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-oncology-diagnostic

Bundle bundle-oncology-diagnostic 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: 2019-03-05

> performer: Practitioner Akerman Philip Prof

> value: 25 Mutations/Megabase (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: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: 2019-03-05

> performer: Practitioner Akerman Philip Prof

> value: Present

> method: Sequencing

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

> > component

> > code: Human reference sequence assembly version

> > value: GRCh37

> > component

> > code: Genomic DNA change (gHGVS)

> > value: NC_000007.13:g.140453136A>T

> > component

> > code: Discrete genetic variant

> > value: Clinvar ID 13961

> > component

> > code: Amino acid change (pHGVS)

> > value: NP_004324.2:p.Val600Glu

> > component

> > code: Gene studied ID

> > value: BRAF

Request:

    POST Observation

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

Resource Observation:

> Profile: Diagnostic Implication

> Related artifact: No display for RelatedArtifact (type: justification; display: https://pmkb.weill.cornell.edu/therapies/103)

> status: Final

> category: Laboratory, Genetics

> code: Diagnostic Implication

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

> effective: 2019-03-05

> 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: Genetic variation clinical significance [Imp]

> > value: Pathogenic

> > component

> > code: Level of Evidence

> > value: Very strong evidence pathogenic

> > component

> > code: Associated phenotype

> > value: melanoma

Request:

    POST Observation

Entry 7 - 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)
> When For | 2019-03-05
> Performer | Practitioner Akerman Philip Prof

> Report Details

> Code | Value | Flags | Reported
> Genetic variant assessment | Present | Final | 2019-03-05 16:04:44+0000
> Diagnostic Implication |  | Final |

Request:

    POST DiagnosticReport