This page is part of the Genetic Reporting Implementation Guide (v0.1.0: STU 1 Ballot 1) based on FHIR v3.3.0. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
Format(s):
Narrative view
Bundle diagnosticreport-pgxexample of type collection
Entry 1 - Full URL = http://hl7.org/fhir/uv/genomics-reporting/DiagnosticReport/pgx-report
Resource DiagnosticReport:
to do (to do) to do
Unable to get Patient Details Report Details
to do to do to do to do to do to doCoded Diagnoses :
Entry 2 - Full URL = http://hl7.org/fhir/uv/genomics-reporting/Patient/patient
Resource Patient:
This would contain patient identifiers, demographics, etc.
Entry 3 - Full URL = http://hl7.org/fhir/uv/genomics-reporting/Specimen/specimen
Resource Specimen:
TODO
Entry 4 - Full URL = http://hl7.org/fhir/uv/genomics-reporting/Organization/lab
Resource Organization:
TODO
Entry 5 - Full URL = http://hl7.org/fhir/uv/genomics-reporting/ServiceRequest/pgx-request
Resource ServiceRequest:
TODO
Entry 6 - Full URL = http://hl7.org/fhir/uv/genomics-reporting/Observation/med-impact-pgx-example
Resource Observation:
Generated Narrative with Details
text:
status: FINAL
category: Laboratory (Details : {http://hl7.org/fhir/observation-category code 'laboratory' = 'Laboratory)
code: Genetic variation's effect on drug metabolism (Details : {LOINC code '53040-2' = 'Genetic variation's effect on drug metabolism', given as 'Genetic variation's effect on drug metabolism'})
subject: This would contain patient identifiers, demographics, etc.Generated Summary:
effective: 01/01/2018
issued: 06/03/2018 12:00:00 AM
performer: TODOGenerated Summary: name: Some lab
value: Rapid metabolizer (Details : {LOINC code 'LA25390-8' = 'LA25390-8', given as 'Rapid metabolizer'})
Components
- Code Value[x] Code Value[x] Code Value[x] * Medication assessed (Details : {LOINC code '51963-7' = 'Medication assessed [ID]', given as 'Medication assessed'}) 6-mercaptopurine (Details : {RxNorm code '103' = 'mercaptopurine', given as '6-mercaptopurine'}) Medication assessed (Details : {LOINC code '51963-7' = 'Medication assessed [ID]', given as 'Medication assessed'}) 6-mercaptopurine (Details : {RxNorm code '103' = 'mercaptopurine', given as '6-mercaptopurine'}) Medication assessed (Details : {LOINC code '51963-7' = 'Medication assessed [ID]', given as 'Medication assessed'}) 6-mercaptopurine (Details : {RxNorm code '103' = 'mercaptopurine', given as '6-mercaptopurine'})
Entry 7 - Full URL = http://hl7.org/fhir/uv/genomics-reporting/Observation/genotype-pgx-example
Resource Observation:
Generated Narrative with Details
text:
status: FINAL
category: Laboratory (Details : {http://hl7.org/fhir/observation-category code 'laboratory' = 'Laboratory)
code: genotype display name (Details : {LOINC code '84413-4' = 'Genotype display name', given as 'genotype display name'})
effective: 01/01/2018
issued: 06/03/2018 12:00:00 AM
value: *4/*35B
specimen: TODOGenerated Summary:
derivedFrom:
- Generated Summary: Laboratory; Haplotype Name; effective: 01/01/2018; issued: 06/03/2018 12:00:00 AM; value: *35B
- Generated Summary: Laboratory; Haplotype Name; effective: 01/01/2018; issued: 06/03/2018 12:00:00 AM; value: *4
Components
- Code Value[x] Code Value[x] Code Value[x] Code Value[x] * Gene studied ID (Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'}) CYP2C9 (Details : {http://www.genenames.org code '2623' = '2623', given as 'CYP2C9'}) Gene studied ID (Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'}) CYP2C9 (Details : {http://www.genenames.org code '2623' = '2623', given as 'CYP2C9'}) Gene studied ID (Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'}) CYP2C9 (Details : {http://www.genenames.org code '2623' = '2623', given as 'CYP2C9'}) Gene studied ID (Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'}) CYP2C9 (Details : {http://www.genenames.org code '2623' = '2623', given as 'CYP2C9'})
Entry 8 - Full URL = http://hl7.org/fhir/uv/genomics-reporting/Observation/haplotype-1-pgx-example
Resource Observation:
Generated Narrative with Details
text:
status: FINAL
category: Laboratory (Details : {http://hl7.org/fhir/observation-category code 'laboratory' = 'Laboratory)
code: Haplotype Name (Details : {LOINC code '84414-2' = 'Haplotype name', given as 'Haplotype Name'})
effective: 01/01/2018
issued: 06/03/2018 12:00:00 AM
value: *35B
specimen: TODOGenerated Summary:
Components
- Code Value[x] Code Value[x] Code Value[x] Code Value[x] * Gene studied ID (Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'}) CYP2C9 (Details : {http://www.genenames.org code '2623' = '2623', given as 'CYP2C9'}) Gene studied ID (Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'}) CYP2C9 (Details : {http://www.genenames.org code '2623' = '2623', given as 'CYP2C9'}) Gene studied ID (Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'}) CYP2C9 (Details : {http://www.genenames.org code '2623' = '2623', given as 'CYP2C9'}) Gene studied ID (Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'}) CYP2C9 (Details : {http://www.genenames.org code '2623' = '2623', given as 'CYP2C9'})
Entry 9 - Full URL = http://hl7.org/fhir/uv/genomics-reporting/Observation/haplotype-2-pgx-example
Resource Observation:
Generated Narrative with Details
text:
status: FINAL
category: Laboratory (Details : {http://hl7.org/fhir/observation-category code 'laboratory' = 'Laboratory)
code: Haplotype Name (Details : {LOINC code '84414-2' = 'Haplotype name', given as 'Haplotype Name'})
effective: 01/01/2018
issued: 06/03/2018 12:00:00 AM
value: *4
specimen: TODOGenerated Summary:
Components
- Code Value[x] Code Value[x] Code Value[x] Code Value[x] * Gene studied ID (Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'}) CYP2C9 (Details : {http://www.genenames.org code '2623' = '2623', given as 'CYP2C9'}) Gene studied ID (Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'}) CYP2C9 (Details : {http://www.genenames.org code '2623' = '2623', given as 'CYP2C9'}) Gene studied ID (Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'}) CYP2C9 (Details : {http://www.genenames.org code '2623' = '2623', given as 'CYP2C9'}) Gene studied ID (Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'}) CYP2C9 (Details : {http://www.genenames.org code '2623' = '2623', given as 'CYP2C9'})
Entry 10 - Full URL = http://hl7.org/fhir/uv/genomics-reporting/Observation/variant-1-pgx-example
Resource Observation:
Generated Narrative with Details
text:
status: FINAL
category: Laboratory (Details : {http://hl7.org/fhir/observation-category code 'laboratory' = 'Laboratory)
code: Genetic variant assessment (Details : {LOINC code 'TBD-Described' = 'TBD-Described', given as 'Genetic variant assessment'})
effective: 01/01/2018
issued: 06/03/2018 12:00:00 AM
value: Present (Details : {LOINC code 'LA9633-4' = 'LA9633-4', given as 'Present'})
specimen: TODOGenerated Summary:
derivedFrom: Generated Summary: DNA; 0
component
code: Gene studied ID (Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'})
value: CYP2C9 (Details : {http://www.genenames.org code '2623' = '2623', given as 'CYP2C9'})
component
code: Genomic reference sequence ID (Details : {LOINC code '48013-7' = 'Genomic reference sequence [ID]', given as 'Genomic reference sequence ID'})
value: NG_007726.3 (Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NG_007726.3' = 'NG_007726.3)
component
code: dbSNP ID (Details : {LOINC code '81255-2' = 'dbSNP [ID]', given as 'dbSNP ID'})
value: rs12345 (Details : {https://www.ncbi.nlm.nih.gov/SNP/ code 'rs12345' = 'rs12345)
component
code: Genomic Ref allele (Details : {LOINC code '69547-8' = 'Genomic ref allele [ID]', given as 'Genomic Ref allele'})
value: T
component
code: Genomic Alt allele (Details : {LOINC code '69551-0' = 'Genomic alt allele [ID]', given as 'Genomic Alt allele'})
value: G
component
code: Genomic Allele start-end (Details : {LOINC code '81254-5' = 'Genomic allele start-end', given as 'Genomic Allele start-end'})
value: 55227976-55227977
Entry 11 - Full URL = http://hl7.org/fhir/uv/genomics-reporting/Observation/variant-2-pgx-example
Resource Observation:
Generated Narrative with Details
text:
status: FINAL
category: Laboratory (Details : {http://hl7.org/fhir/observation-category code 'laboratory' = 'Laboratory)
code: Genetic variant assessment (Details : {LOINC code 'TBD-Described' = 'TBD-Described', given as 'Genetic variant assessment'})
effective: 01/01/2018
issued: 06/03/2018 12:00:00 AM
value: Present (Details : {LOINC code 'LA9633-4' = 'LA9633-4', given as 'Present'})
specimen: TODOGenerated Summary:
derivedFrom: Generated Summary: DNA; 0
component
code: Gene studied ID (Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'})
value: CYP2C9 (Details : {http://www.genenames.org code '2623' = '2623', given as 'CYP2C9'})
component
code: Genomic reference sequence ID (Details : {LOINC code '48013-7' = 'Genomic reference sequence [ID]', given as 'Genomic reference sequence ID'})
value: NG_007726.3 (Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NG_007726.3' = 'NG_007726.3)
component
code: dbSNP ID (Details : {LOINC code '81255-2' = 'dbSNP [ID]', given as 'dbSNP ID'})
value: rs233455 (Details : {https://www.ncbi.nlm.nih.gov/SNP/ code 'rs233455' = 'rs233455)
component
code: Genomic Ref allele (Details : {LOINC code '69547-8' = 'Genomic ref allele [ID]', given as 'Genomic Ref allele'})
value: T
component
code: Genomic Alt allele (Details : {LOINC code '69551-0' = 'Genomic alt allele [ID]', given as 'Genomic Alt allele'})
value: G
component
code: Genomic Allele start-end (Details : {LOINC code '81254-5' = 'Genomic allele start-end', given as 'Genomic Allele start-end'})
value: 55227978-55227979
Entry 12 - Full URL = http://hl7.org/fhir/uv/genomics-reporting/Sequence/sequence-1-pgx-example
Resource Sequence:
Generated Narrative with Details
text:
type: DNA
coordinateSystem: 0
ReferenceSeqs
- Orientation ReferenceSeqId WindowStart WindowEnd * SENSE NG-007726.3 (Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NG-007726.3' = 'NG-007726.3) 55227970 55227980
Entry 13 - Full URL = http://hl7.org/fhir/uv/genomics-reporting/Sequence/sequence-2-pgx-example
Resource Sequence:
Generated Narrative with Details
text:
type: DNA
coordinateSystem: 0
ReferenceSeqs
- Orientation ReferenceSeqId WindowStart WindowEnd * SENSE NG-007726.3 (Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NG-007726.3' = 'NG-007726.3) 55227970 55227980
Entry 14 - Full URL = http://hl7.org/fhir/uv/genomics-reporting/Task/med-usage-impact-task-pgx-example
Resource Task:
Generated Narrative with Details
text:
status: REQUESTED
intent: PROPOSAL
code: Any Increase does Recommendation Text from the provider (Details : {LOINC code 'LA26423-6' = 'LA26423-6', given as 'Increase dose'})
description: Any Increase does Recommendation Text from the provider
focus: Generated Summary: UNKNOWN; 6-mercaptopurine
for: This would contain patient identifiers, demographics, etc.Generated Summary:
reasonReference: Generated Summary: Laboratory; Genetic variation's effect on drug metabolism; effective: 01/01/2018; issued: 06/03/2018 12:00:00 AM; Rapid metabolizer
Entry 15 - Full URL = http://hl7.org/fhir/uv/genomics-reporting/MedicationStatement/current-med-example
Resource MedicationStatement:
Generated Narrative with Details
text:
status: UNKNOWN
medication: 6-mercaptopurine (Details : {RxNorm code '103' = 'mercaptopurine', given as '6-mercaptopurine'})
subject: This would contain patient identifiers, demographics, etc.Generated Summary:
© 2017+ HL7 International Clinical Genomics Work Group. Based on FHIR version (3.3.0-13671). IG generated on Wed, Apr 4, 2018 06:23+1000.
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