bundle-cgexample
type: Bundle
node role: treeRoot
id:
  v: bundle-cgexample
type:
  v: collection
entry:
  full url:
    v: http://example.org/fhir/DiagnosticReport/report
    l: report
  resource: report
entry:
  full url:
    v: http://example.org/fhir/Patient/ExamplePatient
    l: ExamplePatient
  resource: ExamplePatient
entry:
  full url:
    v: http://example.org/fhir/Specimen/ExampleSpecimen
    l: ExampleSpecimen
  resource: ExampleSpecimen
entry:
  full url:
    v: http://example.org/fhir/Organization/ExampleLab
    l: ExampleLab
  resource: ExampleLab
entry:
  full url:
    v: http://example.org/fhir/ServiceRequest/ExampleServiceRequest
    l: ExampleServiceRequest
  resource: ExampleServiceRequest
entry:
  full url:
    v: http://example.org/fhir/Observation/discrete-variant
    l: discrete-variant
  resource: discrete-variant
entry:
  full url:
    v: http://example.org/fhir/Observation/dis-path
    l: dis-path
  resource: dis-path
entry:
  full url:
    v: http://example.org/fhir/Observation/complex-variant
    l: complex-variant
  resource: complex-variant
entry:
  full url:
    v: http://example.org/fhir/Observation/complex-dis-path
    l: complex-dis-path
  resource: complex-dis-path
entry:
  full url:
    v: http://example.org/fhir/Observation/complex-component-D
    l: complex-component-D
  resource: complex-component-D
entry:
  full url:
    v: http://example.org/fhir/Observation/complex-component-E
    l: complex-component-E
  resource: complex-component-E
entry:
  full url:
    v: http://example.org/fhir/Observation/haplotype
    l: haplotype
  resource: haplotype
entry:
  full url:
    v: http://example.org/fhir/Observation/genotype
    l: genotype
  resource: genotype
entry:
  full url:
    v: http://example.org/fhir/Observation/metab
    l: metab
  resource: metab
entry:
  full url:
    v: http://example.org/fhir/Observation/efficacy
    l: efficacy
  resource: efficacy
entry:
  full url:
    v: http://example.org/fhir/Observation/highrisk
    l: highrisk
  resource: highrisk
entry:
  full url:
    v: http://example.org/fhir/Task/usage
    l: usage
  resource: usage

report
type: DiagnosticReport
id:
  v: 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 report Profile: Genomic Report Genetic analysis report (Genetics) Subject Anonymous Patient (no stated gender), DoB Unknown When For 2016 Reported 2016-09-06 00:00:00-0500 Performer Organization Some lab Report Details Code Value Flags Genetic variant assessment Present Final Diagnostic Implication Final Genetic variant assessment Present Final Diagnostic Implication Final Haplotype name *2 Final Genotype display name CYP2C9 *2/*5 Final Therapeutic Implication Final Therapeutic Implication Final Coded Conclusions: Positive Positive
based on:
  l: ExampleServiceRequest
  reference:
    v: ServiceRequest/ExampleServiceRequest
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
subject:
  l: ExamplePatient
  reference:
    v: Patient/ExamplePatient
effective: DateTime
  v: 2016
issued:
  v: 2016-09-06T00:00:00-05:00
performer:
  l: ExampleLab
  reference:
    v: Organization/ExampleLab
result:
  l: discrete-variant
  reference:
    v: Observation/discrete-variant
result:
  l: dis-path
  reference:
    v: Observation/dis-path
result:
  l: complex-variant
  reference:
    v: Observation/complex-variant
result:
  l: complex-dis-path
  reference:
    v: Observation/complex-dis-path
result:
  l: haplotype
  reference:
    v: Observation/haplotype
result:
  l: genotype
  reference:
    v: Observation/genotype
result:
  l: metab
  reference:
    v: Observation/metab
result:
  l: efficacy
  reference:
    v: Observation/efficacy
conclusion code:
  coding: LA6576-8
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: LA6576-8
    display:
      v: Positive
conclusion code:
  coding: http://snomed.info/id/10828004
    system:
      v: http://snomed.info/sct
      l: sct
    code:
      v: 10828004
    display:
      v: Positive
presented form:
  content type:
    v: text/plain

ExamplePatient
type: Patient
id:
  v: ExamplePatient
text:
  status:
    v: additional
  div:
    v: This would contain patient identifiers, demographics, etc.

ExampleSpecimen
type: Specimen
id:
  v: ExampleSpecimen
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Specimen ExampleSpecimen subject: Anonymous Patient (no stated gender), DoB Unknown
subject:
  l: ExamplePatient
  reference:
    v: Patient/ExamplePatient

ExampleLab
type: Organization
id:
  v: ExampleLab
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Organization ExampleLab name: Some lab
name:
  v: Some lab

ExampleServiceRequest
type: ServiceRequest
id:
  v: ExampleServiceRequest
text:
  status:
    v: generated
  div:
    v: Generated Narrative: ServiceRequest ExampleServiceRequest status: Active intent: Original Order code: Genetic analysis report subject: Anonymous Patient (no stated gender), DoB Unknown reasonCode: Worried about family planning
status:
  v: active
intent:
  v: original-order
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
subject:
  l: ExamplePatient
  reference:
    v: Patient/ExamplePatient
reason code:
  text:
    v: Worried about family planning

discrete-variant
type: Observation
id:
  v: discrete-variant
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation discrete-variant Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown effective: 2016 issued: 2016-09-06 00:00:00-0500 performer: Organization Some lab value: Present specimen: Specimen component code: Discrete genetic variant value: NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys) component code: Gene studied [ID] value: ACAD9 component code: Transcript reference sequence [ID] value: NM_014049.4 component code: Genomic reference sequence [ID] value: NG_017064.1 component code: Genomic DNA change (gHGVS) value: T}">NC_000003.11:g.128625063C>T component code: Discrete genetic variant value: rs368949613 component code: DNA change (c.HGVS) value: T}">NM_014049.4:c.1249C>T component code: Amino acid change (pHGVS) value: NP_054768.2:p.Arg417Cys component code: DNA change type value: Substitution component code: Genomic ref allele [ID] value: C component code: Genomic allele start-end value: 31731-31731 component code: Genomic alt allele [ID] value: T component code: Cytogenetic (chromosome) location value: 3q21 component code: Genomic source class [Type] value: Germline component code: Allelic state value: Heterozygous component code: Sample variant allelic frequency [NFr] value: 47 % (Details: UCUM code% = '%') component code: Allelic read depth value: 208 1 (Details: UCUM code1 = '1') component code: Genomic structural variant copy number value: 1 1 (Details: UCUM code1 = '1') component code: Structural variant reported arrCGH [Ratio] value: 0.48 component code: Structural variant [Length] value: 1396929 1 (Details: UCUM code1 = '1') component code: Structural variant outer start and end value: 13200589-15592000 component code: Structural variant inner start and end value: 14184616-15581544
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
subject:
  l: ExamplePatient
  reference:
    v: Patient/ExamplePatient
effective: DateTime
  v: 2016
issued:
  v: 2016-09-06T00:00:00-05:00
performer:
  l: ExampleLab
  reference:
    v: Organization/ExampleLab
value: CodeableConcept
  coding: LA9633-4
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: LA9633-4
    display:
      v: Present
specimen:
  l: ExampleSpecimen
  reference:
    v: Specimen/ExampleSpecimen
component:
  code:
    coding: https://loinc.org/rdf/81252-9
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 81252-9
      display:
        v: Discrete genetic variant
  value: CodeableConcept
    coding:
      system:
        v: http://www.ncbi.nlm.nih.gov/clinvar
        l: clinvar
      code:
        v: 30880
      display:
        v: NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys)
component:
  code:
    coding: https://loinc.org/rdf/48018-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48018-6
  value: CodeableConcept
    coding:
      system:
        v: http://www.genenames.org
        l: www.genenames.org
      code:
        v: HGNC:21497
      display:
        v: ACAD9
component:
  code:
    coding: https://loinc.org/rdf/51958-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51958-7
  value: CodeableConcept
    coding:
      system:
        v: http://www.ncbi.nlm.nih.gov/refseq
        l: refseq
      code:
        v: NM_014049.4
component:
  code:
    coding: https://loinc.org/rdf/48013-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48013-7
  value: CodeableConcept
    coding:
      system:
        v: http://www.ncbi.nlm.nih.gov/refseq
        l: refseq
      code:
        v: NG_017064.1
component:
  code:
    coding: https://loinc.org/rdf/81290-9
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 81290-9
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NC_000003.11:g.128625063C>T
component:
  code:
    coding: https://loinc.org/rdf/81252-9
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 81252-9
  value: CodeableConcept
    coding:
      system:
        v: http://www.ncbi.nlm.nih.gov/projects/SNP
        l: SNP
      version:
        v: 137
      code:
        v: rs368949613
component:
  code:
    coding: https://loinc.org/rdf/48004-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48004-6
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NM_014049.4:c.1249C>T
component:
  code:
    coding: https://loinc.org/rdf/48005-3
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48005-3
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NP_054768.2:p.Arg417Cys
component:
  code:
    coding: https://loinc.org/rdf/48019-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48019-4
  value: CodeableConcept
    coding: LA6690-7
      system:
        v: http://loinc.org
        l: loinc.org

dis-path
type: Observation
id:
  v: dis-path
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 dis-path Profile: Diagnostic Implication status: Final category: Laboratory, Genetics code: Diagnostic Implication subject: Anonymous Patient (no stated gender), DoB Unknown effective: 2016 issued: 2016-09-06 00:00:00-0500 performer: Organization Some lab derivedFrom: Observation Genetic variant assessment component code: Genetic variation clinical significance [Imp] value: Pathogenic component code: Associated phenotype value: acyl-CoA dehydrogenase 9 deficiency
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
subject:
  l: ExamplePatient
  reference:
    v: Patient/ExamplePatient
effective: DateTime
  v: 2016
issued:
  v: 2016-09-06T00:00:00-05:00
performer:
  l: ExampleLab
  reference:
    v: Organization/ExampleLab
derived from:
  l: discrete-variant
  reference:
    v: Observation/discrete-variant
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:0012624
      display:
        v: acyl-CoA dehydrogenase 9 deficiency

complex-variant
type: Observation
id:
  v: complex-variant
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation complex-variant Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown effective: 2016 issued: 2016-09-06 00:00:00-0500 performer: Organization Some lab value: Present specimen: Specimen hasMember: Observation Genetic variant assessment Observation Genetic variant assessment
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
subject:
  l: ExamplePatient
  reference:
    v: Patient/ExamplePatient
effective: DateTime
  v: 2016
issued:
  v: 2016-09-06T00:00:00-05:00
performer:
  l: ExampleLab
  reference:
    v: Organization/ExampleLab
value: CodeableConcept
  coding: LA9633-4
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: LA9633-4
    display:
      v: Present
specimen:
  l: ExampleSpecimen
  reference:
    v: Specimen/ExampleSpecimen
has member:
  l: complex-component-D
  reference:
    v: Observation/complex-component-D
has member:
  l: complex-component-E
  reference:
    v: Observation/complex-component-E

complex-dis-path
type: Observation
id:
  v: complex-dis-path
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 complex-dis-path Profile: Diagnostic Implication status: Final category: Laboratory, Genetics code: Diagnostic Implication subject: Anonymous Patient (no stated gender), DoB Unknown effective: 2016 issued: 2016-09-06 00:00:00-0500 performer: Organization Some lab derivedFrom: Observation Genetic variant assessment component code: Genetic variation clinical significance [Imp] value: Pathogenic component code: Associated phenotype value: Debrisoquine adverse reaction (disorder)
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
subject:
  l: ExamplePatient
  reference:
    v: Patient/ExamplePatient
effective: DateTime
  v: 2016
issued:
  v: 2016-09-06T00:00:00-05:00
performer:
  l: ExampleLab
  reference:
    v: Organization/ExampleLab
derived from:
  l: complex-variant
  reference:
    v: Observation/complex-variant
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: http://snomed.info/id/293498008
      system:
        v: http://snomed.info/sct
        l: sct
      code:
        v: 293498008
      display:
        v: Debrisoquine adverse reaction (disorder)

complex-component-D
type: Observation
id:
  v: complex-component-D
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation complex-component-D Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown effective: 2016 issued: 2016-09-06 00:00:00-0500 performer: Organization Some lab value: Present specimen: Specimen component code: Discrete genetic variant value: NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys) component code: Transcript reference sequence [ID] value: NM_000106.5 component code: DNA change (c.HGVS) value: T}">NM_000106.5:c.886C>T component code: Amino acid change (pHGVS) value: NP_000097.3:p.Arg296Cys component code: DNA change type value: Substitution
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
subject:
  l: ExamplePatient
  reference:
    v: Patient/ExamplePatient
effective: DateTime
  v: 2016
issued:
  v: 2016-09-06T00:00:00-05:00
performer:
  l: ExampleLab
  reference:
    v: Organization/ExampleLab
value: CodeableConcept
  coding: LA9633-4
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: LA9633-4
    display:
      v: Present
specimen:
  l: ExampleSpecimen
  reference:
    v: Specimen/ExampleSpecimen
component:
  code:
    coding: https://loinc.org/rdf/81252-9
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 81252-9
      display:
        v: Discrete genetic variant
  value: CodeableConcept
    coding:
      system:
        v: http://www.ncbi.nlm.nih.gov/clinvar
        l: clinvar
      code:
        v: 31934
      display:
        v: NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys)
component:
  code:
    coding: https://loinc.org/rdf/51958-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51958-7
  value: CodeableConcept
    coding:
      system:
        v: http://www.ncbi.nlm.nih.gov/refseq
        l: refseq
      code:
        v: NM_000106.5
component:
  code:
    coding: https://loinc.org/rdf/48004-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48004-6
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NM_000106.5:c.886C>T
component:
  code:
    coding: https://loinc.org/rdf/48005-3
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48005-3
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NP_000097.3:p.Arg296Cys
component:
  code:
    coding: https://loinc.org/rdf/48019-4
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48019-4
  value: CodeableConcept
    coding: LA6690-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA6690-7
      display:
        v: Substitution

complex-component-E
type: Observation
id:
  v: complex-component-E
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
    l: variant
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation complex-component-E Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown effective: 2016 issued: 2016-09-06 00:00:00-0500 performer: Organization Some lab value: Present specimen: Specimen component code: Discrete genetic variant value: NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr) component code: Transcript reference sequence [ID] value: NM_000106.5 component code: DNA change (c.HGVS) value: C}">NM_000106.5:c.1457G>C
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
subject:
  l: ExamplePatient
  reference:
    v: Patient/ExamplePatient
effective: DateTime
  v: 2016
issued:
  v: 2016-09-06T00:00:00-05:00
performer:
  l: ExampleLab
  reference:
    v: Organization/ExampleLab
value: CodeableConcept
  coding: LA9633-4
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: LA9633-4
    display:
      v: Present
specimen:
  l: ExampleSpecimen
  reference:
    v: Specimen/ExampleSpecimen
component:
  code:
    coding: https://loinc.org/rdf/81252-9
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 81252-9
      display:
        v: Discrete genetic variant
  value: CodeableConcept
    coding:
      system:
        v: http://www.ncbi.nlm.nih.gov/clinvar
        l: clinvar
      version:
        v: ???
      code:
        v: 38486
      display:
        v: NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr)
component:
  code:
    coding: https://loinc.org/rdf/51958-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51958-7
  value: CodeableConcept
    coding:
      system:
        v: http://www.ncbi.nlm.nih.gov/refseq
        l: refseq
      code:
        v: NM_000106.5
component:
  code:
    coding: https://loinc.org/rdf/48004-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48004-6
  value: CodeableConcept
    coding:
      system:
        v: http://varnomen.hgvs.org
        l: varnomen.hgvs.org
      code:
        v: NM_000106.5:c.1457G>C

haplotype
type: Observation
id:
  v: haplotype
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype
    l: haplotype
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation haplotype Profile: Haplotype status: Final category: Laboratory, Genetics code: Haplotype name subject: Anonymous Patient (no stated gender), DoB Unknown effective: 2016 issued: 2016-09-06 00:00:00-0500 performer: Organization Some lab value: *2 specimen: Specimen derivedFrom: Observation Genetic variant assessment
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/84414-2
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 84414-2
subject:
  l: ExamplePatient
  reference:
    v: Patient/ExamplePatient
effective: DateTime
  v: 2016
issued:
  v: 2016-09-06T00:00:00-05:00
performer:
  l: ExampleLab
  reference:
    v: Organization/ExampleLab
value: CodeableConcept
  coding:
    system:
      v: http://www.ebi.ac.uk/ipd/imgt/hla
      l: hla
    code:
      v: *2
specimen:
  l: ExampleSpecimen
  reference:
    v: Specimen/ExampleSpecimen
derived from:
  l: discrete-variant
  reference:
    v: Observation/discrete-variant

genotype
type: Observation
id:
  v: genotype
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype
    l: genotype
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation genotype Profile: Genotype status: Final category: Laboratory, Genetics code: Genotype display name subject: Anonymous Patient (no stated gender), DoB Unknown effective: 2016 issued: 2016-09-06 00:00:00-0500 performer: Organization Some lab value: CYP2C9 *2/*5 specimen: Specimen derivedFrom: Observation Haplotype name component code: Gene studied [ID] value: CYP2C9 component code: Gene studied [ID] value: VKORC1
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/84413-4
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 84413-4
subject:
  l: ExamplePatient
  reference:
    v: Patient/ExamplePatient
effective: DateTime
  v: 2016
issued:
  v: 2016-09-06T00:00:00-05:00
performer:
  l: ExampleLab
  reference:
    v: Organization/ExampleLab
value: CodeableConcept
  coding:
    system:
      v: http://www.pharmvar.org
      l: www.pharmvar.org
    code:
      v: CYP2C9 *2/*5
    display:
      v: CYP2C9 *2/*5
specimen:
  l: ExampleSpecimen
  reference:
    v: Specimen/ExampleSpecimen
derived from:
  l: haplotype
  reference:
    v: Observation/haplotype
component:
  code:
    coding: https://loinc.org/rdf/48018-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48018-6
  value: CodeableConcept
    coding:
      system:
        v: http://www.genenames.org
        l: www.genenames.org
      code:
        v: HGNC:2623
      display:
        v: CYP2C9
component:
  code:
    coding: https://loinc.org/rdf/48018-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 48018-6
  value: CodeableConcept
    coding:
      system:
        v: http://www.genenames.org
        l: www.genenames.org
      code:
        v: HGNC:23663
      display:
        v: VKORC1

metab
type: Observation
id:
  v: metab
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication
    l: therapeutic-implication
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation metab Profile: Therapeutic Implication status: Final category: Laboratory, Genetics code: Therapeutic Implication subject: Anonymous Patient (no stated gender), DoB Unknown effective: 2016 issued: 2016-09-06 00:00:00-0500 performer: Organization Some lab derivedFrom: Observation Genotype display name component code: Medication assessed [ID] value: Warfarin component code: Therapeutic Implication value: Rapid metabolizer
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: therapeutic-implication
subject:
  l: ExamplePatient
  reference:
    v: Patient/ExamplePatient
effective: DateTime
  v: 2016
issued:
  v: 2016-09-06T00:00:00-05:00
performer:
  l: ExampleLab
  reference:
    v: Organization/ExampleLab
derived from:
  l: genotype
  reference:
    v: Observation/genotype
component:
  code:
    coding: https://loinc.org/rdf/51963-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51963-7
  value: CodeableConcept
    coding:
      system:
        v: http://www.nlm.nih.gov/research/umls/rxnorm
        l: rxnorm
      code:
        v: 11289
      display:
        v: Warfarin
component:
  code:
    coding:
      system:
        v: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
        l: tbd-codes-cs
      code:
        v: therapeutic-implication
  value: CodeableConcept
    coding: LA25390-8
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA25390-8
      display:
        v: Rapid metabolizer

efficacy
type: Observation
id:
  v: efficacy
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication
    l: therapeutic-implication
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation efficacy Profile: Therapeutic Implication status: Final category: Laboratory, Genetics code: Therapeutic Implication subject: Anonymous Patient (no stated gender), DoB Unknown effective: 2016 issued: 2016-09-06 00:00:00-0500 performer: Organization Some lab derivedFrom: Observation Genotype display name component code: Therapeutic Implication value: Resistant component code: Medication assessed [ID] value: Warfarin
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: therapeutic-implication
subject:
  l: ExamplePatient
  reference:
    v: Patient/ExamplePatient
effective: DateTime
  v: 2016
issued:
  v: 2016-09-06T00:00:00-05:00
performer:
  l: ExampleLab
  reference:
    v: Organization/ExampleLab
derived from:
  l: genotype
  reference:
    v: Observation/genotype
component:
  code:
    coding:
      system:
        v: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
        l: tbd-codes-cs
      code:
        v: therapeutic-implication
  value: CodeableConcept
    coding: LA6676-6
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA6676-6
      display:
        v: Resistant
component:
  code:
    coding: https://loinc.org/rdf/51963-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51963-7
  value: CodeableConcept
    coding:
      system:
        v: http://www.nlm.nih.gov/research/umls/rxnorm
        l: rxnorm
      code:
        v: 11289
      display:
        v: Warfarin

highrisk
type: Observation
id:
  v: highrisk
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication
    l: therapeutic-implication
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Observation highrisk Profile: Therapeutic Implication status: Final category: Laboratory, Genetics code: Therapeutic Implication subject: Anonymous Patient (no stated gender), DoB Unknown effective: 2016 issued: 2016-09-06 00:00:00-0500 performer: Organization Some lab derivedFrom: Observation Genotype display name component code: Therapeutic Implication value: Low risk component code: Medication assessed [ID] value: Warfarin
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: therapeutic-implication
subject:
  l: ExamplePatient
  reference:
    v: Patient/ExamplePatient
effective: DateTime
  v: 2016
issued:
  v: 2016-09-06T00:00:00-05:00
performer:
  l: ExampleLab
  reference:
    v: Organization/ExampleLab
derived from:
  l: genotype
  reference:
    v: Observation/genotype
component:
  code:
    coding:
      system:
        v: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
        l: tbd-codes-cs
      code:
        v: therapeutic-implication
  value: CodeableConcept
    coding: LA19542-2
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: LA19542-2
      display:
        v: Low risk
component:
  code:
    coding: https://loinc.org/rdf/51963-7
      system:
        v: http://loinc.org
        l: loinc.org
      code:
        v: 51963-7
  value: CodeableConcept
    coding:
      system:
        v: http://www.nlm.nih.gov/research/umls/rxnorm
        l: rxnorm
      code:
        v: 11289
      display:
        v: Warfarin

usage
type: Task
id:
  v: usage
meta:
  profile:
    v: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation
    l: medication-recommendation
text:
  status:
    v: generated
  div:
    v: Generated Narrative: Task usage Profile: Medication Recommendation status: Requested intent: proposal code: May need higher dosage than usual. focus: MedicationStatement: status = unknown; medication[x] = Warfarin for: Anonymous Patient (no stated gender), DoB Unknown requester: Organization Some lab reasonReference: Observation Therapeutic Implication
status:
  v: requested
intent:
  v: proposal
code:
  coding: LA26423-6
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: LA26423-6
    display:
      v: Increase dose
  text:
    v: May need higher dosage than usual.
focus:
  l: MedicationStatementWarfarin
  reference:
    v: MedicationStatement/MedicationStatementWarfarin
for:
  l: ExamplePatient
  reference:
    v: Patient/ExamplePatient
requester:
  l: ExampleLab
  reference:
    v: Organization/ExampleLab
reason reference:
  l: metab
  reference:
    v: Observation/metab

v: LA6690-7

v: Substitution

code:
  coding: https://loinc.org/rdf/69547-8
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 69547-8
value: String
  v: C

code:
  coding: https://loinc.org/rdf/81254-5
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 81254-5
value: Range
  low:
    value:
      v: 31731
  high:
    value:
      v: 31731

code:
  coding: https://loinc.org/rdf/69551-0
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 69551-0
value: String
  v: T

code:
  coding: https://loinc.org/rdf/48001-2
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 48001-2
value: CodeableConcept
  text:
    v: 3q21

code:
  coding: https://loinc.org/rdf/48002-0
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 48002-0
value: CodeableConcept
  coding: LA6683-2
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: LA6683-2
    display:
      v: Germline

code:
  coding: https://loinc.org/rdf/53034-5
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 53034-5
value: CodeableConcept
  coding: LA6706-1
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: LA6706-1
    display:
      v: Heterozygous

code:
  coding: https://loinc.org/rdf/81258-6
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 81258-6
value: Quantity
  value:
    v: 47
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: %

code:
  coding: https://loinc.org/rdf/82121-5
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 82121-5
value: Quantity
  value:
    v: 208
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

code:
  coding: https://loinc.org/rdf/82155-3
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 82155-3
value: Quantity
  value:
    v: 1
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

code:
  coding: https://loinc.org/rdf/81299-0
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 81299-0
value: Quantity
  value:
    v: 0.48

code:
  coding: https://loinc.org/rdf/81300-6
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 81300-6
value: Quantity
  value:
    v: 1396929
  system:
    v: http://unitsofmeasure.org
    l: unitsofmeasure.org
  code:
    v: 1

code:
  coding: https://loinc.org/rdf/81301-4
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 81301-4
value: Range
  low:
    value:
      v: 13200589
  high:
    value:
      v: 15592000

code:
  coding: https://loinc.org/rdf/81302-2
    system:
      v: http://loinc.org
      l: loinc.org
    code:
      v: 81302-2
value: Range
  low:
    value:
      v: 14184616
  high:
    value:
      v: 15581544