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-oncologyexamples-r4

Bundle bundle-oncologyexamples-r4 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

ResourcePractitioner "Inline-Instance-for-oncologyexamples-r4-2"

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:

Generated Narrative: Specimen

ResourceSpecimen "Inline-Instance-for-oncologyexamples-r4-3"

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

ResourceObservation "Inline-Instance-for-oncologyexamples-r4-4"

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: 2023-04-05

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

-CodeValue[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

ResourceObservation "Inline-Instance-for-oncologyexamples-r4-5"

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: 2023-04-05

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

-CodeValue[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

ResourceObservation "Inline-Instance-for-oncologyexamples-r4-6"

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: 2023-04-05

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

ResourceObservation "Inline-Instance-for-oncologyexamples-r4-7"

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: 2023-04-05

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

ResourceObservation "Inline-Instance-for-oncologyexamples-r4-8"

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: 2023-04-05

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

ResourceObservation "Inline-Instance-for-oncologyexamples-r4-9"

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: 2023-04-05

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: Associated phenotype (LOINC#81259-4)

value: Polycythemia vera (PV) ()

component

code: Medication assessed (LOINC#51963-7)

value: Ruxolitinib ()


Entry 10 - fullUrl = urn:uuid:1301943b-55db-4adf-8355-3635f7268a1b

Request:

POST Observation

Resource Observation:

Generated Narrative: Observation

ResourceObservation "Inline-Instance-for-oncologyexamples-r4-10"

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: 2023-04-05

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: Associated 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

ResourceObservation "Inline-Instance-for-oncologyexamples-r4-11"

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: 2023-04-05

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: Associated 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

ResourceObservation "Inline-Instance-for-oncologyexamples-r4-12"

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: 2023-04-05

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: Associated phenotype (LOINC#81259-4)

value: Polycythemia vera (PV) ()

component

code: Medication assessed (LOINC#51963-7)

value: TG02 ()


Entry 13 - fullUrl = urn:uuid:294f1401-e2eb-4df1-b6d2-09e1b7a6ecb6

Request:

POST Observation

Resource Observation:

Generated Narrative: Observation

ResourceObservation "Inline-Instance-for-oncologyexamples-r4-14"

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: 2023-04-05

performer: See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef

derivedFrom: See on this page: urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d

Components

-ExtensionCodeValue[x]
*Associated Therapy (To Be Determined Codes#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.


Entry 14 - fullUrl = urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5

Request:

POST DiagnosticReport

Resource DiagnosticReport:

Genetic analysis report (Genetics)

SubjectNot done yet

Report Details

CodeValueWhen For
Genetic variant assessmentPresent2023-04-05
Genetic variant assessmentPresent2023-04-05
Genetic variant assessmentPresent2023-04-05
Mutations/Megabase [# Ratio] in Tumor25 somatic variants per megabase of sequenced DNA2023-04-05
Microsatellite instability [Interpretation] in Cancer specimen QualitativeStable2023-04-05
Therapeutic Implication2023-04-05
Therapeutic Implication2023-04-05
Therapeutic Implication2023-04-05
Therapeutic Implication2023-04-05