bundle-oncology-report-example
type: Bundle
node role: treeRoot
id:
  v: bundle-oncology-report-example
type:
  v: transaction
entry:
  request:
    method:
      v: POST
    url:
      v: Organization
      l: Organization
    if none exist:
      v: identifier=http://example.org/genomics/NamingSystem/organization|CEGAT
entry:
  request:
    method:
      v: POST
    url:
      v: Patient
      l: Patient
    if none exist:
      v: identifier=http://example.org/genomics/NamingSystem/cegat/patID|11111
entry:
  request:
    method:
      v: POST
    url:
      v: Specimen
      l: Specimen
    if none exist:
      v: identifier=http://example.org/genomics/NamingSystem/cegat/tissueID|UNKNOWN
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: 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: DiagnosticReport
      l: DiagnosticReport

urn:…
type: Organization
id:
  v: Inline-Instance-for-oncology-report-example-1
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Organization Inline-Instance-for-oncology-report-example-1 identifier: http://example.org/genomics/NamingSystem/organization/CEGAT name: CEGAT
identifier:
  system:
    v: http://example.org/genomics/NamingSystem/organization
    l: organization
  value:
    v: CEGAT
name:
  v: CEGAT

urn:…
type: Patient
id:
  v: Inline-Instance-for-oncology-report-example-2
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Patient Inline-Instance-for-oncology-report-example-2 Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)
identifier:
  system:
    v: http://example.org/genomics/NamingSystem/cegat/patID
    l: patID
  value:
    v: 11111

urn:…
type: Specimen
id:
  v: Inline-Instance-for-oncology-report-example-3
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Specimen Inline-Instance-for-oncology-report-example-3 identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN type: Tumor subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) Collections - Method BodySite * Biopsy Malignant neoplasm of cardia
identifier:
  system:
    v: http://example.org/genomics/NamingSystem/cegat/tissueID
    l: tissueID
  value:
    v: UNKNOWN
type:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/v2-0487
      l: v2-0487
    code:
      v: TUMOR
    display:
      v: Tumor
collection:
  method:
    text:
      v: Biopsy
  body site:
    coding:
      system:
        v: http://hl7.org/fhir/sid/icd-10-cm
        l: icd-10-cm
      code:
        v: C16.0

urn:…
type: Observation
id:
  v: Inline-Instance-for-oncology-report-example-4
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation Inline-Instance-for-oncology-report-example-4 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: PIK3CA component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: G}">NM_006218.4:c.3140A>G component code: DNA change type value: substitution component code: Amino acid change (pHGVS) value: NP_006209.2:p.His1047Arg component code: Transcript reference sequence [ID] value: NM_006218.4 component code: Genomic ref allele [ID] value: A component code: Sample VAF value: 0.2188 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 64 reads per base pair (Details: UCUM code1 = '1')
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
    display:
      v: Genetic variant assessment
effective: DateTime
  v: 2023-03-05
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
specimen:
  identifier:
    system:
      v: http://example.org/genomics/NamingSystem/cegat/tissueID
      l: tissueID
    value:
      v: UNKNOWN
component:
  code:
    coding: https://loinc.org/rdf/48002-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48002-0
      display:
        v: Genomic source class
  value: CodeableConcept
    coding: LA6684-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA6684-0
      display:
        v: Somatic
component:
  code:
    coding: https://loinc.org/rdf/48018-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48018-6
      display:
        v: Gene studied [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.genenames.org
        l: www.genenames.org
      code:
        v: HGNC:8975
      display:
        v: PIK3CA
component:
  code:
    coding: https://loinc.org/rdf/62374-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 62374-4
      display:
        v: Human reference sequence assembly version
  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/48004-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48004-6
      display:
        v: DNA change (c.HGVS)
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NM_006218.4:c.3140A>G
      display:
        v: NM_006218.4:c.3140A>G
component:
  code:
    coding: https://loinc.org/rdf/48019-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48019-4
      display:
        v: DNA change type
  value: CodeableConcept
    coding:
      system:
        v: http://www.sequenceontology.org
        l: www.sequenceontology.org
      code:
        v: SO:1000002
      display:
        v: substitution
component:
  code:
    coding: https://loinc.org/rdf/48005-3
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48005-3
      display:
        v: Amino acid change (pHGVS)
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NP_006209.2:p.His1047Arg
      display:
        v: NP_006209.2:p.His1047Arg
component:
  code:
    coding: https://loinc.org/rdf/51958-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51958-7
      display:
        v: Transcript reference sequence [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.ncbi.nlm.nih.gov/refseq
        l: refseq
      code:
        v: NM_006218.3
      display:
        v: NM_006218.4
component:
  code:
    coding: https://loinc.org/rdf/69547-8
      system:
        v: http://loinc.org
        l: loinc.org
  value: String

urn:…
type: Observation
id:
  v: Inline-Instance-for-oncology-report-example-5
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation Inline-Instance-for-oncology-report-example-5 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: NRAS component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: T}">NM_002524.4:c.34G>T component code: DNA change type value: substitution component code: Transcript reference sequence [ID] value: NM_002524.4 component code: Genomic ref allele [ID] value: C component code: Sample VAF value: 0.1793 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 145 reads per base pair (Details: UCUM code1 = '1')
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
    display:
      v: Genetic variant assessment
effective: DateTime
  v: 2023-03-05
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
specimen:
  identifier:
    system:
      v: http://example.org/genomics/NamingSystem/cegat/tissueID
      l: tissueID
    value:
      v: UNKNOWN
component:
  code:
    coding: https://loinc.org/rdf/48002-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48002-0
      display:
        v: Genomic source class
  value: CodeableConcept
    coding: LA6684-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA6684-0
      display:
        v: Somatic
component:
  code:
    coding: https://loinc.org/rdf/48018-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48018-6
      display:
        v: Gene studied [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.genenames.org
        l: www.genenames.org
      code:
        v: HGNC:7989
      display:
        v: NRAS
component:
  code:
    coding: https://loinc.org/rdf/62374-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 62374-4
      display:
        v: Human reference sequence assembly version
  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/48004-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48004-6
      display:
        v: DNA change (c.HGVS)
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NM_002524.4:c.34G>T
      display:
        v: NM_002524.4:c.34G>T
component:
  code:
    coding: https://loinc.org/rdf/48019-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48019-4
      display:
        v: DNA change type
  value: CodeableConcept
    coding:
      system:
        v: http://www.sequenceontology.org
        l: www.sequenceontology.org
      code:
        v: SO:1000002
      display:
        v: substitution
component:
  code:
    coding: https://loinc.org/rdf/51958-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51958-7
      display:
        v: Transcript reference sequence [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.ncbi.nlm.nih.gov/refseq
        l: refseq
      code:
        v: NM_002524.4
      display:
        v: NM_002524.4
component:
  code:
    coding: https://loinc.org/rdf/69547-8
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 69547-8
      display:
        v: Genomic ref allele [ID]
  value: String
    v: C
component:
  code:
    coding: https://loinc.org/rdf/81258-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 81258-6
      display:
        v: Sample VAF
  value: Quantity
    value:
      v: 0.1793

urn:…
type: Observation
id:
  v: Inline-Instance-for-oncology-report-example-6
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation Inline-Instance-for-oncology-report-example-6 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: FBXW7 component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: A}">NM_001349798.2:c.1394G>A component code: DNA change type value: substitution component code: Amino acid change (pHGVS) value: NP_001336727.1:p.Arg465His component code: Transcript reference sequence [ID] value: NM_001349798.2 component code: Genomic ref allele [ID] value: C component code: Sample VAF value: 0.1053 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 57 reads per base pair (Details: UCUM code1 = '1')
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
    display:
      v: Genetic variant assessment
effective: DateTime
  v: 2023-03-05
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
specimen:
  identifier:
    system:
      v: http://example.org/genomics/NamingSystem/cegat/tissueID
      l: tissueID
    value:
      v: UNKNOWN
component:
  code:
    coding: https://loinc.org/rdf/48002-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48002-0
      display:
        v: Genomic source class
  value: CodeableConcept
    coding: LA6684-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA6684-0
      display:
        v: Somatic
component:
  code:
    coding: https://loinc.org/rdf/48018-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48018-6
      display:
        v: Gene studied [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.genenames.org
        l: www.genenames.org
      code:
        v: HGNC:16712
      display:
        v: FBXW7
component:
  code:
    coding: https://loinc.org/rdf/62374-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 62374-4
      display:
        v: Human reference sequence assembly version
  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/48004-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48004-6
      display:
        v: DNA change (c.HGVS)
  value: CodeableConcept
    coding:
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        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NM_001349798.2:c.1394G>A
      display:
        v: NM_001349798.2:c.1394G>A
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    coding: https://loinc.org/rdf/48019-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48019-4
      display:
        v: DNA change type
  value: CodeableConcept
    coding:
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        v: http://www.sequenceontology.org
        l: www.sequenceontology.org
      code:
        v: SO:1000002
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component:
  code:
    coding: https://loinc.org/rdf/48005-3
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48005-3
      display:
        v: Amino acid change (pHGVS)
  value: CodeableConcept
    coding:
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        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NP_001336727.1:p.Arg465His
      display:
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component:
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    coding: https://loinc.org/rdf/51958-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51958-7
      display:
        v: Transcript reference sequence [ID]
  value: CodeableConcept
    coding:
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        v: http://www.ncbi.nlm.nih.gov/refseq
        l: refseq
      code:
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      display:
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component:
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    coding: https://loinc.org/rdf/69547-8
      system:
        v: http://loinc.org
        l: loinc.org
  value: String

urn:…
type: Observation
id:
  v: Inline-Instance-for-oncology-report-example-7
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation Inline-Instance-for-oncology-report-example-7 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: KMT2D component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: NM_003482.3:c.7900_7901delCA component code: DNA change type value: deletion component code: Transcript reference sequence [ID] value: NM_003482.3 component code: Genomic ref allele [ID] value: CTG component code: Sample VAF value: 0.188 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 117 reads per base pair (Details: UCUM code1 = '1')
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
    display:
      v: Genetic variant assessment
effective: DateTime
  v: 2023-03-05
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
specimen:
  identifier:
    system:
      v: http://example.org/genomics/NamingSystem/cegat/tissueID
      l: tissueID
    value:
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component:
  code:
    coding: https://loinc.org/rdf/48002-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48002-0
      display:
        v: Genomic source class
  value: CodeableConcept
    coding: LA6684-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA6684-0
      display:
        v: Somatic
component:
  code:
    coding: https://loinc.org/rdf/48018-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48018-6
      display:
        v: Gene studied [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.genenames.org
        l: www.genenames.org
      code:
        v: HGNC:7133
      display:
        v: KMT2D
component:
  code:
    coding: https://loinc.org/rdf/62374-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 62374-4
      display:
        v: Human reference sequence assembly version
  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/48004-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48004-6
      display:
        v: DNA change (c.HGVS)
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NM_003482.3:c.7900_7901delCA
      display:
        v: NM_003482.3:c.7900_7901delCA
component:
  code:
    coding: https://loinc.org/rdf/48019-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48019-4
      display:
        v: DNA change type
  value: CodeableConcept
    coding:
      system:
        v: http://www.sequenceontology.org
        l: www.sequenceontology.org
      code:
        v: SO:0000159
      display:
        v: deletion
component:
  code:
    coding: https://loinc.org/rdf/51958-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51958-7
      display:
        v: Transcript reference sequence [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.ncbi.nlm.nih.gov/refseq
        l: refseq
      code:
        v: NM_003482.3
      display:
        v: NM_003482.3
component:
  code:
    coding: https://loinc.org/rdf/69547-8
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 69547-8
      display:
        v: Genomic ref allele [ID]
  value: String
    v: CTG
component:
  code:
    coding: https://loinc.org/rdf/81258-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 81258-6
      display:
        v: Sample VAF
  value: Quantity
    value:
      v: 0.188

urn:…
type: Observation
id:
  v: Inline-Instance-for-oncology-report-example-8
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation Inline-Instance-for-oncology-report-example-8 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: PIK3CA component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: T}">NM_006218.3:c.333G>T component code: DNA change type value: substitution component code: Transcript reference sequence [ID] value: NM_006218.3 component code: Genomic ref allele [ID] value: G component code: Sample VAF value: 0.1471 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 68 reads per base pair (Details: UCUM code1 = '1')
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
    display:
      v: Genetic variant assessment
effective: DateTime
  v: 2023-03-05
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
specimen:
  identifier:
    system:
      v: http://example.org/genomics/NamingSystem/cegat/tissueID
      l: tissueID
    value:
      v: UNKNOWN
component:
  code:
    coding: https://loinc.org/rdf/48002-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48002-0
      display:
        v: Genomic source class
  value: CodeableConcept
    coding: LA6684-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA6684-0
      display:
        v: Somatic
component:
  code:
    coding: https://loinc.org/rdf/48018-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48018-6
      display:
        v: Gene studied [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.genenames.org
        l: www.genenames.org
      code:
        v: HGNC:8975
      display:
        v: PIK3CA
component:
  code:
    coding: https://loinc.org/rdf/62374-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 62374-4
      display:
        v: Human reference sequence assembly version
  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/48004-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48004-6
      display:
        v: DNA change (c.HGVS)
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NM_006218.3:c.333G>T
      display:
        v: NM_006218.3:c.333G>T
component:
  code:
    coding: https://loinc.org/rdf/48019-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48019-4
      display:
        v: DNA change type
  value: CodeableConcept
    coding:
      system:
        v: http://www.sequenceontology.org
        l: www.sequenceontology.org
      code:
        v: SO:1000002
      display:
        v: substitution
component:
  code:
    coding: https://loinc.org/rdf/51958-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51958-7
      display:
        v: Transcript reference sequence [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.ncbi.nlm.nih.gov/refseq
        l: refseq
      code:
        v: NM_006218.3
      display:
        v: NM_006218.3
component:
  code:
    coding: https://loinc.org/rdf/69547-8
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 69547-8
      display:
        v: Genomic ref allele [ID]
  value: String
    v: G
component:
  code:
    coding: https://loinc.org/rdf/81258-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 81258-6
      display:
        v: Sample VAF
  value: Quantity
    value:
      v: 0.1471

urn:…
type: Observation
id:
  v: Inline-Instance-for-oncology-report-example-9
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation Inline-Instance-for-oncology-report-example-9 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: IRS2 component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: T}">NM_003749.2:c.3960C>T component code: DNA change type value: substitution component code: Transcript reference sequence [ID] value: NM_003749.2 component code: Genomic ref allele [ID] value: G component code: Sample VAF value: 0.1343 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 134 reads per base pair (Details: UCUM code1 = '1')
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
    display:
      v: Genetic variant assessment
effective: DateTime
  v: 2023-03-05
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
specimen:
  identifier:
    system:
      v: http://example.org/genomics/NamingSystem/cegat/tissueID
      l: tissueID
    value:
      v: UNKNOWN
component:
  code:
    coding: https://loinc.org/rdf/48002-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48002-0
      display:
        v: Genomic source class
  value: CodeableConcept
    coding: LA6684-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA6684-0
      display:
        v: Somatic
component:
  code:
    coding: https://loinc.org/rdf/48018-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48018-6
      display:
        v: Gene studied [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.genenames.org
        l: www.genenames.org
      code:
        v: HGNC:6126
      display:
        v: IRS2
component:
  code:
    coding: https://loinc.org/rdf/62374-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 62374-4
      display:
        v: Human reference sequence assembly version
  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/48004-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48004-6
      display:
        v: DNA change (c.HGVS)
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NM_003749.2:c.3960C>T
      display:
        v: NM_003749.2:c.3960C>T
component:
  code:
    coding: https://loinc.org/rdf/48019-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48019-4
      display:
        v: DNA change type
  value: CodeableConcept
    coding:
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        v: http://www.sequenceontology.org
        l: www.sequenceontology.org
      code:
        v: SO:1000002
      display:
        v: substitution
component:
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    coding: https://loinc.org/rdf/51958-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51958-7
      display:
        v: Transcript reference sequence [ID]
  value: CodeableConcept
    coding:
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        v: http://www.ncbi.nlm.nih.gov/refseq
        l: refseq
      code:
        v: NM_003749.2
      display:
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component:
  code:
    coding: https://loinc.org/rdf/69547-8
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 69547-8
      display:
        v: Genomic ref allele [ID]
  value: String
    v: G
component:
  code:
    coding: https://loinc.org/rdf/81258-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 81258-6
      display:
        v: Sample VAF
  value: Quantity
    value:
      v: 0.1343

urn:…
type: Observation
id:
  v: Inline-Instance-for-oncology-report-example-10
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation Inline-Instance-for-oncology-report-example-10 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: CDKN2A component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: NM_000077.4:c.9_32del component code: DNA change type value: deletion component code: Amino acid change (pHGVS) value: NP_000068.1:p.Ala4_Pro11del component code: Transcript reference sequence [ID] value: NM_000077.4 component code: Genomic ref allele [ID] value: AGGCTCCATGCTGCTCCCCGCCGCC component code: Sample VAF value: 0.0536 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 112 reads per base pair (Details: UCUM code1 = '1')
status:
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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
    display:
      v: Genetic variant assessment
effective: DateTime
  v: 2023-03-05
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
specimen:
  identifier:
    system:
      v: http://example.org/genomics/NamingSystem/cegat/tissueID
      l: tissueID
    value:
      v: UNKNOWN
component:
  code:
    coding: https://loinc.org/rdf/48002-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48002-0
      display:
        v: Genomic source class
  value: CodeableConcept
    coding: LA6684-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA6684-0
      display:
        v: Somatic
component:
  code:
    coding: https://loinc.org/rdf/48018-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48018-6
      display:
        v: Gene studied [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.genenames.org
        l: www.genenames.org
      code:
        v: HGNC:1787
      display:
        v: CDKN2A
component:
  code:
    coding: https://loinc.org/rdf/62374-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 62374-4
      display:
        v: Human reference sequence assembly version
  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/48004-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48004-6
      display:
        v: DNA change (c.HGVS)
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NM_000077.4:c.9_32del
component:
  code:
    coding: https://loinc.org/rdf/48019-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48019-4
      display:
        v: DNA change type
  value: CodeableConcept
    coding:
      system:
        v: http://www.sequenceontology.org
        l: www.sequenceontology.org
      code:
        v: SO:0000159
      display:
        v: deletion
component:
  code:
    coding: https://loinc.org/rdf/48005-3
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48005-3
      display:
        v: Amino acid change (pHGVS)
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NP_000068.1:p.Ala4_Pro11del
component:
  code:
    coding: https://loinc.org/rdf/51958-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51958-7
      display:
        v: Transcript reference sequence [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.ncbi.nlm.nih.gov/refseq
        l: refseq
      code:
        v: NM_000077.4
      display:
        v: NM_000077.4
component:
  code:
    coding: https://loinc.org/rdf/69547-8
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 69547-8
      display:
        v: Genomic ref allele [ID]
  value: String

urn:…
type: Observation
id:
  v: Inline-Instance-for-oncology-report-example-11
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation Inline-Instance-for-oncology-report-example-11 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: RECQL4 component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: T}">NM_004260.4:c.2086C>T component code: DNA change type value: substitution component code: Amino acid change (pHGVS) value: NP_004251.4:p.Arg696Cys component code: Transcript reference sequence [ID] value: NM_004260.4 component code: Genomic ref allele [ID] value: G component code: Sample VAF value: 0.2568 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 148 reads per base pair (Details: UCUM code1 = '1')
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
    display:
      v: Genetic variant assessment
effective: DateTime
  v: 2023-03-05
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
specimen:
  identifier:
    system:
      v: http://example.org/genomics/NamingSystem/cegat/tissueID
      l: tissueID
    value:
      v: UNKNOWN
component:
  code:
    coding: https://loinc.org/rdf/48002-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48002-0
      display:
        v: Genomic source class
  value: CodeableConcept
    coding: LA6684-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA6684-0
      display:
        v: Somatic
component:
  code:
    coding: https://loinc.org/rdf/48018-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48018-6
      display:
        v: Gene studied [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.genenames.org
        l: www.genenames.org
      code:
        v: HGNC:9949
      display:
        v: RECQL4
component:
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      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 62374-4
      display:
        v: Human reference sequence assembly version
  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/48004-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48004-6
      display:
        v: DNA change (c.HGVS)
  value: CodeableConcept
    coding:
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        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NM_004260.4:c.2086C>T
component:
  code:
    coding: https://loinc.org/rdf/48019-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48019-4
      display:
        v: DNA change type
  value: CodeableConcept
    coding:
      system:
        v: http://www.sequenceontology.org
        l: www.sequenceontology.org
      code:
        v: SO:1000002
      display:
        v: substitution
component:
  code:
    coding: https://loinc.org/rdf/48005-3
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48005-3
      display:
        v: Amino acid change (pHGVS)
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NP_004251.4:p.Arg696Cys
component:
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    coding: https://loinc.org/rdf/51958-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51958-7
      display:
        v: Transcript reference sequence [ID]
  value: CodeableConcept
    coding:
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        v: http://www.ncbi.nlm.nih.gov/refseq
        l: refseq
      code:
        v: NM_004260.4
      display:
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component:
  code:
    coding: https://loinc.org/rdf/69547-8
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 69547-8
      display:
        v: Genomic ref allele [ID]
  value: String

urn:…
type: Observation
id:
  v: Inline-Instance-for-oncology-report-example-12
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation Inline-Instance-for-oncology-report-example-12 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: RYR1 component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: A}">NM_000540.3:c.4964G>A component code: DNA change type value: substitution component code: Amino acid change (pHGVS) value: NP_000531.2:p.Arg1655Leu component code: Transcript reference sequence [ID] value: NM_000540.3 component code: Genomic ref allele [ID] value: G component code: Sample VAF value: 0.2151 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 93 reads per base pair (Details: UCUM code1 = '1')
status:
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category:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/observation-category
      l: observation-category
    code:
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category:
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      l: v2-0074
    code:
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code:
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    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 69548-6
    display:
      v: Genetic variant assessment
effective: DateTime
  v: 2023-03-05
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
specimen:
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      v: http://example.org/genomics/NamingSystem/cegat/tissueID
      l: tissueID
    value:
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component:
  code:
    coding: https://loinc.org/rdf/48002-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48002-0
      display:
        v: Genomic source class
  value: CodeableConcept
    coding: LA6684-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA6684-0
      display:
        v: Somatic
component:
  code:
    coding: https://loinc.org/rdf/48018-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48018-6
      display:
        v: Gene studied [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.genenames.org
        l: www.genenames.org
      code:
        v: HGNC:10483
      display:
        v: RYR1
component:
  code:
    coding: https://loinc.org/rdf/62374-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 62374-4
      display:
        v: Human reference sequence assembly version
  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/48004-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48004-6
      display:
        v: DNA change (c.HGVS)
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NM_000540.3:c.4964G>A
component:
  code:
    coding: https://loinc.org/rdf/48019-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48019-4
      display:
        v: DNA change type
  value: CodeableConcept
    coding:
      system:
        v: http://www.sequenceontology.org
        l: www.sequenceontology.org
      code:
        v: SO:1000002
      display:
        v: substitution
component:
  code:
    coding: https://loinc.org/rdf/48005-3
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48005-3
      display:
        v: Amino acid change (pHGVS)
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NP_000531.2:p.Arg1655Leu
component:
  code:
    coding: https://loinc.org/rdf/51958-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51958-7
      display:
        v: Transcript reference sequence [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.ncbi.nlm.nih.gov/refseq
        l: refseq
      code:
        v: NM_000540.2
      display:
        v: NM_000540.3
component:
  code:
    coding: https://loinc.org/rdf/69547-8
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 69547-8
      display:
        v: Genomic ref allele [ID]
  value: String

urn:…
type: Observation
id:
  v: Inline-Instance-for-oncology-report-example-13
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation Inline-Instance-for-oncology-report-example-13 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: SACS component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: A}">NM_014363.5:c.12118G>A component code: DNA change type value: substitution component code: Transcript reference sequence [ID] value: NM_014363.5 component code: Genomic ref allele [ID] value: C component code: Sample VAF value: 0.3333 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 60 reads per base pair (Details: UCUM code1 = '1')
status:
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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
    display:
      v: Genetic variant assessment
effective: DateTime
  v: 2023-03-05
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
specimen:
  identifier:
    system:
      v: http://example.org/genomics/NamingSystem/cegat/tissueID
      l: tissueID
    value:
      v: UNKNOWN
component:
  code:
    coding: https://loinc.org/rdf/48002-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48002-0
      display:
        v: Genomic source class
  value: CodeableConcept
    coding: LA6684-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA6684-0
      display:
        v: Somatic
component:
  code:
    coding: https://loinc.org/rdf/48018-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48018-6
      display:
        v: Gene studied [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.genenames.org
        l: www.genenames.org
      code:
        v: HGNC:10519
      display:
        v: SACS
component:
  code:
    coding: https://loinc.org/rdf/62374-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 62374-4
      display:
        v: Human reference sequence assembly version
  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/48004-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48004-6
      display:
        v: DNA change (c.HGVS)
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
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component:
  code:
    coding: https://loinc.org/rdf/48019-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48019-4
      display:
        v: DNA change type
  value: CodeableConcept
    coding:
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        v: http://www.sequenceontology.org
        l: www.sequenceontology.org
      code:
        v: SO:1000002
      display:
        v: substitution
component:
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    coding: https://loinc.org/rdf/51958-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51958-7
      display:
        v: Transcript reference sequence [ID]
  value: CodeableConcept
    coding:
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        v: http://www.ncbi.nlm.nih.gov/refseq
        l: refseq
      code:
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      display:
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component:
  code:
    coding: https://loinc.org/rdf/69547-8
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 69547-8
      display:
        v: Genomic ref allele [ID]
  value: String
    v: C
component:
  code:
    coding: https://loinc.org/rdf/81258-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
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      display:
        v: Sample VAF
  value: Quantity
    value:
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    unit:
      v: relative frequency of a particular allele in the specimen

urn:…
type: Observation
id:
  v: Inline-Instance-for-oncology-report-example-14
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
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  div:
    v: Generated Narrative: Observation Inline-Instance-for-oncology-report-example-14 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: SLIT2 component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: A}">NM_004787.3:c.1290C>A component code: DNA change type value: substitution component code: Transcript reference sequence [ID] value: NM_004787.3 component code: Genomic ref allele [ID] value: C component code: Sample VAF value: 0.2642 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 53 reads per base pair (Details: UCUM code1 = '1')
status:
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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
    display:
      v: Genetic variant assessment
effective: DateTime
  v: 2023-03-05
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
specimen:
  identifier:
    system:
      v: http://example.org/genomics/NamingSystem/cegat/tissueID
      l: tissueID
    value:
      v: UNKNOWN
component:
  code:
    coding: https://loinc.org/rdf/48002-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48002-0
      display:
        v: Genomic source class
  value: CodeableConcept
    coding: LA6684-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA6684-0
      display:
        v: Somatic
component:
  code:
    coding: https://loinc.org/rdf/48018-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48018-6
      display:
        v: Gene studied [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.genenames.org
        l: www.genenames.org
      code:
        v: HGNC:11086
      display:
        v: SLIT2
component:
  code:
    coding: https://loinc.org/rdf/62374-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 62374-4
      display:
        v: Human reference sequence assembly version
  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/48004-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48004-6
      display:
        v: DNA change (c.HGVS)
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NM_004787.3:c.1290C>A
component:
  code:
    coding: https://loinc.org/rdf/48019-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48019-4
      display:
        v: DNA change type
  value: CodeableConcept
    coding:
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        v: http://www.sequenceontology.org
        l: www.sequenceontology.org
      code:
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      display:
        v: substitution
component:
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    coding: https://loinc.org/rdf/51958-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51958-7
      display:
        v: Transcript reference sequence [ID]
  value: CodeableConcept
    coding:
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        v: http://www.ncbi.nlm.nih.gov/refseq
        l: refseq
      code:
        v: NM_004787.3
      display:
        v: NM_004787.3
component:
  code:
    coding: https://loinc.org/rdf/69547-8
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 69547-8
      display:
        v: Genomic ref allele [ID]
  value: String
    v: C
component:
  code:
    coding: https://loinc.org/rdf/81258-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 81258-6
      display:
        v: Sample VAF
  value: Quantity
    value:
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    unit:
      v: relative frequency of a particular allele in the specimen

urn:…
type: Observation
id:
  v: Inline-Instance-for-oncology-report-example-15
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation Inline-Instance-for-oncology-report-example-15 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: SMARCA4 component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: T}">NM_003072.5:c.2372C>T component code: DNA change type value: substitution component code: Amino acid change (pHGVS) value: NP_003063.2:p.Ala791Val component code: Transcript reference sequence [ID] value: NM_003072.5 component code: Genomic ref allele [ID] value: C component code: Sample VAF value: 0.1938 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 160 reads per base pair (Details: UCUM code1 = '1')
status:
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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
    display:
      v: Genetic variant assessment
effective: DateTime
  v: 2023-03-05
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
specimen:
  identifier:
    system:
      v: http://example.org/genomics/NamingSystem/cegat/tissueID
      l: tissueID
    value:
      v: UNKNOWN
component:
  code:
    coding: https://loinc.org/rdf/48002-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48002-0
      display:
        v: Genomic source class
  value: CodeableConcept
    coding: LA6684-0
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA6684-0
      display:
        v: Somatic
component:
  code:
    coding: https://loinc.org/rdf/48018-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48018-6
      display:
        v: Gene studied [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.genenames.org
        l: www.genenames.org
      code:
        v: HGNC:11100
      display:
        v: SMARCA4
component:
  code:
    coding: https://loinc.org/rdf/62374-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 62374-4
      display:
        v: Human reference sequence assembly version
  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/48004-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48004-6
      display:
        v: DNA change (c.HGVS)
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NM_003072.5:c.2372C>T
component:
  code:
    coding: https://loinc.org/rdf/48019-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48019-4
      display:
        v: DNA change type
  value: CodeableConcept
    coding:
      system:
        v: http://www.sequenceontology.org
        l: www.sequenceontology.org
      code:
        v: SO:1000002
      display:
        v: substitution
component:
  code:
    coding: https://loinc.org/rdf/48005-3
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48005-3
      display:
        v: Amino acid change (pHGVS)
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NP_003063.2:p.Ala791Val
component:
  code:
    coding: https://loinc.org/rdf/51958-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51958-7
      display:
        v: Transcript reference sequence [ID]
  value: CodeableConcept
    coding:
      system:
        v: http://www.ncbi.nlm.nih.gov/refseq
        l: refseq
      code:
        v: NM_003072.5
      display:
        v: NM_003072.5
component:
  code:
    coding: https://loinc.org/rdf/69547-8
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 69547-8
      display:
        v: Genomic ref allele [ID]
  value: String

urn:…
type: DiagnosticReport
id:
  v: Inline-Instance-for-oncology-report-example-16
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 Inline-Instance-for-oncology-report-example-16 Profile: Genomic Report Genetic analysis report (Genetics) Subject Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) Reported 2019-09-15 11:35:05-0400 Performer Organization CEGAT Identifier http://example.org/genomics/NamingSystem/cegat/reportID/42867 Report Details Code Value Flags When For Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05
identifier:
  system:
    v: http://example.org/genomics/NamingSystem/cegat/reportID
    l: reportID
  value:
    v: 42867
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
    display:
      v: Genetic analysis report
issued:
  v: 2019-09-15T11:35:05.722-04:00

v: 69547-8

v: Genomic ref allele [ID]

String
v: A

code:
  coding: https://loinc.org/rdf/81258-6
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 81258-6
    display:
      v: Sample VAF
value: Quantity
  value:
    v: 0.2188
  unit:
    v: relative frequency of a particular allele in the specimen
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

code:
  coding: https://loinc.org/rdf/82121-5
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 82121-5
    display:
      v: Allelic read depth
value: Quantity
  value:
    v: 64
  unit:
    v: reads per base pair
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

v: relative frequency of a particular allele in the specimen

v: 1

code:
  coding: https://loinc.org/rdf/82121-5
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 82121-5
    display:
      v: Allelic read depth
value: Quantity
  value:
    v: 145
  unit:
    v: reads per base pair
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

v: 69547-8

v: Genomic ref allele [ID]

String
v: C

code:
  coding: https://loinc.org/rdf/81258-6
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 81258-6
    display:
      v: Sample VAF
value: Quantity
  value:
    v: 0.1053
  unit:
    v: relative frequency of a particular allele in the specimen
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

code:
  coding: https://loinc.org/rdf/82121-5
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 82121-5
    display:
      v: Allelic read depth
value: Quantity
  value:
    v: 57
  unit:
    v: reads per base pair
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

v: relative frequency of a particular allele in the specimen

v: 1

code:
  coding: https://loinc.org/rdf/82121-5
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 82121-5
    display:
      v: Allelic read depth
value: Quantity
  value:
    v: 117
  unit:
    v: reads per base pair
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

v: relative frequency of a particular allele in the specimen

v: 1

code:
  coding: https://loinc.org/rdf/82121-5
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 82121-5
    display:
      v: Allelic read depth
value: Quantity
  value:
    v: 68
  unit:
    v: reads per base pair
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

v: relative frequency of a particular allele in the specimen

v: 1

code:
  coding: https://loinc.org/rdf/82121-5
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 82121-5
    display:
      v: Allelic read depth
value: Quantity
  value:
    v: 134
  unit:
    v: reads per base pair
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

String
v: AGGCTCCATGCTGCTCCCCGCCGCC

code:
  coding: https://loinc.org/rdf/81258-6
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 81258-6
    display:
      v: Sample VAF
value: Quantity
  value:
    v: 0.0536
  unit:
    v: relative frequency of a particular allele in the specimen
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

code:
  coding: https://loinc.org/rdf/82121-5
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 82121-5
    display:
      v: Allelic read depth
value: Quantity
  value:
    v: 112
  unit:
    v: reads per base pair
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

String
v: G

code:
  coding: https://loinc.org/rdf/81258-6
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 81258-6
    display:
      v: Sample VAF
value: Quantity
  value:
    v: 0.2568
  unit:
    v: relative frequency of a particular allele in the specimen
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

code:
  coding: https://loinc.org/rdf/82121-5
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 82121-5
    display:
      v: Allelic read depth
value: Quantity
  value:
    v: 148
  unit:
    v: reads per base pair
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

String
v: G

code:
  coding: https://loinc.org/rdf/81258-6
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 81258-6
    display:
      v: Sample VAF
value: Quantity
  value:
    v: 0.2151
  unit:
    v: relative frequency of a particular allele in the specimen
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

code:
  coding: https://loinc.org/rdf/82121-5
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 82121-5
    display:
      v: Allelic read depth
value: Quantity
  value:
    v: 93
  unit:
    v: reads per base pair
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

v: 1

code:
  coding: https://loinc.org/rdf/82121-5
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 82121-5
    display:
      v: Allelic read depth
value: Quantity
  value:
    v: 60
  unit:
    v: reads per base pair
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

v: 1

code:
  coding: https://loinc.org/rdf/82121-5
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 82121-5
    display:
      v: Allelic read depth
value: Quantity
  value:
    v: 53
  unit:
    v: reads per base pair
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

String
v: C

code:
  coding: https://loinc.org/rdf/81258-6
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 81258-6
    display:
      v: Sample VAF
value: Quantity
  value:
    v: 0.1938
  unit:
    v: relative frequency of a particular allele in the specimen
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

code:
  coding: https://loinc.org/rdf/82121-5
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 82121-5
    display:
      v: Allelic read depth
value: Quantity
  value:
    v: 160
  unit:
    v: reads per base pair
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1