Genomics Reporting Implementation Guide
3.0.0 - release International flag

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

Example Bundle: bundle-cgexample

Generated Narrative: Bundle bundle-cgexample

Bundle bundle-cgexample of type collection

Entry 1 - fullUrl = http://example.org/fhir/DiagnosticReport/report

Resource DiagnosticReport:

Generated Narrative: DiagnosticReport report

Genetic analysis report (Genetics)

SubjectAnonymous Patient (no stated gender), DoB Unknown
When For2016
Reported2016-09-06 00:00:00-0500
Performer Organization Some lab

Report Details

CodeValue

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

subject: Anonymous Patient (no stated gender), DoB Unknown

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)

subject: Anonymous Patient (no stated gender), DoB Unknown

Entry 6 - fullUrl = http://example.org/fhir/Observation/discrete-variant

Resource Observation:

Generated Narrative: Observation discrete-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 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

Entry 7 - fullUrl = http://example.org/fhir/Observation/dis-path

Resource Observation:

Generated Narrative: Observation dis-path

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

Resource Observation:

Generated Narrative: Observation complex-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

Resource Observation:

Generated Narrative: Observation complex-dis-path

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

Resource Observation:

Generated Narrative: Observation complex-component-D

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

Resource Observation:

Generated Narrative: Observation complex-component-E

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/haplotype

Resource Observation:

Generated Narrative: Observation 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: Bundle: type = collection

Entry 13 - fullUrl = http://example.org/fhir/Observation/genotype

Resource Observation:

Generated Narrative: Observation 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: Bundle: type = collection

component

code: Gene studied [ID]

value: CYP2C9

component

code: Gene studied [ID]

value: VKORC1

Entry 14 - fullUrl = http://example.org/fhir/Observation/metab

Resource Observation:

Generated Narrative: Observation metab

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 15 - fullUrl = http://example.org/fhir/Observation/efficacy

Resource Observation:

Generated Narrative: Observation efficacy

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 16 - fullUrl = http://example.org/fhir/Observation/highrisk

Resource Observation:

Generated Narrative: Observation highrisk

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 17 - fullUrl = http://example.org/fhir/Task/usage

Resource Task:

Generated Narrative: Task usage

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