bundle-prequel-prenatal-trisomy13
type: Bundle
node role: treeRoot
id:
  v: bundle-prequel-prenatal-trisomy13
type:
  v: transaction
entry:
  request:
    method:
      v: POST
    url:
      v: Patient
      l: Patient
entry:
  request:
    method:
      v: POST
    url:
      v: Practitioner
      l: Practitioner
entry:
  request:
    method:
      v: POST
    url:
      v: Organization
      l: Organization
entry:
  request:
    method:
      v: POST
    url:
      v: Organization
      l: Organization
entry:
  request:
    method:
      v: POST
    url:
      v: ServiceRequest
      l: ServiceRequest
entry:
  request:
    method:
      v: POST
    url:
      v: Specimen
      l: Specimen
entry:
  request:
    method:
      v: POST
    url:
      v: Observation
      l: Observation
entry:
  request:
    method:
      v: POST
    url:
      v: Observation
      l: Observation
entry:
  request:
    method:
      v: POST
    url:
      v: Observation
      l: Observation
entry:
  request:
    method:
      v: POST
    url:
      v: Observation
      l: Observation
entry:
  request:
    method:
      v: POST
    url:
      v: Observation
      l: Observation
entry:
  request:
    method:
      v: POST
    url:
      v: Observation
      l: Observation
entry:
  request:
    method:
      v: POST
    url:
      v: Observation
      l: Observation
entry:
  request:
    method:
      v: POST
    url:
      v: Task
      l: Task
entry:
  request:
    method:
      v: POST
    url:
      v: DiagnosticReport
      l: DiagnosticReport

urn:…
type: Patient
id:
  v: prequel-patient-jane-miller
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Patient prequel-patient-jane-miller Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)
identifier:
  system:
    v: http://example.org/mrn
    l: mrn
  value:
    v: FAKERQIHPT13S
name:
  family:
    v: Miller
  given:
    v: Jane
gender:
  v: female
birth date:
  v: 1997-11-11

urn:…
type: Practitioner
id:
  v: prequel-practitioner-paul-smith
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Practitioner prequel-practitioner-paul-smith identifier: United States National Provider Identifier/4253506008 name: Paul Smith
identifier:
  system:
    v: http://hl7.org/fhir/sid/us-npi
    l: us-npi
  value:
    v: 4253506008
name:
  family:
    v: Smith
  given:
    v: Paul
  prefix:
    v: Dr.

urn:…
type: Organization
id:
  v: prequel-org-umc
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Organization prequel-org-umc name: University Medical Center Contacts - Telecom Address * ph: (800) 555-1212, fax: (800) 555-1212 123 Main Street City CA 10231
name:
  v: University Medical Center
contact:
  telecom:
    system:
      v: phone
    value:
      v: (800) 555-1212
  telecom:
    system:
      v: fax
    value:
      v: (800) 555-1212
  address:
    line:
      v: 123 Main Street
    city:
      v: City
    state:
      v: CA
    postal code:
      v: 10231

urn:…
type: Organization
id:
  v: prequel-org-myriad
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Organization prequel-org-myriad identifier: <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.#xD;#xA;#xD;#xA;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."#xD;#xA;#xD;#xA;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."#xD;#xA;#xD;#xA;CLIA is maintained by CMS. It is in the public domain and free to use without restriction.#xD;#xA;#xD;#xA;See http://cms.gov/regulations-and-guidance/legislation/clia.">Clinical Laboratory Improvement Amendments/05D1102604 name: Myriad Women's Health, Inc. Contacts - Telecom Address * ph: (888) 268-6795, http://www.myriadwomenshealth.com 180 Kimball Way South San Francisco CA 94080
identifier:
  system:
    v: urn:oid:2.16.840.1.113883.4.7
    l: 2.16.840.1.113883.4.7
  value:
    v: 05D1102604
name:
  v: Myriad Women's Health, Inc.
contact:
  telecom:
    system:
      v: phone
    value:
      v: (888) 268-6795
  telecom:
    system:
      v: url
    value:
      v: http://www.myriadwomenshealth.com
  address:
    line:
      v: 180 Kimball Way
    city:
      v: South San Francisco
    state:
      v: CA
    postal code:
      v: 94080

urn:…
type: ServiceRequest
id:
  v: prequel-service-request
text:
  status:
    v: generated
  div:
    v: Generated Narrative: ServiceRequest prequel-service-request status: Completed intent: Order Codes - Concept * Myriad Prequel Prenatal Screen with AMPLIFY technology — Chromosomes 13, 18, 21 aneuploidy screening (NIPS v4.0) subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S) authoredOn: 2024-06-06 requester: Practitioner Paul Smith performer: Organization Myriad Women's Health, Inc. specimen: Specimen: identifier = http://example.org/barcode#31200020477415; status = available; type = Blood venous; receivedTime = 2024-06-09 note: 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
status:
  v: completed
intent:
  v: order
code:
  concept:
    coding: https://loinc.org/rdf/24364-2
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 24364-2
      display:
        v: Obstetric 1996 panel - Serum and Blood
    text:
      v: Myriad Prequel Prenatal Screen with AMPLIFY technology — Chromosomes 13, 18, 21 aneuploidy screening (NIPS v4.0)
authored on:
  v: 2024-06-06
note:
  text:
    v: 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

urn:…
type: Specimen
id:
  v: prequel-specimen-cfdna
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Specimen prequel-specimen-cfdna identifier: http://example.org/barcode/31200020477415 status: Available type: Streck Cell-Free DNA Blood Tube (cell-free DNA) subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S) receivedTime: 2024-06-09 Collections - Collector Collected[x] * Practitioner Paul Smith 2024-06-06
identifier:
  system:
    v: http://example.org/barcode
    l: barcode
  value:
    v: 31200020477415
status:
  v: available
type:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/v2-0487
      l: v2-0487
    code:
      v: BLDV
    display:
      v: Blood venous
  text:
    v: Streck Cell-Free DNA Blood Tube (cell-free DNA)
received time:
  v: 2024-06-09
collection:
  collected: DateTime
    v: 2024-06-06

urn:…
type: Observation
id:
  v: prequel-biomarker-fetal-fraction
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker
    l: molecular-biomarker
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation prequel-biomarker-fetal-fraction Profile: Molecular Biomarker status: Final category: Laboratory, Biomarker Category, Genetics code: Cell-free DNA.fetal/Cell-free DNA.total in Plasma cell-free DNA by Dosage of chromosome-specific cfDNA subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S) effective: 2024-06-16 performer: Organization Myriad Women's Health, Inc. value: 25 % (Details: UCUM code% = '%') note: Fetal fraction is one component of the algorithm used and is combined with other quality metrics to determine the aneuploidy screening result. specimen: Specimen: identifier = http://example.org/barcode#31200020477415; status = available; type = Blood venous; receivedTime = 2024-06-09 Components - Code Value[x] * Biomarker Category Cell-free fetal DNA fraction
status:
  v: final
category:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/observation-category
      l: observation-category
    code:
      v: laboratory
category:
  coding:
    system:
      v: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
      l: tbd-codes-cs
    code:
      v: biomarker-category
category:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/v2-0074
      l: v2-0074
    code:
      v: GE
code:
  coding: https://loinc.org/rdf/75605-6
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 75605-6
    display:
      v: Cell-free DNA.fetal/Cell-free DNA.total in Plasma cell-free DNA by Dosage of chromosome-specific cfDNA
effective: DateTime
  v: 2024-06-16
value: Quantity
  value:
    v: 25
  unit:
    v: %
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: %
note:
  text:
    v: Fetal fraction is one component of the algorithm used and is combined with other quality metrics to determine the aneuploidy screening result.
component:
  code:
    coding:
      system:
        v: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
        l: tbd-codes-cs
      code:
        v: biomarker-category
  value: CodeableConcept
    text:
      v: Cell-free fetal DNA fraction

urn:…
type: Observation
id:
  v: prequel-variant-chr13-trisomy
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation prequel-variant-chr13-trisomy Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S) effective: 2024-06-16 performer: Organization Myriad Women's Health, Inc. value: Present method: Sequencing with fetal chromosome analysis (NIPS v4.0); Genome Reference Consortium Human Build 37 (GRCh37)/hg19 specimen: Specimen: identifier = http://example.org/barcode#31200020477415; status = available; type = Blood venous; receivedTime = 2024-06-09 component code: Chromosome [Identifier] in Blood or Tissue by Molecular genetics method value: Chromosome 13 component code: Human reference sequence assembly version value: GRCh37 component code: Genomic source class [Type] value: Fetal component code: Genomic structural variant copy number value: 3 1 (Details: UCUM code1 = '1') component code: DNA change type value: copy_number_gain component code: Conclusion Text value: 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).
status:
  v: final
category:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/observation-category
      l: observation-category
    code:
      v: laboratory
category:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/v2-0074
      l: v2-0074
    code:
      v: GE
code:
  coding: https://loinc.org/rdf/69548-6
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 69548-6
effective: DateTime
  v: 2024-06-16
value: CodeableConcept
  coding: LA9633-4
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: LA9633-4
    display:
      v: Present
method:
  coding: LA26398-0
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: LA26398-0
    display:
      v: Sequencing
  text:
    v: Sequencing with fetal chromosome analysis (NIPS v4.0); Genome Reference Consortium Human Build 37 (GRCh37)/hg19
component:
  code:
    coding: https://loinc.org/rdf/48000-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48000-4
  value: CodeableConcept
    coding: LA21266-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA21266-4
      display:
        v: Chromosome 13
component:
  code:
    coding: https://loinc.org/rdf/62374-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 62374-4
  value: CodeableConcept
    coding: LA14029-5
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA14029-5
      display:
        v: GRCh37
component:
  code:
    coding: https://loinc.org/rdf/48002-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48002-0
  value: CodeableConcept
    coding: LA10429-1
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA10429-1
      display:
        v: Fetal
component:
  code:
    coding: https://loinc.org/rdf/82155-3
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 82155-3
  value: Quantity
    value:
      v: 3
    system:
      v: http://unitsofmeasure.org
      l: unitsofmeasure.org
    code:
      v: 1
component:
  code:
    coding: https://loinc.org/rdf/48019-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48019-4
  value: CodeableConcept
    coding:
      system:
        v: http://www.sequenceontology.org
        l: www.sequenceontology.org
      code:
        v: SO:0001742
      display:
        v: copy_number_gain
component:
  code:
    coding:
      system:
        v: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
        l: tbd-codes-cs
      code:
        v: conclusion-string
  value: String
    v: 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).

urn:…
type: Observation
id:
  v: prequel-variant-chr18-negative
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation prequel-variant-chr18-negative Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S) effective: 2024-06-16 performer: Organization Myriad Women's Health, Inc. value: Absent method: Sequencing with fetal chromosome analysis (NIPS v4.0); GRCh37/hg19 specimen: Specimen: identifier = http://example.org/barcode#31200020477415; status = available; type = Blood venous; receivedTime = 2024-06-09 component code: Chromosome [Identifier] in Blood or Tissue by Molecular genetics method value: Chromosome 18 component code: Human reference sequence assembly version value: GRCh37 component code: Genomic source class [Type] value: Fetal component code: Genomic structural variant copy number value: 2 1 (Details: UCUM code1 = '1') component code: Conclusion Text 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).
status:
  v: final
category:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/observation-category
      l: observation-category
    code:
      v: laboratory
category:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/v2-0074
      l: v2-0074
    code:
      v: GE
code:
  coding: https://loinc.org/rdf/69548-6
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 69548-6
effective: DateTime
  v: 2024-06-16
value: CodeableConcept
  coding: LA9634-2
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: LA9634-2
    display:
      v: Absent
method:
  coding: LA26398-0
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: LA26398-0
    display:
      v: Sequencing
  text:
    v: Sequencing with fetal chromosome analysis (NIPS v4.0); GRCh37/hg19
component:
  code:
    coding: https://loinc.org/rdf/48000-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48000-4
  value: CodeableConcept
    coding: LA21271-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA21271-4
      display:
        v: Chromosome 18
component:
  code:
    coding: https://loinc.org/rdf/62374-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 62374-4
  value: CodeableConcept
    coding: LA14029-5
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA14029-5
      display:
        v: GRCh37
component:
  code:
    coding: https://loinc.org/rdf/48002-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48002-0
  value: CodeableConcept
    coding: LA10429-1
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA10429-1
      display:
        v: Fetal
component:
  code:
    coding: https://loinc.org/rdf/82155-3
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 82155-3
  value: Quantity
    value:
      v: 2
    system:
      v: http://unitsofmeasure.org
      l: unitsofmeasure.org
    code:
      v: 1
component:
  code:
    coding:
      system:
        v: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
        l: tbd-codes-cs
      code:
        v: conclusion-string
  value: String
    v: 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).

urn:…
type: Observation
id:
  v: prequel-variant-chr21-negative
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation prequel-variant-chr21-negative Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S) effective: 2024-06-16 performer: Organization Myriad Women's Health, Inc. value: Absent method: Sequencing with fetal chromosome analysis (NIPS v4.0); GRCh37/hg19 specimen: Specimen: identifier = http://example.org/barcode#31200020477415; status = available; type = Blood venous; receivedTime = 2024-06-09 component code: Chromosome [Identifier] in Blood or Tissue by Molecular genetics method value: Chromosome 21 component code: Human reference sequence assembly version value: GRCh37 component code: Genomic source class [Type] value: Fetal component code: Genomic structural variant copy number value: 2 1 (Details: UCUM code1 = '1') component code: Conclusion Text 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).
status:
  v: final
category:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/observation-category
      l: observation-category
    code:
      v: laboratory
category:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/v2-0074
      l: v2-0074
    code:
      v: GE
code:
  coding: https://loinc.org/rdf/69548-6
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 69548-6
effective: DateTime
  v: 2024-06-16
value: CodeableConcept
  coding: LA9634-2
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: LA9634-2
    display:
      v: Absent
method:
  coding: LA26398-0
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: LA26398-0
    display:
      v: Sequencing
  text:
    v: Sequencing with fetal chromosome analysis (NIPS v4.0); GRCh37/hg19
component:
  code:
    coding: https://loinc.org/rdf/48000-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48000-4
  value: CodeableConcept
    coding: LA21274-8
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA21274-8
      display:
        v: Chromosome 21
component:
  code:
    coding: https://loinc.org/rdf/62374-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 62374-4
  value: CodeableConcept
    coding: LA14029-5
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA14029-5
      display:
        v: GRCh37
component:
  code:
    coding: https://loinc.org/rdf/48002-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48002-0
  value: CodeableConcept
    coding: LA10429-1
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA10429-1
      display:
        v: Fetal
component:
  code:
    coding: https://loinc.org/rdf/82155-3
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 82155-3
  value: Quantity
    value:
      v: 2
    system:
      v: http://unitsofmeasure.org
      l: unitsofmeasure.org
    code:
      v: 1
component:
  code:
    coding:
      system:
        v: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
        l: tbd-codes-cs
      code:
        v: conclusion-string
  value: String
    v: 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).

urn:…
type: Observation
id:
  v: prequel-dx-implication-patau
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication
    l: diagnostic-implication
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation prequel-dx-implication-patau Profile: Diagnostic Implication status: Final category: Laboratory, Genetics code: Diagnostic Implication subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S) effective: 2024-06-16 performer: Organization Myriad Women's Health, Inc. derivedFrom: Observation Genetic variant assessment component code: Genetic variation clinical significance [Imp] value: Pathogenic component code: Associated phenotype value: Trisomy 13 (Patau Syndrome) component code: Condition Inheritance value: Contiguous gene syndrome (chromosomal aneuploidy; typically sporadic) component code: Conclusion Text 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.
status:
  v: final
category:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/observation-category
      l: observation-category
    code:
      v: laboratory
category:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/v2-0074
      l: v2-0074
    code:
      v: GE
code:
  coding:
    system:
      v: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
      l: tbd-codes-cs
    code:
      v: diagnostic-implication
effective: DateTime
  v: 2024-06-16
component:
  code:
    coding: https://loinc.org/rdf/53037-8
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 53037-8
  value: CodeableConcept
    coding: LA6668-3
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA6668-3
      display:
        v: Pathogenic
component:
  code:
    coding: https://loinc.org/rdf/81259-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 81259-4
  value: CodeableConcept
    coding:
      system:
        v: http://purl.obolibrary.org/obo/mondo.owl
        l: mondo.owl
      code:
        v: MONDO:0009141
      display:
        v: trisomy 13
    text:
      v: Trisomy 13 (Patau Syndrome)
component:
  code:
    coding:
      system:
        v: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
        l: tbd-codes-cs
      code:
        v: condition-inheritance
  value: CodeableConcept
    coding:
      system:
        v: http://purl.obolibrary.org/obo/hp.owl
        l: hp.owl
      code:
        v: HP:0001466
    text:
      v: Contiguous gene syndrome (chromosomal aneuploidy; typically sporadic)
component:
  code:
    coding:
      system:
        v: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
        l: tbd-codes-cs
      code:
        v: conclusion-string
  value: String
    v: 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.

urn:…
type: Observation
id:
  v: prequel-dx-implication-edwards-negative
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication
    l: diagnostic-implication
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation prequel-dx-implication-edwards-negative Profile: Diagnostic Implication status: Final category: Laboratory, Genetics code: Diagnostic Implication subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S) effective: 2024-06-16 performer: Organization Myriad Women's Health, Inc. derivedFrom: Observation Genetic variant assessment component code: Genetic variation clinical significance [Imp] value: Likely benign component code: Associated phenotype value: Trisomy 18 (Edwards Syndrome) component code: Conclusion Text 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).
status:
  v: final
category:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/observation-category
      l: observation-category
    code:
      v: laboratory
category:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/v2-0074
      l: v2-0074
    code:
      v: GE
code:
  coding:
    system:
      v: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
      l: tbd-codes-cs
    code:
      v: diagnostic-implication
effective: DateTime
  v: 2024-06-16
component:
  code:
    coding: https://loinc.org/rdf/53037-8
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 53037-8
  value: CodeableConcept
    coding: LA26334-5
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA26334-5
      display:
        v: Likely benign
component:
  code:
    coding: https://loinc.org/rdf/81259-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 81259-4
  value: CodeableConcept
    coding:
      system:
        v: http://purl.obolibrary.org/obo/mondo.owl
        l: mondo.owl
      code:
        v: MONDO:0009869
      display:
        v: trisomy 18
    text:
      v: Trisomy 18 (Edwards Syndrome)
component:
  code:
    coding:
      system:
        v: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
        l: tbd-codes-cs
      code:
        v: conclusion-string
  value: String
    v: 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).

urn:…
type: Observation
id:
  v: prequel-dx-implication-down-negative
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication
    l: diagnostic-implication
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation prequel-dx-implication-down-negative Profile: Diagnostic Implication status: Final category: Laboratory, Genetics code: Diagnostic Implication subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S) effective: 2024-06-16 performer: Organization Myriad Women's Health, Inc. derivedFrom: Observation Genetic variant assessment component code: Genetic variation clinical significance [Imp] value: Likely benign component code: Associated phenotype value: Trisomy 21 (Down Syndrome) component code: Conclusion Text 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).
status:
  v: final
category:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/observation-category
      l: observation-category
    code:
      v: laboratory
category:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/v2-0074
      l: v2-0074
    code:
      v: GE
code:
  coding:
    system:
      v: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
      l: tbd-codes-cs
    code:
      v: diagnostic-implication
effective: DateTime
  v: 2024-06-16
component:
  code:
    coding: https://loinc.org/rdf/53037-8
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 53037-8
  value: CodeableConcept
    coding: LA26334-5
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA26334-5
      display:
        v: Likely benign
component:
  code:
    coding: https://loinc.org/rdf/81259-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 81259-4
  value: CodeableConcept
    coding:
      system:
        v: http://purl.obolibrary.org/obo/mondo.owl
        l: mondo.owl
      code:
        v: MONDO:0008608
      display:
        v: trisomy 21
    text:
      v: Trisomy 21 (Down Syndrome)
component:
  code:
    coding:
      system:
        v: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
        l: tbd-codes-cs
      code:
        v: conclusion-string
  value: String
    v: 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).

urn:…
type: Task
id:
  v: prequel-task-genetic-counseling
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation
    l: followup-recommendation
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Task prequel-task-genetic-counseling Profile: Followup Recommendation status: Requested intent: proposal code: Genetic counseling recommended 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: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S) Reasons - Reference * Observation Diagnostic Implication
status:
  v: requested
intent:
  v: proposal
code:
  coding: LA14020-4
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: LA14020-4
    display:
      v: Genetic counseling recommended
description:
  v: 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.

urn:…
type: DiagnosticReport
id:
  v: prequel-genomic-report
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report
    l: genomic-report
text:
  status:
    v: generated
  div:
    v: Generated Narrative: DiagnosticReport prequel-genomic-report Profile: Genomic Report Genetic analysis report (Genetics) Subject Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S) When For 2024-06-17 Reported 2024-06-17 00:00:00+0000 Performer Organization Myriad Women's Health, Inc. Report Details Code Value Flags Note When For Cell-free DNA.fetal/Cell-free DNA.total in Plasma cell-free DNA by Dosage of chromosome-specific cfDNA 25 % (Details: UCUM code% = '%') Final Fetal fraction is one component of the algorithm used and is combined with other quality metrics to determine the aneuploidy screening result. 2024-06-16 Genetic variant assessment Present Final 2024-06-16 Genetic variant assessment Absent Final 2024-06-16 Genetic variant assessment Absent Final 2024-06-16 Diagnostic Implication Final 2024-06-16 Diagnostic Implication Final 2024-06-16 Diagnostic Implication Final 2024-06-16 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. Coded Conclusions: POSITIVE: Pregnancy at Increased Risk for Trisomy 13 (Patau Syndrome)
extension:
  url:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
    l: recommended-action
  value: Reference
status:
  v: final
category:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/v2-0074
      l: v2-0074
    code:
      v: GE
code:
  coding: https://loinc.org/rdf/51969-4
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 51969-4
effective: DateTime
  v: 2024-06-17
issued:
  v: 2024-06-17T00:00:00Z
conclusion:
  v: 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.
conclusion code:
  concept:
    coding: http://snomed.info/id/10828004
      system:
        v: http://snomed.info/sct
        l: sct
      code:
        v: 10828004
      display:
        v: Positive (qualifier value)
    text:
      v: POSITIVE: Pregnancy at Increased Risk for Trisomy 13 (Patau Syndrome)
presented form:
  content type:
    v: application/pdf
  title:
    v: Myriad Prequel Prenatal Screen with AMPLIFY — Positive Sample Report (PDF)
  creation:
    v: 2024-06-17