Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions
Bundle bundle-cgexample of type collection
Entry 1 - fullUrl = http://example.org/fhir/DiagnosticReport/report
Resource DiagnosticReport:
Gene analysis narr rpt Doc (Genetics)
Subject Anonymous Patient (no stated gender), DoB Unknown When For 2016 Reported 2016-09-06 00:00:00-0500 Report Details
Code Value When For Reported Genetic variant assessment Present 2016 Diagnostic Implication 2016 Genetic var assess Present 2016 Diagnostic Implication 2016 Haplotype name Bld/T *2 2016 Genotype name Patient CYP2C9 *2/*5 2016 Therapeutic Implication 2016 Therapeutic Implication 2016 Coded Conclusions :
- Positive
- Positive
Entry 2 - fullUrl = http://example.org/fhir/Patient/ExamplePatient
Resource Patient:
This would contain patient identifiers, demographics, etc.
Entry 3 - fullUrl = http://example.org/fhir/Specimen/ExampleSpecimen
Resource Specimen:
Resource Specimen "ExampleSpecimen"
Entry 4 - fullUrl = http://example.org/fhir/Organization/ExampleLab
Resource Organization:
Generated Narrative: Organization
Resource Organization "ExampleLab"
name: Some lab
Entry 5 - fullUrl = http://example.org/fhir/ServiceRequest/ExampleServiceRequest
Resource ServiceRequest:
Generated Narrative: ServiceRequest
Resource ServiceRequest "ExampleServiceRequest"
status: ACTIVE
intent: ORIGINALORDER
code: Genetic analysis report (LOINC#51969-4)
Entry 6 - fullUrl = http://example.org/fhir/Observation/discrete-variant
Resource Observation:
Generated Narrative: Observation
Resource Observation "discrete-variant"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See on this page: Patient/ExamplePatient
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See on this page: Organization/ExampleLab
value: Present (LOINC#LA9633-4)
specimen: See on this page: Specimen/ExampleSpecimen
component
code: Discrete genetic variant (LOINC#81252-9)
value: NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys) (ClinVar Variant ID#30880)
component
code: Gene studied ID (LOINC#48018-6)
value: ACAD9 (HUGO Gene Nomenclature Committee Genes#HGNC:21497)
component
code: Transcript ref sequence ID (LOINC#51958-7)
value: NM_014049.4 (Gene Reference Sequence Collection#NM_014049.4)
component
code: Genomic reference sequence ID (LOINC#48013-7)
value: NG_017064.1 (Gene Reference Sequence Collection#NG_017064.1)
component
code: Struct var HGVS name (LOINC#81290-9)
value: NC_000003.11:g.128625063C>T (Human Genome Variation Society nomenclature#NC_000003.11:g.128625063C>T)
component
code: Simple var ID (LOINC#81252-9)
value: rs368949613 (Genetic Sequence polymorphism database[137]#rs368949613)
component
code: DNA change (LOINC#48004-6)
value: NM_014049.4:c.1249C>T (Human Genome Variation Society nomenclature#NM_014049.4:c.1249C>T)
component
code: Amino acid change (LOINC#48005-3)
value: NP_054768.2:p.Arg417Cys (Human Genome Variation Society nomenclature#NP_054768.2:p.Arg417Cys)
component
code: DNA Change Type (LOINC#48019-4)
value: Substitution (LOINC#LA6690-7)
component
code: Ref nucleotide (LOINC#69547-8)
value: C
component
code: Gen allele loc ID (LOINC#81254-5)
value: 31731-31731
component
code: Alt allele (LOINC#69551-0)
value: T
component
code: Cyto loc ID (LOINC#48001-2)
value: 3q21 ()
component
code: Genomic source class (LOINC#48002-0)
value: Germline (LOINC#LA6683-2)
component
code: Allelic state (LOINC#53034-5)
value: Heterozygous (LOINC#LA6706-1)
component
code: Sample VAF (LOINC#81258-6)
value: 47 % (Details: UCUM code % = '%')
component
code: Allelic read depth (LOINC#82121-5)
value: 208 1 (Details: UCUM code 1 = '1')
component
code: Gen struct var copy num (LOINC#82155-3)
value: 1 1 (Details: UCUM code 1 = '1')
component
code: Struct var rep arrCGH Rto (LOINC#81299-0)
value: 0.48
component
code: Struct var len (LOINC#81300-6)
value: 1396929 1 (Details: UCUM code 1 = '1')
component
code: Struct var outer start-end NumRange (LOINC#81301-4)
value: 13200589-15592000
component
code: Struct var inner start-end NumRange (LOINC#81302-2)
value: 14184616-15581544
Entry 7 - fullUrl = http://example.org/fhir/Observation/dis-path
Resource Observation:
Generated Narrative: Observation
Resource Observation "dis-path"
Profile: Diagnostic Implication
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Diagnostic Implication (To Be Determined Codes#diagnostic-implication)
subject: See on this page: Patient/ExamplePatient
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See on this page: Organization/ExampleLab
derivedFrom: See on this page: Observation/discrete-variant
component
code: Gene dis seq var interp-Imp (LOINC#53037-8)
value: Pathogenic (LOINC#LA6668-3)
component
code: Prob assoc phenotype (LOINC#81259-4)
value: acyl-CoA dehydrogenase 9 deficiency (Mondo Disease Ontology#MONDO:0012624)
Entry 8 - fullUrl = http://example.org/fhir/Observation/complex-variant
Resource Observation:
Generated Narrative: Observation
Resource Observation "complex-variant"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic var assess (LOINC#69548-6)
subject: See on this page: Patient/ExamplePatient
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See on this page: Organization/ExampleLab
value: Present (LOINC#LA9633-4)
specimen: See on this page: Specimen/ExampleSpecimen
hasMember:
Entry 9 - fullUrl = http://example.org/fhir/Observation/complex-dis-path
Resource Observation:
Generated Narrative: Observation
Resource Observation "complex-dis-path"
Profile: Diagnostic Implication
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Diagnostic Implication (To Be Determined Codes#diagnostic-implication)
subject: See on this page: Patient/ExamplePatient
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See on this page: Organization/ExampleLab
derivedFrom: See on this page: Observation/complex-variant
component
code: Gene dis seq var interp-Imp (LOINC#53037-8)
value: Pathogenic (LOINC#LA6668-3)
component
code: Prob assoc phenotype (LOINC#81259-4)
value: Debrisoquine adverse reaction (disorder) (SNOMED CT#293498008)
Entry 10 - fullUrl = http://example.org/fhir/Observation/complex-component-D
Resource Observation:
Generated Narrative: Observation
Resource Observation "complex-component-D"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See on this page: Patient/ExamplePatient
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See on this page: Organization/ExampleLab
value: Present (LOINC#LA9633-4)
specimen: See on this page: Specimen/ExampleSpecimen
component
code: Discrete genetic variant (LOINC#81252-9)
value: NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys) (ClinVar Variant ID#31934)
component
code: Transcript ref sequence ID (LOINC#51958-7)
value: NM_000106.5 (Gene Reference Sequence Collection#NM_000106.5)
component
code: DNA change (LOINC#48004-6)
value: NM_000106.5:c.886C>T (Human Genome Variation Society nomenclature#NM_000106.5:c.886C>T)
component
code: Amino acid change (LOINC#48005-3)
value: NP_000097.3:p.Arg296Cys (Human Genome Variation Society nomenclature#NP_000097.3:p.Arg296Cys)
component
code: DNA Change Type (LOINC#48019-4)
value: Substitution (LOINC#LA6690-7)
Entry 11 - fullUrl = http://example.org/fhir/Observation/complex-component-E
Resource Observation:
Generated Narrative: Observation
Resource Observation "complex-component-E"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See on this page: Patient/ExamplePatient
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See on this page: Organization/ExampleLab
value: Present (LOINC#LA9633-4)
specimen: See on this page: Specimen/ExampleSpecimen
component
code: Discrete genetic variant (LOINC#81252-9)
value: NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr) (ClinVar Variant ID[???]#38486)
component
code: Transcript ref sequence ID (LOINC#51958-7)
value: NM_000106.5 (Gene Reference Sequence Collection#NM_000106.5)
component
code: DNA change (LOINC#48004-6)
value: NM_000106.5:c.1457G>C (Human Genome Variation Society nomenclature#NM_000106.5:c.1457G>C)
Entry 12 - fullUrl = http://example.org/fhir/Observation/haplotype
Resource Observation:
Generated Narrative: Observation
Resource Observation "haplotype"
Profile: Haplotype
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Haplotype name Bld/T (LOINC#84414-2)
subject: See on this page: Patient/ExamplePatient
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See on this page: Organization/ExampleLab
value: *2 (hla#*2)
specimen: See on this page: Specimen/ExampleSpecimen
derivedFrom: See on this page: Observation/discrete-variant
Entry 13 - fullUrl = http://example.org/fhir/Observation/genotype
Resource Observation:
Generated Narrative: Observation
Resource Observation "genotype"
Profile: Genotype
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genotype name Patient (LOINC#84413-4)
subject: See on this page: Patient/ExamplePatient
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See on this page: Organization/ExampleLab
value: CYP2C9 *2/*5 (www.pharmvar.org#CYP2C9 *2/*5)
specimen: See on this page: Specimen/ExampleSpecimen
derivedFrom: See on this page: Observation/haplotype
component
code: Gene studied ID (LOINC#48018-6)
value: CYP2C9 (HUGO Gene Nomenclature Committee Genes#HGNC:2623)
component
code: Gene studied ID (LOINC#48018-6)
value: VKORC1 (HUGO Gene Nomenclature Committee Genes#HGNC:23663)
Entry 14 - fullUrl = http://example.org/fhir/Observation/metab
Resource Observation:
Generated Narrative: Observation
Resource Observation "metab"
Profile: Therapeutic Implication
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
subject: See on this page: Patient/ExamplePatient
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See on this page: Organization/ExampleLab
derivedFrom: See on this page: Observation/genotype
component
code: Medication assessed (LOINC#51963-7)
value: Warfarin (RxNorm#11289)
component
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
value: Rapid metabolizer (LOINC#LA25390-8)
Entry 15 - fullUrl = http://example.org/fhir/Observation/efficacy
Resource Observation:
Generated Narrative: Observation
Resource Observation "efficacy"
Profile: Therapeutic Implication
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
subject: See on this page: Patient/ExamplePatient
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See on this page: Organization/ExampleLab
derivedFrom: See on this page: Observation/genotype
component
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
value: Resistant (LOINC#LA6676-6)
component
code: Medication assessed (LOINC#51963-7)
value: Warfarin (RxNorm#11289)
Entry 16 - fullUrl = http://example.org/fhir/Observation/highrisk
Resource Observation:
Generated Narrative: Observation
Resource Observation "highrisk"
Profile: Therapeutic Implication
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
subject: See on this page: Patient/ExamplePatient
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See on this page: Organization/ExampleLab
derivedFrom: See on this page: Observation/genotype
component
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
value: Low risk (LOINC#LA19542-2)
component
code: Medication assessed (LOINC#51963-7)
value: Warfarin (RxNorm#11289)
Entry 17 - fullUrl = http://example.org/fhir/Task/usage
Resource Task:
Resource Task "usage"
Profile: Medication Recommendation
status: REQUESTED
intent: PROPOSAL
code: May need higher dosage than usual. (LOINC#LA26423-6 "Increase dose")
focus: MedicationStatement/MedicationStatementWarfarin
for: See on this page: Patient/ExamplePatient
requester: See on this page: Organization/ExampleLab