ct-xG-bundle - GenomeX Data Exchange FHIR IG v0.2.0

GenomeX Data Exchange FHIR IG, published by MITRE. This guide is not an authorized publication; it is the continuous build for version 0.2.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/CodeX-HL7-FHIR-Accelerator/GenomeX-DataExchange/ and changes regularly. See the Directory of published versions

Example Bundle: ct-xG-bundle

Generated Narrative: Bundle ct-xG-bundle

Bundle ct-xG-bundle of type transaction

Entry 1 - fullUrl = urn:uuid:43e09316-c616-4b23-81df-e546d2b95c41

Resource Patient:

Generated Narrative: Patient ct-cancer-patient-C3PO

C3P0 Test Male, DoB: 1950-01-01 ( Medical Record Number: 123456789)
Other Id: Patient external identifier/0754aeb3-dd9c-458a-9b06-2da7d62ejh7k (use: usual, )
Contact Detail 987 Main St Anytown 12345 US

Request:

POST Patient

Entry 2 - fullUrl = urn:uuid:d90e9857-574a-4fc6-98c6-6d61d6e024cd

Resource DiagnosticReport:

Generated Narrative: DiagnosticReport gx-genomics-report-C3PO

Genetic analysis report (Genetics, DNA, Genetics)
Subject Not done yet
When For 2022-02-15 19:28:58+0500
Performer Bundle: type = transaction
Identifiers Accession ID/TL-22-D3MTCAU4 Pipeline Version/3.9.3 Placer Identifier/d6eeedd1-92d3-45b9-bf33-6401e804425f
Report Details
Code Value

Request:

POST DiagnosticReport

Entry 3 - fullUrl = urn:uuid:150a3549-3114-4dea-bd1d-e24c036b2934

Resource ServiceRequest:

Generated Narrative: ServiceRequest ct-xG-ServiceRequest

identifier: Filler Identifier/22hosvx
requisition: Accession ID/TL-24-D3MTCAH8
status: Completed
intent: Order
code: No display for ServiceRequest.code (concept: CancerNext)
subject: Bundle: type = transaction
requester: Bundle: type = transaction

Request:

POST ServiceRequest

Entry 4 - fullUrl = urn:uuid:775af36d-3c44-4647-b120-5d5a6b490a1e

Resource Practitioner:

Generated Narrative: Practitioner ct-xG-practitioner

identifier: United States National Provider Identifier/9988776345
name: Luke Skywalker
gender: Male
address: 600 Chicago Drive Everywhere TX 16789 US (work)
Qualifications
- Code
* Doctor of Medicine

Request:

POST Practitioner

Entry 5 - fullUrl = urn:uuid:eb4e82bd-2162-4b01-bfd7-19bac0828abe

Resource PractitionerRole:

Generated Narrative: PractitionerRole ct-genomic-practitionerRole

practitioner: Bundle: type = transaction
organization: Bundle: type = transaction

Request:

POST PractitionerRole

Entry 6 - fullUrl = urn:uuid:19fc189e-7287-4a4b-bf1c-1ab222bbfe3d

Resource Organization:

Generated Narrative: Organization ct-ordering-organization

identifier: http://example.emr.com/organization/12345
active: true
name: TriHealth Cancer Institute - Cincinnati
Contacts
- Name Address
* 1234 Brooks River Cincinnati OH 11111-1111 (work)
* Steve Jobs
partOf: Identifier: Oncology Group

Request:

POST Organization

Entry 7 - fullUrl = urn:uuid:aeea668a-a035-4963-9e56-249d735916a5

Resource Organization:

Generated Narrative: Organization ct-organization-tempus-inc

identifier: Clinical Laboratory Improvement Amendments/14D2114007
active: true
name: Tempus Labs, Inc
Contacts
- Name Telecom Address
* support@tempus.com 600 W Chicago Avenue, Ste 510 Chicago IL 60654 USA
* Nike Beaubier, M,FCAP,MGAP

Request:

POST Organization

Entry 8 - fullUrl = urn:uuid:26242dd9-b9c7-40cb-838c-7f5007fde86f

Resource Practitioner:

Generated Narrative: Practitioner Inline-Instance-for-ct-xG-bundle-1

Last updated: 2023-10-02 07:03:06+0000
Profile: http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner
identifier: http://www.acme.com/identifiers/patient/123456
name: Test Pathologist

Request:

POST Practitioner

Entry 9 - fullUrl = urn:uuid:1a9edfe1-1620-4882-a81c-30c2f254f34f

Resource Specimen:

Generated Narrative: Specimen Inline-Instance-for-ct-xG-bundle-2

status: Available
type: Whole blood
subject: Bundle: type = transaction
receivedTime: 2022-02-11 11:00:00+0500
Collections
- Collected[x]
* 2022-02-06 05:00:00+0500

Request:

POST Specimen

Entry 10 - fullUrl = urn:uuid:82a8b9db-a68e-4e06-897e-77ed3ea5aced

Resource Observation:

Generated Narrative: Observation ct-xG-OverallInterpretation

status: Final
category: Laboratory, Genetics
code: Discrete variation analysis overall interpretation
subject: Bundle: type = transaction
effective: 2019-04-01
performer: Bundle: type = transaction
value: Positive
specimen: Bundle: type = transaction

Request:

POST Observation

Entry 11 - fullUrl = urn:uuid:6320918e-f5da-41fa-9481-6b75c2a0d712

Resource Observation:

Generated Narrative: Observation ct-xG-observation1

status: Final
category: Laboratory, Genetics, Laboratory, Genetics
code: Genetic variant assessment
subject: Bundle: type = transaction
value: Present
method: Sequencing
component
code: Gene studied [ID]
value: LZTR1
component
code: Human reference sequence assembly version
value: GRCh37
component
code: Genomic source class [Type]
value: Germline
component
code: Transcript reference sequence [ID]
value: NM_006767.3
component
code: DNA change (c.HGVS)
value: c.439A>G
component
code: Amino acid change (pHGVS)
value: p.K147E
component
code: Genomic allele start-end
value: 21342337-?
component
code: Chromosome [Identifier] in Blood or Tissue by Molecular genetics method
value: Chromosome 22

Request:

POST Observation

Entry 12 - fullUrl = urn:uuid:92f37846-46db-41f2-b0f5-edd46b61880a

Resource Observation:

Generated Narrative: Observation ct-xG-observation2

status: Final
category: Laboratory, Genetics, Laboratory, Genetics
code: Genetic variant assessment
subject: Bundle: type = transaction
value: Present
method: Sequencing
component
code: Gene studied [ID]
value: MUTYH
component
code: Human reference sequence assembly version
value: GRCh37
component
code: Genomic source class [Type]
value: Germline
component
code: Transcript reference sequence [ID]
value: NM_001128425.1
component
code: DNA change (c.HGVS)
value: c.481G>C
component
code: Amino acid change (pHGVS)
value: p.D161H
component
code: Genomic allele start-end
value: 45798613-?
component
code: Chromosome [Identifier] in Blood or Tissue by Molecular genetics method
value: Chromosome 1

Request:

POST Observation

Entry 13 - fullUrl = urn:uuid:5a506248-dad9-441e-b898-6fd4be77974b

Resource Observation:

Generated Narrative: Observation ct-diagnostic-implication-1

status: Final
category: Laboratory, Genetics, Laboratory, Genetics
code: Diagnostic Implication
subject: Bundle: type = transaction
effective: 2019-04-01
derivedFrom: Bundle: type = transaction
Components
- Code Value[x]
* Genetic variation clinical significance [Imp] Uncertain Significance

Request:

POST Observation

Entry 14 - fullUrl = urn:uuid:e44b5631-a39a-43c6-b189-de68720d66fa

Resource Observation:

Generated Narrative: Observation ct-diagnostic-implication-2

status: Final
category: Laboratory, Genetics, Laboratory, Genetics
code: Diagnostic Implication
subject: Bundle: type = transaction
effective: 2019-04-01
derivedFrom: Bundle: type = transaction
Components
- Code Value[x]
* Genetic variation clinical significance [Imp] Likely Pathogenic

Request:

POST Observation

Entry 15 - fullUrl = urn:uuid:33a4f8bb-eae5-4927-b20b-5915cbd862ab

Resource Observation:

Generated Narrative: Observation ct-OverallInterp

status: Final
category: Laboratory, Genetics
code: Discrete variation analysis overall interpretation
subject: Bundle: type = transaction
effective: 2019-04-01
performer: Bundle: type = transaction
value: Positive
specimen: Bundle: type = transaction

Request:

POST Observation

Entry 16 - fullUrl = urn:uuid:c5s0f176-e402-4eaf-989c-959e80d91a11

Resource DocumentReference:

Generated Narrative: DocumentReference ct-xT-GeneList3

identifier: https://www.tempus.com/11120
status: Current
docStatus: Preliminary
description:
Gene List

content
Attachments
- Url Title Creation
* https://edge-api-demo.stagingtempus.com/fhir/R4/static/Gene_List_1.json GeneList 2019-03-01 01:02:01+0100

Request:

POST DocumentReference

Entry 17 - fullUrl = urn:uuid:22263097-6033-41af-9f6a-d7b012e27bbb

Resource Procedure:

Generated Narrative: Procedure ct-xT-genomicStudyAnalysis8

Genomic Study Analysis Regions
studied: Bundle: type = transaction
Genomic Study Analysis Specimen: Bundle: type = transaction
Genomic Study Analysis Focus: Bundle: type = transaction
status: Completed
category: Laboratory
subject: Bundle: type = transaction

Request:

POST Procedure

Entry 18 - fullUrl = urn:uuid:88f2715b-10ea-42ae-a3a2-185b14e6e666

Resource Procedure:

Generated Narrative: Procedure ct-xT-genomicStudy-9

Genomic Study Analysis Extension: Bundle: type = transaction
basedOn: Bundle: type = transaction
status: Completed
category: Laboratory
code: xT panel
subject: Bundle: type = transaction

Request:

POST Procedure