Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild 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-withGrouping

Bundle bundle-oncologyexamples-r4-withGrouping of type transaction

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

Resource Patient:

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

> Links: | General Practitioner: Practitioner Akerman Philip Prof

Request:

    POST Patient

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

Resource Practitioner:

> 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:

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

> status: Available

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

> ### Collections

> - | Collector
> * | Practitioner Akerman Philip Prof

Request:

    POST Specimen

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

Resource Observation:

> Profile: Molecular Biomarker

> status: Final

> category: Laboratory, Biomarker Category, Genetics

> code: Mutations/Megabase [# Ratio] in Tumor

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

> effective: 2023-05-01

> performer: Practitioner Akerman Philip Prof

> value: 25 somatic variants per megabase of sequenced DNA (Details: UCUM code1/1000000 = '1/1000000')

> specimen: Specimen: identifier = 076e1948-2217-11e9-94d8-12e241dc1f66; status = available

> ### Components

> - | Code | Value[x]
> * | Biomarker Category | molecular sequence adjacent category

Request:

    POST Observation

Entry 5 - fullUrl = urn:uuid:64b91716-6431-41bd-8fd4-7ac99bebdee9

Resource Observation:

> Profile: Molecular Biomarker

> status: Final

> category: Laboratory, Biomarker Category, Genetics

> code: Microsatellite instability [Interpretation] in Cancer specimen Qualitative

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

> effective: 2023-05-01

> performer: Practitioner Akerman Philip Prof

> value: Stable

> specimen: Specimen: identifier = 076e1948-2217-11e9-94d8-12e241dc1f66; status = available

> ### Components

> - | Code | Value[x]
> * | Biomarker Category | molecular sequence adjacent category

Request:

    POST Observation

Entry 6 - fullUrl = urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

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

> effective: 2023-05-01

> performer: Practitioner Akerman Philip Prof

> value: Present

> method: Sequencing

> specimen: Specimen: identifier = 076e1948-2217-11e9-94d8-12e241dc1f66; status = available

> > 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:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

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

> effective: 2023-05-01

> performer: Practitioner Akerman Philip Prof

> value: Present

> method: Sequencing

> specimen: Specimen: identifier = 076e1948-2217-11e9-94d8-12e241dc1f66; status = available

> > 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:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

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

> effective: 2023-05-01

> performer: Practitioner Akerman Philip Prof

> value: Present

> method: Sequencing

> specimen: Specimen: identifier = 076e1948-2217-11e9-94d8-12e241dc1f66; status = available

> > 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:

> Profile: Therapeutic Implication

> status: Final

> category: Laboratory, Genetics

> code: Therapeutic Implication

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

> effective: 2023-05-01

> performer: Practitioner Akerman Philip Prof

> method: Computational analysis

> specimen: Specimen: identifier = 076e1948-2217-11e9-94d8-12e241dc1f66; status = available

> derivedFrom: Observation Genetic variant assessment

> > 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

> > Medication Assessed reference to a FHIR resource: MedicationKnowledge Ruxolitinib

> > code: Medication assessed [ID]

> > value: Ruxolitinib

> > code: Ruxolitinib

> > status: active

Request:

    POST Observation

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

Resource Observation:

> Profile: Therapeutic Implication

> status: Final

> category: Laboratory, Genetics

> code: Therapeutic Implication

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

> effective: 2023-05-01

> performer: Practitioner Akerman Philip Prof

> method: Computational analysis

> specimen: Specimen: identifier = 076e1948-2217-11e9-94d8-12e241dc1f66; status = available

> derivedFrom: Observation Genetic variant assessment

> > 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:

> Profile: Therapeutic Implication

> status: Final

> category: Laboratory, Genetics

> code: Therapeutic Implication

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

> effective: 2023-05-01

> performer: Practitioner Akerman Philip Prof

> method: Computational analysis

> specimen: Specimen: identifier = 076e1948-2217-11e9-94d8-12e241dc1f66; status = available

> derivedFrom: Observation Genetic variant assessment

> > 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:

> Profile: Therapeutic Implication

> status: Final

> category: Laboratory, Genetics

> code: Therapeutic Implication

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

> effective: 2023-05-01

> performer: Practitioner Akerman Philip Prof

> method: Computational analysis

> specimen: Specimen: identifier = 076e1948-2217-11e9-94d8-12e241dc1f66; status = available

> derivedFrom: Observation Genetic variant assessment

> > 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:16fdd5fc-e665-48af-99e4-48d603f3e12f

Resource Observation:

> status: Final

> category: Laboratory, Genetics

> code: Group

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

> effective: 2023-05-01

> performer: Practitioner Akerman Philip Prof

> hasMember:

> - SNV analysis for JAK2 variant
> - SNV analysis for KDR variant
> - SNV analysis for ERBB4 variant
> - TMB value analysis
> - MSI status analysis

Request:

    POST Observation

Entry 14 - fullUrl = urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e

Resource Observation:

> status: Final

> category: Laboratory, Genetics

> code: Group

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

> effective: 2023-05-01

> performer: Practitioner Akerman Philip Prof

> hasMember:

> - Therapy match result 1
> - Therapy match result 2
> - Therapy match result 3
> - Therapy match result 4

Request:

    POST Observation

Entry 15 - fullUrl = urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5

Resource DiagnosticReport:

> Profile: Genomic Report

> ## Genetic analysis report (Genetics)

> Subject | Carrot John Mr Male, DoB: 1962-12-31 ( 1007)
> Performer | Practitioner Akerman Philip Prof

> Report Details

> Code | Value | Flags | When For | Reported
> Group |  | Final | 2023-05-01 |
> Genetic variant assessment | Present | Final | 2019-03-05 | 2019-03-05 16:04:44+0000
> Genetic variant assessment | Present | Final | 2023-05-01 |
> Genetic variant assessment | Present | Final | 2023-05-01 |
> Mutations/Megabase [# Ratio] in Tumor | 25 Mutations/Megabase (Details: UCUM code1/1000000 = '1/1000000') | Final | 2019-03-05 |
> Microsatellite instability [Interpretation] in Cancer specimen Qualitative | Stable | Final | 2023-05-01 |
> Genetic variant assessment | Present | Final | 2019-03-05 | 2019-03-05 16:04:44+0000
> Diagnostic Implication |  | Final | 2019-03-05 |
> Therapeutic Implication |  | Final | 2023-05-01 |
> Therapeutic Implication |  | Final | 2023-05-01 |
> Therapeutic Implication |  | Final | 2023-05-01 |

Request:

    POST DiagnosticReport