Genomics Reporting Implementation Guide
3.0.0 - STU3
Genomics Reporting Implementation Guide
3.0.0 - STU3
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
Generated Narrative: Bundle bundle-oncologyexamples-r4
Bundle bundle-oncologyexamples-r4 of type transaction
Entry 1 - fullUrl = urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
Resource Patient:
Generated Narrative: Patient Inline-Instance-for-oncologyexamples-r4-1
Carrot John Mr Male, DoB: 1962-12-31 ( 1007)
Links:
- General Practitioner: Bundle: type = transaction
Request:
POST Patient
Entry 2 - fullUrl = urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
Resource Practitioner:
Generated Narrative: Practitioner Inline-Instance-for-oncologyexamples-r4-2
identifier: 4654765876
name: Akerman Philip Prof
address: Castro Valley CA
Request:
POST Practitioner
Entry 3 - fullUrl = urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d
Resource Specimen:
Generated Narrative: Specimen Inline-Instance-for-oncologyexamples-r4-3
identifier: 076e1948-2217-11e9-94d8-12e241dc1f66
status: Available
subject: Bundle: type = transaction
Collections
Collector Bundle: type = transaction
Request:
POST Specimen
Entry 4 - fullUrl = urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f
Resource Observation:
Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-4
status: Final
category: Laboratory, A characterization of a given biomarker observation., Genetics
code: Mutations/Megabase [# Ratio] in Tumor
subject: Bundle: type = transaction
effective: 2023-04-05
performer: Bundle: type = transaction
value: 25 somatic variants per megabase of sequenced DNA (Details: UCUM code1/1000000 = '1/1000000')
specimen: Bundle: type = transaction
Components
Code Value[x] A characterization of a given biomarker observation. molecular sequence adjacent category
Request:
POST Observation
Entry 5 - fullUrl = urn:uuid:64b91716-6431-41bd-8fd4-7ac99bebdee9
Resource Observation:
Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-5
status: Final
category: Laboratory, A characterization of a given biomarker observation., Genetics
code: Microsatellite instability [Interpretation] in Cancer specimen Qualitative
subject: Bundle: type = transaction
effective: 2023-04-05
performer: Bundle: type = transaction
value: Stable
specimen: Bundle: type = transaction
Components
Code Value[x] A characterization of a given biomarker observation. molecular sequence adjacent category
Request:
POST Observation
Entry 6 - fullUrl = urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d
Resource Observation:
Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-6
status: Final
category: Laboratory, Genetics
code: Genetic variant assessment
subject: Bundle: type = transaction
effective: 2023-04-05
performer: Bundle: type = transaction
value: Present
method: Sequencing
specimen: Bundle: type = transaction
component
code: Genomic DNA change (gHGVS)
value: NC_000009.12:g.5073770G>T
component
code: Amino acid change (pHGVS)
value: NP_004963.1:p.Val617Phe
component
code: Genomic source class
value: Germline
component
code: Gene studied ID
value: JAK2
Request:
POST Observation
Entry 7 - fullUrl = urn:uuid:772de7d7-e1bd-4183-bdb5-cea8eda317cd
Resource Observation:
Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-7
status: Final
category: Laboratory, Genetics
code: Genetic variant assessment
subject: Bundle: type = transaction
effective: 2023-04-05
performer: Bundle: type = transaction
value: Present
method: Sequencing
specimen: Bundle: type = transaction
component
code: Genomic DNA change (gHGVS)
value: NC_000004.11:g.55972974T>A
component
code: Amino acid change (pHGVS)
value: NP_002244.1:p.Gln472His
component
code: Genomic source class
value: Germline
component
code: Gene studied ID
value: KDR
Request:
POST Observation
Entry 8 - fullUrl = urn:uuid:b33eb7ec-d83e-49d2-b0f3-729d024ebe01
Resource Observation:
Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-8
status: Final
category: Laboratory, Genetics
code: Genetic variant assessment
subject: Bundle: type = transaction
effective: 2023-04-05
performer: Bundle: type = transaction
value: Present
method: Sequencing
specimen: Bundle: type = transaction
component
code: Genomic DNA change (gHGVS)
value: NC_000002.12:g.211713666_211713668del
component
code: Genomic source class
value: Germline
component
code: Gene studied ID
value: ERBB4
Request:
POST Observation
Entry 9 - fullUrl = urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524
Resource Observation:
Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-9
status: Final
category: Laboratory, Genetics
code: Therapeutic Implication
subject: Bundle: type = transaction
effective: 2023-04-05
performer: Bundle: type = transaction
method: Computational analysis
specimen: Bundle: type = transaction
derivedFrom: Bundle: type = transaction
component
code: Therapeutic Implication
value: Responsive
component
code: Level of Evidence
value: Very strong evidence pathogenic
component
code: Associated phenotype
value: Polycythemia vera (PV)
component
code: Medication assessed
value: Ruxolitinib
Request:
POST Observation
Entry 10 - fullUrl = urn:uuid:1301943b-55db-4adf-8355-3635f7268a1b
Resource Observation:
Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-10
status: Final
category: Laboratory, Genetics
code: Therapeutic Implication
subject: Bundle: type = transaction
effective: 2023-04-05
performer: Bundle: type = transaction
method: Computational analysis
specimen: Bundle: type = transaction
derivedFrom: Bundle: type = transaction
component
code: Therapeutic Implication
value: Responsive
component
code: Level of Evidence
value: Very strong evidence pathogenic
component
code: Associated phenotype
value: Polycythemia vera (PV)
component
code: Medication assessed
value: AT9283
Request:
POST Observation
Entry 11 - fullUrl = urn:uuid:05713d1c-0df5-46d5-a5a9-2085eef56c20
Resource Observation:
Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-11
status: Final
category: Laboratory, Genetics
code: Therapeutic Implication
subject: Bundle: type = transaction
effective: 2023-04-05
performer: Bundle: type = transaction
method: Computational analysis
specimen: Bundle: type = transaction
derivedFrom: Bundle: type = transaction
component
code: Therapeutic Implication
value: Responsive
component
code: Level of Evidence
value: Very strong evidence pathogenic
component
code: Associated phenotype
value: Polycythemia vera (PV)
component
code: Medication assessed
value: SNX-5422
Request:
POST Observation
Entry 12 - fullUrl = urn:uuid:294f1401-e2eb-4df1-b6d2-09e1b7a6eca4
Resource Observation:
Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-12
status: Final
category: Laboratory, Genetics
code: Therapeutic Implication
subject: Bundle: type = transaction
effective: 2023-04-05
performer: Bundle: type = transaction
method: Computational analysis
specimen: Bundle: type = transaction
derivedFrom: Bundle: type = transaction
component
code: Therapeutic Implication
value: Responsive
component
code: Level of Evidence
value: Very strong evidence pathogenic
component
code: Associated phenotype
value: Polycythemia vera (PV)
component
code: Medication assessed
value: TG02
Request:
POST Observation
Entry 13 - fullUrl = urn:uuid:294f1401-e2eb-4df1-b6d2-09e1b7a6ecb6
Resource Observation:
Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-14
status: Final
category: Laboratory, Genetics
code: Therapeutic Implication
subject: Bundle: type = transaction
effective: 2023-04-05
performer: Bundle: type = transaction
derivedFrom: Bundle: type = transaction
Components
Extension Code Value[x] Associated Therapy Ruxolitinib Generated Narrative: PlanDefinition #PlanDefRuxolitinib
name: RuxolitinibPlan
status: Draft
description:
This is not a fully defined resource, just here as a place holder to show how a PlanDefinition could be packaged.
Request:
POST Observation
Entry 14 - fullUrl = urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5
Resource DiagnosticReport:
Generated Narrative: DiagnosticReport Inline-Instance-for-oncologyexamples-r4-13
Genetic analysis report (Genetics)
Subject Not done yet Performer Bundle: type = transaction Report Details
Code Value
Request:
POST DiagnosticReport
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-12-12
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