Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build
Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild 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-withGrouping of type collection
Entry 1 - fullUrl = http://example.org/fhir/DiagnosticReport/report-withGrouping
Resource DiagnosticReport:
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 Group Final Haplotype name HLA-A*02:01 Final Genotype display name CYP2C9 *2/*5 Final Therapeutic Implication Final Therapeutic Implication Final Coded Conclusions:
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:
Entry 4 - fullUrl = http://example.org/fhir/Organization/ExampleLab
Resource Organization:
name: Some lab
Entry 5 - fullUrl = http://example.org/fhir/ServiceRequest/ExampleServiceRequest
Resource ServiceRequest:
status: Active
intent: Original Order
Codes
Concept Genetic analysis report subject: Anonymous Patient (no stated gender), DoB Unknown
Reasons
Concept Worried about family planning
Entry 6 - fullUrl = http://example.org/fhir/Observation/discrete-variant-1a
Resource Observation:
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: 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:
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
Entry 8 - fullUrl = http://example.org/fhir/Observation/complex-variant-1a
Resource Observation:
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:
Entry 9 - fullUrl = http://example.org/fhir/Observation/complex-dis-path-1a
Resource Observation:
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)
Entry 10 - fullUrl = http://example.org/fhir/Observation/complex-component-D-1a
Resource Observation:
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: 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:
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: NM_000106.5:c.1457G>C
Entry 12 - fullUrl = http://example.org/fhir/Observation/pharmPanel-1a
Resource Observation:
Recommended Action: Task Increase dose
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:
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: HLA-A*02:01
specimen: Specimen
derivedFrom: Observation Genetic variant assessment
Entry 14 - fullUrl = http://example.org/fhir/Observation/genotype-1a
Resource Observation:
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
Entry 15 - fullUrl = http://example.org/fhir/Observation/metab-1a
Resource Observation:
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
Entry 16 - fullUrl = http://example.org/fhir/Observation/efficacy-1a
Resource Observation:
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
Entry 17 - fullUrl = http://example.org/fhir/Observation/highrisk-1a
Resource Observation:
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
Entry 18 - fullUrl = http://example.org/fhir/Task/usage-1a
Resource Task:
Profile: Medication Recommendation
status: Requested
intent: Proposal
code: May need higher dosage than usual.
focus: MedicationStatement: status = recorded
for: Anonymous Patient (no stated gender), DoB Unknown
requester: Organization Some lab
Reasons
Reference Observation Therapeutic Implication
IG © 2025+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#4.0.0-cibuild based on FHIR 6.0.0-ballot3. Generated 2025-12-19
Links: Table of Contents |
QA Report
| Version History |
|
Propose a change