Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions
Bundle bundle-cgexample-withGrouping of type collection
Entry 1 - fullUrl = http://example.org/fhir/DiagnosticReport/report-withGrouping
Resource DiagnosticReport:
Genetic analysis report (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 Discrete variation analysis overall interpretation Positive 2016 Genetic variant assessment Present 2016 Diagnostic Implication 2016 Genetic variant assessment Present 2016 Diagnostic Implication 2016 Group 2016 Haplotype name *2 2016 Genotype display name CYP2C9 *2/*5 2016 Therapeutic Implication 2016 Therapeutic Implication 2016
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"
subject: See above (Patient/ExamplePatient)
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)
subject: See above (Patient/ExamplePatient)
Entry 6 - fullUrl = http://example.org/fhir/Observation/overall-interp-1a
Resource Observation:
Generated Narrative: Observation
Resource Observation "overall-interp-1a"
Profile: Overall Interpretation
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Discrete variation analysis overall interpretation (LOINC#51968-6)
subject: See above (Patient/ExamplePatient)
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See above (Organization/ExampleLab)
value: Positive (LOINC#LA6576-8; SNOMED CT#10828004)
specimen: See above (Specimen/ExampleSpecimen)
Entry 7 - fullUrl = http://example.org/fhir/Observation/discrete-variant-1a
Resource Observation:
Generated Narrative: Observation
Resource Observation "discrete-variant-1a"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (Patient/ExamplePatient)
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See above (Organization/ExampleLab)
value: Present (LOINC#LA9633-4)
specimen: See above (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 reference 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: Genomic DNA change (gHGVS) (LOINC#81290-9)
value: NC_000003.11:g.128625063C>T (Human Genome Variation Society nomenclature#NC_000003.11:g.128625063C>T)
component
code: Discrete genetic variant (LOINC#81252-9)
value: rs368949613 (Genetic Sequence polymorphism database#rs368949613)
component
code: DNA change (c.HGVS) (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 (pHGVS) (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: Genomic ref allele [ID] (LOINC#69547-8)
value: C
component
code: Genomic allele start-end (LOINC#81254-5)
value: 31731-31731
component
code: Genomic alt allele [ID] (LOINC#69551-0)
value: T
component
code: Cytogenetic (chromosome) location (LOINC#48001-2)
value: 3q21 ()
component
code: Genomic source class [Type] (LOINC#48002-0)
value: Germline (LOINC#LA6683-2)
component
code: Allelic state (LOINC#53034-5)
value: Heterozygous (LOINC#LA6706-1)
component
code: Sample variant allelic frequency [NFr] (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: Genomic structural variant copy number (LOINC#82155-3)
value: 1 1 (Details: UCUM code 1 = '1')
component
code: Structural variant outer start and end (LOINC#81301-4)
value: 13200589-15592000
component
code: Structural variant inner start and end (LOINC#81302-2)
value: 14184616-15581544
Entry 8 - fullUrl = http://example.org/fhir/Observation/dis-path-1a
Resource Observation:
Generated Narrative: Observation
Resource Observation "dis-path-1a"
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 above (Patient/ExamplePatient)
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See above (Organization/ExampleLab)
derivedFrom: See above (Observation/discrete-variant-1a)
component
code: Genetic variation clinical significance [Imp] (LOINC#53037-8)
value: Pathogenic (LOINC#LA6668-3)
component
code: Associated phenotype (LOINC#81259-4)
value: acyl-CoA dehydrogenase 9 deficiency (Mondo Disease Ontology#MONDO:0012624)
Entry 9 - fullUrl = http://example.org/fhir/Observation/complex-variant-1a
Resource Observation:
Generated Narrative: Observation
Resource Observation "complex-variant-1a"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (Patient/ExamplePatient)
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See above (Organization/ExampleLab)
value: Present (LOINC#LA9633-4)
specimen: See above (Specimen/ExampleSpecimen)
hasMember:
Entry 10 - fullUrl = http://example.org/fhir/Observation/complex-dis-path-1a
Resource Observation:
Generated Narrative: Observation
Resource Observation "complex-dis-path-1a"
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 above (Patient/ExamplePatient)
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See above (Organization/ExampleLab)
derivedFrom: See above (Observation/complex-variant-1a)
component
code: Genetic variation clinical significance [Imp] (LOINC#53037-8)
value: Pathogenic (LOINC#LA6668-3)
component
code: Associated phenotype (LOINC#81259-4)
value: Debrisoquine adverse reaction (disorder) (SNOMED CT#293498008)
Entry 11 - fullUrl = http://example.org/fhir/Observation/complex-component-D-1a
Resource Observation:
Generated Narrative: Observation
Resource Observation "complex-component-D-1a"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (Patient/ExamplePatient)
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See above (Organization/ExampleLab)
value: Present (LOINC#LA9633-4)
specimen: See above (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 reference sequence [ID] (LOINC#51958-7)
value: NM_000106.5 (Gene Reference Sequence Collection#NM_000106.5)
component
code: DNA change (c.HGVS) (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 (pHGVS) (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 12 - fullUrl = http://example.org/fhir/Observation/complex-component-E-1a
Resource Observation:
Generated Narrative: Observation
Resource Observation "complex-component-E-1a"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (Patient/ExamplePatient)
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See above (Organization/ExampleLab)
value: Present (LOINC#LA9633-4)
specimen: See above (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 reference sequence [ID] (LOINC#51958-7)
value: NM_000106.5 (Gene Reference Sequence Collection#NM_000106.5)
component
code: DNA change (c.HGVS) (LOINC#48004-6)
value: NM_000106.5:c.1457G>C (Human Genome Variation Society nomenclature#NM_000106.5:c.1457G>C)
Entry 13 - fullUrl = http://example.org/fhir/Observation/pharmPanel-1a
Resource Observation:
Generated Narrative: Observation
Resource Observation "pharmPanel-1a"
Recommended Action: See above (Task/usage-1a)
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Group (NCI Thesaurus#C43359)
subject: See above (Patient/ExamplePatient)
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See above (Organization/ExampleLab)
hasMember:
Entry 14 - fullUrl = http://example.org/fhir/Observation/haplotype-1a
Resource Observation:
Generated Narrative: Observation
Resource Observation "haplotype-1a"
Profile: Haplotype
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Haplotype name (LOINC#84414-2)
subject: See above (Patient/ExamplePatient)
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See above (Organization/ExampleLab)
value: *2 (hla#*2)
specimen: See above (Specimen/ExampleSpecimen)
derivedFrom: See above (Observation/discrete-variant-1a)
Entry 15 - fullUrl = http://example.org/fhir/Observation/genotype-1a
Resource Observation:
Generated Narrative: Observation
Resource Observation "genotype-1a"
Profile: Genotype
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genotype display name (LOINC#84413-4)
subject: See above (Patient/ExamplePatient)
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See above (Organization/ExampleLab)
value: CYP2C9 *2/*5 (www.pharmvar.org#CYP2C9*2*5")
specimen: See above (Specimen/ExampleSpecimen)
derivedFrom: See above (Observation/haplotype-1a)
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 16 - fullUrl = http://example.org/fhir/Observation/metab-1a
Resource Observation:
Generated Narrative: Observation
Resource Observation "metab-1a"
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 above (Patient/ExamplePatient)
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See above (Organization/ExampleLab)
derivedFrom: See above (Observation/genotype-1a)
component
code: Medication assessed [ID] (LOINC#51963-7)
value: Warfarin (RxNorm#11289)
component
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
value: Rapid metabolizer (LOINC#LA25390-8)
Entry 17 - fullUrl = http://example.org/fhir/Observation/efficacy-1a
Resource Observation:
Generated Narrative: Observation
Resource Observation "efficacy-1a"
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 above (Patient/ExamplePatient)
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See above (Organization/ExampleLab)
derivedFrom: See above (Observation/genotype-1a)
component
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
value: Resistant (LOINC#LA6676-6)
component
code: Medication assessed [ID] (LOINC#51963-7)
value: Warfarin (RxNorm#11289)
Entry 18 - fullUrl = http://example.org/fhir/Observation/highrisk-1a
Resource Observation:
Generated Narrative: Observation
Resource Observation "highrisk-1a"
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 above (Patient/ExamplePatient)
effective: 2016
issued: Sep 6, 2016, 5:00:00 AM
performer: See above (Organization/ExampleLab)
derivedFrom: See above (Observation/genotype-1a)
component
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
value: Low risk (LOINC#LA19542-2)
component
code: Medication assessed [ID] (LOINC#51963-7)
value: Warfarin (RxNorm#11289)
Entry 19 - fullUrl = http://example.org/fhir/Task/usage-1a
Resource Task:
Resource Task "usage-1a"
Profile: Medication Recommendation
status: REQUESTED
intent: PROPOSAL
code: May need higher dosage than usual. (LOINC#LA26423-6 "Increase dose")
focus: MedicationStatement/MedicationStatementWarfarin
for: See above (Patient/ExamplePatient)
requester: See above (Organization/ExampleLab)
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0-ballot based on FHIR 4.0.1. Generated 2023-12-18
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