Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot 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 3.0.1-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

Example Bundle: bundle-cgexample

Bundle bundle-cgexample of type collection

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

Resource DiagnosticReport:

Gene analysis narr rpt Doc (Genetics)

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

Report Details

CodeValueWhen ForReported
Genetic variant assessmentPresent2016
Diagnostic Implication2016
Genetic var assessPresent2016
Diagnostic Implication2016
Haplotype name Bld/T*22016
Genotype name PatientCYP2C9 *2/*52016
Therapeutic Implication2016
Therapeutic Implication2016

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

Resource Specimen "ExampleSpecimen"

subject: See on this page: 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 on this page: Patient/ExamplePatient

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:

Generated Narrative: 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