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-oncology-diagnostic

Bundle bundle-oncology-diagnostic of type transaction

Entry 1 - Full URL = urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d

Request:

POST Patient

Resource Patient:

Carrot John Mr Male, DoB: 1962-12-31 ( id: 1007)

Entry 2 - Full URL = urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef

Request:

POST Practitioner

Resource Practitioner:

Generated Narrative

Resource "Inline-Instance-for-oncology-diagnostic-2"

identifier: id: 4654765876

name: Akerman Philip Prof

address: Castro Valley CA

Entry 3 - Full URL = urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d

Request:

POST Specimen

Resource Specimen:

Generated Narrative

Resource "Inline-Instance-for-oncology-diagnostic-3"

identifier: id: 076e1948-2217-11e9-94d8-12e241dc1f66

status: AVAILABLE

subject: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d

Collections

-Collector
*urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef

Entry 4 - Full URL = urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f

Request:

POST Observation

Resource Observation:

Generated Narrative

Resource "Inline-Instance-for-oncology-diagnostic-4"

status: FINAL

code: Tumor Mutational Burden ()

subject: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d

performer: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef

value: 25 Mutations/Megabase (Details: UCUM code 1/1000000{Base} = '1/1000000{Base}')

specimen: urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d

Entry 5 - Full URL = urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d

Request:

POST Observation

Resource Observation:

Generated Narrative

Resource "Inline-Instance-for-oncology-diagnostic-5"

Profile: Variant

status: FINAL

category: Laboratory (Observation Category Codes#laboratory)

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

subject: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d

performer: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef

value: Present (LOINC#LA9633-4)

method: Sequencing (LOINC#LA26398-0)

specimen: urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d

component

code: Human reference sequence assembly version (LOINC#62374-4)

value: GRCh37 (LOINC#LA14029-5)

component

code: Genomic DNA change (gHGVS) (LOINC#81290-9)

value: NC_000007.13:g.140453136A>T (Human Genome Variation Society nomenclature#NC_000007.13:g.140453136A>T)

component

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

value: Clinvar ID 13961 (clinvar#13961)

component

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

value: p.Val600Glu (Human Genome Variation Society nomenclature#p.Val600Glu)

component

code: Amino acid change type (LOINC#48006-1)

value: Missense (LOINC#LA6698-0)

component

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

value: BRAF (geneId#HGNC:1097)

Entry 6 - Full URL = urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524

Request:

POST Observation

Resource Observation:

Generated Narrative

Resource "Inline-Instance-for-oncology-diagnostic-6"

Profile: Diagnostic Implication

Genomics Artifact:

Exception generating Narrative: type org.hl7.fhir.r5.model.RelatedArtifact not handled - should not be here

Entry 7 - Full URL = urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5

Request:

POST DiagnosticReport

Resource DiagnosticReport:

Genetic analysis report (Genetics)

SubjectNot done yet

Report Details

CodeValue