%"
},
"note" : [
{
"text" : "Fetal fraction is one component of the algorithm used and is combined with other quality metrics to determine the aneuploidy screening result."
}
],
"specimen" : {
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000006"
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "biomarker-category"
}
]
},
"valueCodeableConcept" : {
"text" : "Cell-free fetal DNA fraction"
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000008",
"resource" : {
"resourceType" : "Observation",
"id" : "prequel-variant-chr13-trisomy",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text" : {
"status" : "generated",
"div" : "<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>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
},
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69548-6"
}
]
},
"subject" : {
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"code" : "1"
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{
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"code" : {
"coding" : [
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"valueString" : "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)."
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"url" : "Observation"
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{
"fullUrl" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000009",
"resource" : {
"resourceType" : "Observation",
"id" : "prequel-variant-chr18-negative",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text" : {
"status" : "generated",
"div" : "<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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"category" : [
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"code" : "GE"
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{
"system" : "http://loinc.org",
"code" : "69548-6"
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"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26398-0",
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"specimen" : {
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000006"
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"valueString" : "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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"resource" : {
"resourceType" : "Observation",
"id" : "prequel-variant-chr21-negative",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
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"text" : {
"status" : "generated",
"div" : "<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>"
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"category" : [
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"coding" : [
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"code" : "laboratory"
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{
"coding" : [
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"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
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]
}
],
"code" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "69548-6"
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},
"subject" : {
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"
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"effectiveDateTime" : "2024-06-16",
"performer" : [
{
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000004"
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],
"valueCodeableConcept" : {
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"code" : "LA9634-2",
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"method" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26398-0",
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],
"text" : "Sequencing with fetal chromosome analysis (NIPS v4.0); GRCh37/hg19"
},
"specimen" : {
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000006"
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"component" : [
{
"code" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "48000-4"
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"valueCodeableConcept" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "LA21274-8",
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{
"code" : {
"coding" : [
{
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"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA14029-5",
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]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48002-0"
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},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA10429-1",
"display" : "Fetal"
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},
{
"code" : {
"coding" : [
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"valueQuantity" : {
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"code" : "1"
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{
"code" : {
"coding" : [
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"valueString" : "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)."
}
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},
"request" : {
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"url" : "Observation"
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},
{
"fullUrl" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000011",
"resource" : {
"resourceType" : "Observation",
"id" : "prequel-dx-implication-patau",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
]
},
"text" : {
"status" : "generated",
"div" : "<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>"
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"system" : "http://purl.obolibrary.org/obo/mondo.owl",
"code" : "MONDO:0009141",
"display" : "trisomy 13"
}
],
"text" : "Trisomy 13 (Patau Syndrome)"
}
},
{
"code" : {
"coding" : [
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"text" : "Contiguous gene syndrome (chromosomal aneuploidy; typically sporadic)"
}
},
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"code" : {
"coding" : [
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}
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"request" : {
"method" : "POST",
"url" : "Observation"
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{
"fullUrl" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000014",
"resource" : {
"resourceType" : "Observation",
"id" : "prequel-dx-implication-edwards-negative",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
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"status" : "generated",
"div" : "<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>"
},
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"coding" : [
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"code" : "diagnostic-implication"
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"subject" : {
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"
},
"effectiveDateTime" : "2024-06-16",
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{
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000004"
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"derivedFrom" : [
{
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000009"
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],
"component" : [
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"code" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "53037-8"
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"coding" : [
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{
"system" : "http://purl.obolibrary.org/obo/mondo.owl",
"code" : "MONDO:0009869",
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],
"text" : "Trisomy 18 (Edwards Syndrome)"
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},
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
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}
]
},
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"method" : "POST",
"url" : "Observation"
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},
{
"fullUrl" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000015",
"resource" : {
"resourceType" : "Observation",
"id" : "prequel-dx-implication-down-negative",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
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"text" : {
"status" : "generated",
"div" : "<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>"
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"coding" : [
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"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
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],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "diagnostic-implication"
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]
},
"subject" : {
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"
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"effectiveDateTime" : "2024-06-16",
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{
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000004"
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],
"derivedFrom" : [
{
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000010"
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"component" : [
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"coding" : [
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],
"text" : "Trisomy 21 (Down Syndrome)"
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},
{
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"coding" : [
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"valueString" : "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)."
}
]
},
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},
{
"fullUrl" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000012",
"resource" : {
"resourceType" : "Task",
"id" : "prequel-task-genetic-counseling",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation"
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"text" : {
"status" : "generated",
"div" : "<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>\n</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>"
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"code" : {
"coding" : [
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"system" : "http://loinc.org",
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"description" : "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" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001"
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"reason" : [
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"reference" : {
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000011"
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"request" : {
"method" : "POST",
"url" : "Task"
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{
"fullUrl" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000013",
"resource" : {
"resourceType" : "DiagnosticReport",
"id" : "prequel-genomic-report",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"
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"text" : {
"status" : "generated",
"div" : "<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>\n</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>\n</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>"
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{
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000009"
},
{
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000010"
},
{
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000011"
},
{
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000014"
},
{
"reference" : "urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000015"
}
],
"conclusion" : "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.",
"conclusionCode" : [
{
"concept" : {
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "10828004",
"display" : "Positive (qualifier value)"
}
],
"text" : "POSITIVE: Pregnancy at Increased Risk for Trisomy 13 (Patau Syndrome)"
}
}
],
"presentedForm" : [
{
"contentType" : "application/pdf",
"data" : "JVBERi0xLjQKJeLjz9MKICAgICAgICAgICAgICAgICAgICAgICAgICAgICAKJSUgUGxhY2Vob2xkZXIgYmFzZTY0LWVuY29kZWQgUERGIGRhdGEgJSUK",
"title" : "Myriad Prequel Prenatal Screen with AMPLIFY — Positive Sample Report (PDF)",
"creation" : "2024-06-17"
}
]
},
"request" : {
"method" : "POST",
"url" : "DiagnosticReport"
}
}
]
}
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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