Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot
Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot
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
Bundle bundle-oncologyexamples-r4-withGrouping of type transaction
Entry 1 - fullUrl = urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
Request:
POST Patient
Resource Patient:
Anonymous Patient Male, DoB: 1962-12-31 ( 1007)
Entry 2 - fullUrl = urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
Request:
POST Practitioner
Resource Practitioner:
Generated Narrative: Practitioner
Resource Practitioner "Inline-Instance-for-oncologyexamples-r4-withGrouping-2"
identifier: 4654765876
name: Akerman Philip Prof
address: Castro Valley CA
Entry 3 - fullUrl = urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d
Request:
POST Specimen
Resource Specimen:
Resource Specimen "Inline-Instance-for-oncologyexamples-r4-withGrouping-3"
identifier: 076e1948-2217-11e9-94d8-12e241dc1f66
status: AVAILABLE
subject: See on this page: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
Collections
Collector See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
Entry 4 - fullUrl = urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncologyexamples-r4-withGrouping-4"
Profile: Molecular Biomarker
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), A characterization of a given biomarker observation. (To Be Determined Codes#biomarker-category), Genetics (diagnosticServiceSectionId#GE)
code: Mutations/Megabase [# Ratio] in Tumor (LOINC#94076-7)
subject: See on this page: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
effective: 2023-05-01
performer: See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
value: 25 somatic variants per megabase of sequenced DNA (Details: UCUM code 1/1000000 = '1/1000000')
specimen: See on this page: urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d
Components
Code Value[x] A characterization of a given biomarker observation. (To Be Determined Codes#biomarker-category) molecular sequence adjacent category (Molecular Biomarker Ontology Codes#molgen)
Entry 5 - fullUrl = urn:uuid:64b91716-6431-41bd-8fd4-7ac99bebdee9
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncologyexamples-r4-withGrouping-5"
Profile: Molecular Biomarker
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), A characterization of a given biomarker observation. (To Be Determined Codes#biomarker-category), Genetics (diagnosticServiceSectionId#GE)
code: Microsatellite instability [Interpretation] in Cancer specimen Qualitative (LOINC#81695-9)
subject: See on this page: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
effective: 2023-05-01
performer: See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
value: Stable (LOINC#LA14122-8)
specimen: See on this page: urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d
Components
Code Value[x] A characterization of a given biomarker observation. (To Be Determined Codes#biomarker-category) molecular sequence adjacent category (Molecular Biomarker Ontology Codes#molgen)
Entry 6 - fullUrl = urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncologyexamples-r4-withGrouping-6"
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: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
effective: 2023-05-01
performer: See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
specimen: See on this page: urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d
component
code: Genomic DNA change (gHGVS) (LOINC#81290-9)
value: NC_000009.12:g.5073770G>T (Human Genome Variation Society nomenclature#NC_000009.12:g.5073770G>T)
component
code: Amino acid change (pHGVS) (LOINC#48005-3)
value: NP_004963.1:p.Val617Phe (Human Genome Variation Society nomenclature#NP_004963.1:p.Val617Phe)
component
code: Genomic source class (LOINC#48002-0)
value: Germline (LOINC#LA6683-2)
component
code: Gene studied ID (LOINC#48018-6)
value: JAK2 (HUGO Gene Nomenclature Committee Genes)
Entry 7 - fullUrl = urn:uuid:772de7d7-e1bd-4183-bdb5-cea8eda317cd
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncologyexamples-r4-withGrouping-7"
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: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
effective: 2023-05-01
performer: See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
specimen: See on this page: urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d
component
code: Genomic DNA change (gHGVS) (LOINC#81290-9)
value: NC_000004.11:g.55972974T>A (Human Genome Variation Society nomenclature#NC_000004.11:g.55972974T>A)
component
code: Amino acid change (pHGVS) (LOINC#48005-3)
value: NP_002244.1:p.Gln472His (Human Genome Variation Society nomenclature#NP_002244.1:p.Gln472His)
component
code: Genomic source class (LOINC#48002-0)
value: Germline (LOINC#LA6683-2)
component
code: Gene studied ID (LOINC#48018-6)
value: KDR (HUGO Gene Nomenclature Committee Genes)
Entry 8 - fullUrl = urn:uuid:b33eb7ec-d83e-49d2-b0f3-729d024ebe01
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncologyexamples-r4-withGrouping-8"
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: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
effective: 2023-05-01
performer: See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
specimen: See on this page: urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d
component
code: Genomic DNA change (gHGVS) (LOINC#81290-9)
value: NC_000002.12:g.211713666_211713668del (Human Genome Variation Society nomenclature#NC_000002.12:g.211713666_211713668del)
component
code: Genomic source class (LOINC#48002-0)
value: Germline (LOINC#LA6683-2)
component
code: Gene studied ID (LOINC#48018-6)
value: ERBB4 (HUGO Gene Nomenclature Committee Genes)
Entry 9 - fullUrl = urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncologyexamples-r4-withGrouping-9"
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: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
effective: 2023-05-01
performer: See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
method: Computational analysis (LOINC#LA26811-2)
specimen: See on this page: urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d
derivedFrom: See on this page: urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d
component
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
value: Responsive (LOINC#LA6677-4)
component
code: Level of evidence (LOINC#93044-6)
value: Very strong evidence pathogenic (LOINC#LA30200-2)
component
code: Prob assoc phenotype (LOINC#81259-4)
value: Polycythemia vera (PV) ()
component
Medication Assessed reference to a FHIR resource:
code: Ruxolitinib (RxNorm#1193326)
status: ACTIVE
code: Medication assessed (LOINC#51963-7)
value: Ruxolitinib (RxNorm#1193326)
Generated Narrative: MedicationKnowledge #Inline-MedicationKnowledgeRuxolitinib
code: Ruxolitinib (RxNorm#1193326)
status: ACTIVE
Entry 10 - fullUrl = urn:uuid:1301943b-55db-4adf-8355-3635f7268a1b
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncologyexamples-r4-withGrouping-10"
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: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
effective: 2023-05-01
performer: See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
method: Computational analysis (LOINC#LA26811-2)
specimen: See on this page: urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d
derivedFrom: See on this page: urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d
component
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
value: Responsive (LOINC#LA6677-4)
component
code: Level of Evidence (LOINC#93044-6)
value: Very strong evidence pathogenic (LOINC#LA30200-2)
component
code: Prob assoc phenotype (LOINC#81259-4)
value: Polycythemia vera (PV) ()
component
code: Medication assessed (LOINC#51963-7)
value: AT9283 ()
Entry 11 - fullUrl = urn:uuid:05713d1c-0df5-46d5-a5a9-2085eef56c20
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncologyexamples-r4-withGrouping-11"
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: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
effective: 2023-05-01
performer: See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
method: Computational analysis (LOINC#LA26811-2)
specimen: See on this page: urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d
derivedFrom: See on this page: urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d
component
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
value: Responsive (LOINC#LA6677-4)
component
code: Level of Evidence (LOINC#93044-6)
value: Very strong evidence pathogenic (LOINC#LA30200-2)
component
code: Prob assoc phenotype (LOINC#81259-4)
value: Polycythemia vera (PV) ()
component
code: Medication assessed (LOINC#51963-7)
value: SNX-5422 ()
Entry 12 - fullUrl = urn:uuid:294f1401-e2eb-4df1-b6d2-09e1b7a6eca4
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncologyexamples-r4-withGrouping-12"
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: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
effective: 2023-05-01
performer: See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
method: Computational analysis (LOINC#LA26811-2)
specimen: See on this page: urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d
derivedFrom: See on this page: urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d
component
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
value: Responsive (LOINC#LA6677-4)
component
code: Level of Evidence (LOINC#93044-6)
value: Very strong evidence pathogenic (LOINC#LA30200-2)
component
code: Prob assoc phenotype (LOINC#81259-4)
value: Polycythemia vera (PV) ()
component
code: Medication assessed (LOINC#51963-7)
value: TG02 ()
Entry 13 - fullUrl = urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12f
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncologyexamples-r4-withGrouping-13"
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Group (NCI Thesaurus#C43359)
subject: See on this page: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
effective: 2023-05-01
performer: See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
hasMember:
- See on this page: urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d: SNV analysis for JAK2 variant
- See on this page: urn:uuid:772de7d7-e1bd-4183-bdb5-cea8eda317cd: SNV analysis for KDR variant
- See on this page: urn:uuid:b33eb7ec-d83e-49d2-b0f3-729d024ebe01: SNV analysis for ERBB4 variant
- See on this page: urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f: TMB value analysis
- See on this page: urn:uuid:64b91716-6431-41bd-8fd4-7ac99bebdee9: MSI status analysis
Entry 14 - fullUrl = urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncologyexamples-r4-withGrouping-14"
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Group (NCI Thesaurus#C43359)
subject: See on this page: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
effective: 2023-05-01
performer: See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
hasMember:
- See on this page: urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524: Therapy match result 1
- See on this page: urn:uuid:1301943b-55db-4adf-8355-3635f7268a1b: Therapy match result 2
- See on this page: urn:uuid:05713d1c-0df5-46d5-a5a9-2085eef56c20: Therapy match result 3
- See on this page: urn:uuid:294f1401-e2eb-4df1-b6d2-09e1b7a6eca4: Therapy match result 4
Entry 15 - fullUrl = urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5
Request:
POST DiagnosticReport
Resource DiagnosticReport:
Genetic analysis report (Genetics)
Subject Not done yet Report Details
Code Value When For Group 2023-05-01 Genetic variant assessment Present 2023-05-01 Genetic variant assessment Present 2023-05-01 Genetic variant assessment Present 2023-05-01 Mutations/Megabase [# Ratio] in Tumor 25 somatic variants per megabase of sequenced DNA 2023-05-01 Microsatellite instability [Interpretation] in Cancer specimen Qualitative Stable 2023-05-01 Group 2023-05-01 Therapeutic Implication 2023-05-01 Therapeutic Implication 2023-05-01 Therapeutic Implication 2023-05-01 Therapeutic Implication 2023-05-01
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.1-SNAPSHOT based on FHIR 4.0.1. Generated 2024-04-09
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