Genomics Reporting Implementation Guide
2.0.0 - trial-use

This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

Example Bundle: bundle-cgexample-withGrouping

Bundle bundle-cgexample-withGrouping of type collection

Entry 1 - Full URL = http://example.org/fhir/DiagnosticReport/report-withGrouping

Resource DiagnosticReport:

Master HL7 genetic variant reporting panel (Genetics)

SubjectAnonymous Patient (no stated gender), DoB Unknown
When For2016
Reported2016-09-06 12:00:00-0500

Report Details

CodeValue

Entry 2 - Full URL = http://example.org/fhir/Patient/ExamplePatient

Resource Patient:

This would contain patient identifiers, demographics, etc.

Entry 3 - Full URL = http://example.org/fhir/Specimen/ExampleSpecimen

Resource Specimen:

Generated Narrative

Resource "ExampleSpecimen"

subject: Patient/ExamplePatient

Entry 4 - Full URL = http://example.org/fhir/Organization/ExampleLab

Resource Organization:

Generated Narrative

Resource "ExampleLab"

name: Some lab

Entry 5 - Full URL = http://example.org/fhir/ServiceRequest/ExampleServiceRequest

Resource ServiceRequest:

Generated Narrative

Resource "ExampleServiceRequest"

status: ACTIVE

intent: ORIGINALORDER

code: Master HL7 genetic variant reporting panel (LOINC#81247-9)

subject: Patient/ExamplePatient

Entry 6 - Full URL = http://example.org/fhir/Observation/overall-interp-1a

Resource Observation:

Generated Narrative

Resource "overall-interp-1a"

Profile: Overall Interpretation

status: FINAL

category: Laboratory (Observation Category Codes#laboratory)

code: Discrete variation analysis overall interpretation (LOINC#51968-6)

subject: Patient/ExamplePatient

effective: 2016

issued: Sep 6, 2016 5:00:00 AM

performer: Organization/ExampleLab "Some lab"

value: Positive (LOINC#LA6576-8; SNOMED CT#10828004)

specimen: Specimen/ExampleSpecimen

Entry 7 - Full URL = http://example.org/fhir/Observation/discrete-variant-1a

Resource Observation:

Generated Narrative

Resource "discrete-variant-1a"

Profile: Variant

status: FINAL

category: Laboratory (Observation Category Codes#laboratory)

code: Genetic variant assessment (LOINC#69548-6)

subject: Patient/ExamplePatient

effective: 2016

issued: Sep 6, 2016 5:00:00 AM

performer: Organization/ExampleLab "Some lab"

value: Present (LOINC#LA9633-4)

specimen: Specimen/ExampleSpecimen

component

code: Discrete genetic variant (LOINC#81252-9)

value: NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys) (clinvar[???]#30880)

component

code: Gene studied [ID] (LOINC#48018-6)

value: ACAD9 (geneId#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[137]#rs368949613)

component

code: DNA change (c.HGVS) (LOINC#48004-6)

value: c.1249C>T (Human Genome Variation Society nomenclature[15.11]#c.1249C>T)

component

code: Amino acid change (pHGVS) (LOINC#48005-3)

value: p.Arg417Cys (Human Genome Variation Society nomenclature[15.11]#p.Arg417Cys)

component

code: DNA Change Type (LOINC#48019-4)

value: Substitution (LOINC#LA6690-7)

component

code: Amino acid change [Type] (LOINC#48006-1)

value: Missense (LOINC#LA6698-0)

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 reported arrCGH [Ratio] (LOINC#81299-0)

value: 0.48

component

code: Structural variant [Length] (LOINC#81300-6)

value: 1396929 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 - Full URL = http://example.org/fhir/Observation/dis-path-1a

Resource Observation:

Generated Narrative

Resource "dis-path-1a"

Profile: Diagnostic Implication

status: FINAL

category: Laboratory (Observation Category Codes#laboratory)

code: Diagnostic Implication (To Be Determined Codes#diagnostic-implication)

subject: Patient/ExamplePatient

effective: 2016

issued: Sep 6, 2016 5:00:00 AM

performer: Organization/ExampleLab "Some lab"

derivedFrom: 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 family, member 9, deficiency of (medgen#C1970173)

Entry 9 - Full URL = http://example.org/fhir/Observation/complex-variant-1a

Resource Observation:

Generated Narrative

Resource "complex-variant-1a"

Profile: Variant

status: FINAL

category: Laboratory (Observation Category Codes#laboratory)

code: Genetic variant assessment (LOINC#69548-6)

subject: Patient/ExamplePatient

effective: 2016

issued: Sep 6, 2016 5:00:00 AM

performer: Organization/ExampleLab "Some lab"

value: Present (LOINC#LA9633-4)

specimen: Specimen/ExampleSpecimen

hasMember:

Components

-CodeValue[x]
*Complex variant type (LOINC#81263-6)Haplotype (LOINC#LA26218-0)

Entry 10 - Full URL = http://example.org/fhir/Observation/complex-dis-path-1a

Resource Observation:

Generated Narrative

Resource "complex-dis-path-1a"

Profile: Diagnostic Implication

status: FINAL

category: Laboratory (Observation Category Codes#laboratory)

code: Diagnostic Implication (To Be Determined Codes#diagnostic-implication)

subject: Patient/ExamplePatient

effective: 2016

issued: Sep 6, 2016 5:00:00 AM

performer: Organization/ExampleLab "Some lab"

derivedFrom: 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 - Full URL = http://example.org/fhir/Observation/complex-component-D-1a

Resource Observation:

Generated Narrative

Resource "complex-component-D-1a"

Profile: Variant

status: FINAL

category: Laboratory (Observation Category Codes#laboratory)

code: Genetic variant assessment (LOINC#69548-6)

subject: Patient/ExamplePatient

effective: 2016

issued: Sep 6, 2016 5:00:00 AM

performer: Organization/ExampleLab "Some lab"

value: Present (LOINC#LA9633-4)

specimen: Specimen/ExampleSpecimen

component

code: Discrete genetic variant (LOINC#81252-9)

value: NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys) (clinvar#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: c.886C>T (Human Genome Variation Society nomenclature[15.11]#c.886C>T)

component

code: Amino acid change (pHGVS) (LOINC#48005-3)

value: p.Arg296Cys (Human Genome Variation Society nomenclature[15.11]#p.Arg296Cys)

component

code: DNA Change Type (LOINC#48019-4)

value: Substitution (LOINC#LA6690-7)

component

code: Amino acid change [Type] (LOINC#48006-1)

value: Missense (LOINC#LA6698-0)

Entry 12 - Full URL = http://example.org/fhir/Observation/complex-component-E-1a

Resource Observation:

Generated Narrative

Resource "complex-component-E-1a"

Profile: Variant

status: FINAL

category: Laboratory (Observation Category Codes#laboratory)

code: Genetic variant assessment (LOINC#69548-6)

subject: Patient/ExamplePatient

effective: 2016

issued: Sep 6, 2016 5:00:00 AM

performer: Organization/ExampleLab "Some lab"

value: Present (LOINC#LA9633-4)

specimen: Specimen/ExampleSpecimen

component

code: Discrete genetic variant (LOINC#81252-9)

value: NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr) (clinvar[???]#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: c.1457G>C (Human Genome Variation Society nomenclature[15.11]#c.1457G>C)

Entry 13 - Full URL = http://example.org/fhir/Observation/pharmPanel-1a

Resource Observation:

Generated Narrative

Resource "pharmPanel-1a"

Recommended Action: Task/usage-1a

status: FINAL

category: Laboratory (Observation Category Codes#laboratory)

code: Panel (ncimeta.nci.nih.gov#C43359)

subject: Patient/ExamplePatient

effective: 2016

issued: Sep 6, 2016 5:00:00 AM

performer: Organization/ExampleLab "Some lab"

hasMember:

Entry 14 - Full URL = http://example.org/fhir/Observation/haplotype-1a

Resource Observation:

Generated Narrative

Resource "haplotype-1a"

Profile: Haplotype

status: FINAL

category: Laboratory (Observation Category Codes#laboratory)

code: Haplotype name (LOINC#84414-2)

subject: Patient/ExamplePatient

effective: 2016

issued: Sep 6, 2016 5:00:00 AM

performer: Organization/ExampleLab "Some lab"

value: *2 (hla#*2)

specimen: Specimen/ExampleSpecimen

derivedFrom: Observation/discrete-variant-1a

Entry 15 - Full URL = http://example.org/fhir/Observation/genotype-1a

Resource Observation:

Generated Narrative

Resource "genotype-1a"

Profile: Genotype

status: FINAL

category: Laboratory (Observation Category Codes#laboratory)

code: Genotype display name (LOINC#84413-4)

subject: Patient/ExamplePatient

effective: 2016

issued: Sep 6, 2016 5:00:00 AM

performer: Organization/ExampleLab "Some lab"

value: CYP2C9 *2/*5 (www.pharmvar.org#CYP2C9 *2/*5)

specimen: Specimen/ExampleSpecimen

derivedFrom: Observation/haplotype-1a

component

code: Gene studied [ID] (LOINC#48018-6)

value: CYP2C9 (geneId#2623)

component

code: Gene studied [ID] (LOINC#48018-6)

value: VKORC1 (geneId#23663)

Entry 16 - Full URL = http://example.org/fhir/Observation/metab-1a

Resource Observation:

Generated Narrative

Resource "metab-1a"

Profile: Therapeutic Implication

status: FINAL

category: Laboratory (Observation Category Codes#laboratory)

code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)

subject: Patient/ExamplePatient

effective: 2016

issued: Sep 6, 2016 5:00:00 AM

performer: Organization/ExampleLab "Some lab"

derivedFrom: Observation/genotype-1a

component

code: Medication assessed [ID] (LOINC#51963-7)

value: Warfarin (RxNorm#11289)

component

code: Predicted Therapeutic Implication (To Be Determined Codes#predicted-therapeutic-implication)

value: Rapid metabolizer (LOINC#LA25390-8)

Entry 17 - Full URL = http://example.org/fhir/Observation/efficacy-1a

Resource Observation:

Generated Narrative

Resource "efficacy-1a"

Profile: Therapeutic Implication

status: FINAL

category: Laboratory (Observation Category Codes#laboratory)

code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)

subject: Patient/ExamplePatient

effective: 2016

issued: Sep 6, 2016 5:00:00 AM

performer: Organization/ExampleLab "Some lab"

derivedFrom: Observation/genotype-1a

component

code: Predicted Therapeutic Implication (To Be Determined Codes#predicted-therapeutic-implication)

value: Resistant (LOINC#LA6676-6)

component

code: Medication assessed [ID] (LOINC#51963-7)

value: Warfarin (RxNorm#11289)

Entry 18 - Full URL = http://example.org/fhir/Observation/highrisk-1a

Resource Observation:

Generated Narrative

Resource "highrisk-1a"

Profile: Therapeutic Implication

status: FINAL

category: Laboratory (Observation Category Codes#laboratory)

code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)

subject: Patient/ExamplePatient

effective: 2016

issued: Sep 6, 2016 5:00:00 AM

performer: Organization/ExampleLab "Some lab"

derivedFrom: Observation/genotype-1a

component

code: Predicted Therapeutic Implication (To Be Determined Codes#predicted-therapeutic-implication)

value: Low risk (LOINC#LA19542-2)

component

code: Medication assessed [ID] (LOINC#51963-7)

value: Warfarin (RxNorm#11289)

Entry 19 - Full URL = http://example.org/fhir/Task/usage-1a

Resource Task:

Generated Narrative

Resource "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: Patient/ExamplePatient

requester: Organization/ExampleLab "Some lab"

reasonReference: Observation/metab-1a