Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 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
Generated Narrative: Bundle bundle-cgexample-withGrouping
Bundle bundle-cgexample-withGrouping of type collection
Entry 1 - fullUrl = http://example.org/fhir/DiagnosticReport/report-withGrouping
Resource DiagnosticReport:
Generated Narrative: DiagnosticReport report-withGrouping
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 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:
Generated Narrative: Specimen ExampleSpecimen
Entry 4 - fullUrl = http://example.org/fhir/Organization/ExampleLab
Resource Organization:
Generated Narrative: Organization ExampleLab
name: Some lab
Entry 5 - fullUrl = http://example.org/fhir/ServiceRequest/ExampleServiceRequest
Resource ServiceRequest:
Generated Narrative: ServiceRequest ExampleServiceRequest
status: Active
intent: Original Order
code: No display for ServiceRequest.code (concept: Genetic analysis report)
Entry 6 - fullUrl = http://example.org/fhir/Observation/discrete-variant-1a
Resource Observation:
Generated Narrative: Observation discrete-variant-1a
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: NC_000003.11:g.128625063C>T
component
code: Discrete genetic variant
value: rs368949613
component
code: DNA change (c.HGVS)
value: 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 outer start and end
value: 13200589-15592000
component
code: Structural variant inner start and end
value: 14184616-15581544
Entry 7 - fullUrl = http://example.org/fhir/Observation/dis-path-1a
Resource Observation:
Generated Narrative: Observation dis-path-1a
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: Bundle: type = collection
component
code: Genetic variation clinical significance [Imp]
value: Pathogenic
component
code: Associated phenotype
value: acyl-CoA dehydrogenase 9 deficiency
Entry 8 - fullUrl = http://example.org/fhir/Observation/complex-variant-1a
Resource Observation:
Generated Narrative: Observation complex-variant-1a
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:
Entry 9 - fullUrl = http://example.org/fhir/Observation/complex-dis-path-1a
Resource Observation:
Generated Narrative: Observation complex-dis-path-1a
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: Bundle: type = collection
component
code: Genetic variation clinical significance [Imp]
value: Pathogenic
component
code: Associated phenotype
value: Debrisoquine adverse reaction (disorder)
Entry 10 - fullUrl = http://example.org/fhir/Observation/complex-component-D-1a
Resource Observation:
Generated Narrative: Observation complex-component-D-1a
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: 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
Entry 11 - fullUrl = http://example.org/fhir/Observation/complex-component-E-1a
Resource Observation:
Generated Narrative: Observation complex-component-E-1a
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: NM_000106.5:c.1457G>C
Entry 12 - fullUrl = http://example.org/fhir/Observation/pharmPanel-1a
Resource Observation:
Generated Narrative: Observation pharmPanel-1a
Recommended Action: Bundle: type = collection
status: Final
category: Laboratory, Genetics
code: Group
subject: Anonymous Patient (no stated gender), DoB Unknown
effective: 2016
issued: 2016-09-06 00:00:00-0500
performer: Organization Some lab
hasMember:
Entry 13 - fullUrl = http://example.org/fhir/Observation/haplotype-1a
Resource Observation:
Generated Narrative: Observation haplotype-1a
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: Bundle: type = collection
Entry 14 - fullUrl = http://example.org/fhir/Observation/genotype-1a
Resource Observation:
Generated Narrative: Observation genotype-1a
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: Bundle: type = collection
component
code: Gene studied [ID]
value: CYP2C9
component
code: Gene studied [ID]
value: VKORC1
Entry 15 - fullUrl = http://example.org/fhir/Observation/metab-1a
Resource Observation:
Generated Narrative: Observation metab-1a
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: Bundle: type = collection
component
code: Medication assessed [ID]
value: Warfarin
component
code: Therapeutic Implication
value: Rapid metabolizer
Entry 16 - fullUrl = http://example.org/fhir/Observation/efficacy-1a
Resource Observation:
Generated Narrative: Observation efficacy-1a
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: Bundle: type = collection
component
code: Therapeutic Implication
value: Resistant
component
code: Medication assessed [ID]
value: Warfarin
Entry 17 - fullUrl = http://example.org/fhir/Observation/highrisk-1a
Resource Observation:
Generated Narrative: Observation highrisk-1a
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: Bundle: type = collection
component
code: Therapeutic Implication
value: Low risk
component
code: Medication assessed [ID]
value: Warfarin
Entry 18 - fullUrl = http://example.org/fhir/Task/usage-1a
Resource Task:
Generated Narrative: Task usage-1a
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
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-11-19
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