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-report-example

Bundle bundle-oncology-report-example of type transaction

Entry 1 - fullUrl = urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17

Resource Organization:

> identifier: `http://example.org/genomics/NamingSystem/organization`/CEGAT

> name: CEGAT

Request:

    POST Organization
    If-None-Exist = identifier=http://example.org/genomics/NamingSystem/organization|CEGAT

Entry 2 - fullUrl = urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648

Resource Patient:

> Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)

Request:

    POST Patient
    If-None-Exist = identifier=http://example.org/genomics/NamingSystem/cegat/patID|11111

Entry 3 - fullUrl = urn:uuid:a2041c83-b73d-4fc8-9466-4ba4a92da516

Resource Specimen:

> identifier: `http://example.org/genomics/NamingSystem/cegat/tissueID`/UNKNOWN

> type: Tumor

> subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)

> ### Collections

> - | Method | BodySite
> * | Biopsy | No display for Specimen.collection.bodySite (concept: Malignant neoplasm of cardia)

Request:

    POST Specimen
    If-None-Exist = identifier=http://example.org/genomics/NamingSystem/cegat/tissueID|UNKNOWN

Entry 4 - fullUrl = urn:uuid:dac358c3-403a-4dbb-b478-4259aed882ae

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)

> effective: 2023-03-05

> performer: Organization CEGAT

> value: Present

> method: Sequencing

> specimen: Identifier: `http://example.org/genomics/NamingSystem/cegat/tissueID`/UNKNOWN

> > component

> > code: Genomic source class

> > value: Somatic

> > component

> > code: Gene studied [ID]

> > value: PIK3CA

> > component

> > code: Human reference sequence assembly version

> > value: GRCh37

> > component

> > code: DNA change (c.HGVS)

> > value: NM_006218.4:c.3140A>G

> > component

> > code: DNA change type

> > value: substitution

> > component

> > code: Amino acid change (pHGVS)

> > value: NP_006209.2:p.His1047Arg

> > component

> > code: Transcript reference sequence [ID]

> > value: NM_006218.4

> > component

> > code: Genomic ref allele [ID]

> > value: A

> > component

> > code: Sample VAF

> > value: 0.2188 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1')

> > component

> > code: Allelic read depth

> > value: 64 reads per base pair (Details: UCUM code1 = '1')

Request:

    POST Observation

Entry 5 - fullUrl = urn:uuid:1d773d66-cec7-44a2-b92a-46d00adeae00

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)

> effective: 2023-03-05

> performer: Organization CEGAT

> value: Present

> method: Sequencing

> specimen: Identifier: `http://example.org/genomics/NamingSystem/cegat/tissueID`/UNKNOWN

> > component

> > code: Genomic source class

> > value: Somatic

> > component

> > code: Gene studied [ID]

> > value: NRAS

> > component

> > code: Human reference sequence assembly version

> > value: GRCh37

> > component

> > code: DNA change (c.HGVS)

> > value: NM_002524.4:c.34G>T

> > component

> > code: DNA change type

> > value: substitution

> > component

> > code: Transcript reference sequence [ID]

> > value: NM_002524.4

> > component

> > code: Genomic ref allele [ID]

> > value: C

> > component

> > code: Sample VAF

> > value: 0.1793 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1')

> > component

> > code: Allelic read depth

> > value: 145 reads per base pair (Details: UCUM code1 = '1')

Request:

    POST Observation

Entry 6 - fullUrl = urn:uuid:842d9ab9-d940-4f0c-adf9-e5c528f5c0e5

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)

> effective: 2023-03-05

> performer: Organization CEGAT

> value: Present

> method: Sequencing

> specimen: Identifier: `http://example.org/genomics/NamingSystem/cegat/tissueID`/UNKNOWN

> > component

> > code: Genomic source class

> > value: Somatic

> > component

> > code: Gene studied [ID]

> > value: FBXW7

> > component

> > code: Human reference sequence assembly version

> > value: GRCh37

> > component

> > code: DNA change (c.HGVS)

> > value: NM_001349798.2:c.1394G>A

> > component

> > code: DNA change type

> > value: substitution

> > component

> > code: Amino acid change (pHGVS)

> > value: NP_001336727.1:p.Arg465His

> > component

> > code: Transcript reference sequence [ID]

> > value: NM_001349798.2

> > component

> > code: Genomic ref allele [ID]

> > value: C

> > component

> > code: Sample VAF

> > value: 0.1053 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1')

> > component

> > code: Allelic read depth

> > value: 57 reads per base pair (Details: UCUM code1 = '1')

Request:

    POST Observation

Entry 7 - fullUrl = urn:uuid:9a9f9a4a-52e3-4738-bd0b-a25374bbf358

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)

> effective: 2023-03-05

> performer: Organization CEGAT

> value: Present

> method: Sequencing

> specimen: Identifier: `http://example.org/genomics/NamingSystem/cegat/tissueID`/UNKNOWN

> > component

> > code: Genomic source class

> > value: Somatic

> > component

> > code: Gene studied [ID]

> > value: KMT2D

> > component

> > code: Human reference sequence assembly version

> > value: GRCh37

> > component

> > code: DNA change (c.HGVS)

> > value: NM_003482.3:c.7900_7901delCA

> > component

> > code: DNA change type

> > value: deletion

> > component

> > code: Transcript reference sequence [ID]

> > value: NM_003482.3

> > component

> > code: Genomic ref allele [ID]

> > value: CTG

> > component

> > code: Sample VAF

> > value: 0.188 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1')

> > component

> > code: Allelic read depth

> > value: 117 reads per base pair (Details: UCUM code1 = '1')

Request:

    POST Observation

Entry 8 - fullUrl = urn:uuid:58828523-8893-45fc-973b-16290366c5e5

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)

> effective: 2023-03-05

> performer: Organization CEGAT

> value: Present

> method: Sequencing

> specimen: Identifier: `http://example.org/genomics/NamingSystem/cegat/tissueID`/UNKNOWN

> > component

> > code: Genomic source class

> > value: Somatic

> > component

> > code: Gene studied [ID]

> > value: PIK3CA

> > component

> > code: Human reference sequence assembly version

> > value: GRCh37

> > component

> > code: DNA change (c.HGVS)

> > value: NM_006218.3:c.333G>T

> > component

> > code: DNA change type

> > value: substitution

> > component

> > code: Transcript reference sequence [ID]

> > value: NM_006218.3

> > component

> > code: Genomic ref allele [ID]

> > value: G

> > component

> > code: Sample VAF

> > value: 0.1471 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1')

> > component

> > code: Allelic read depth

> > value: 68 reads per base pair (Details: UCUM code1 = '1')

Request:

    POST Observation

Entry 9 - fullUrl = urn:uuid:2c28b23f-3e9f-4c03-8c8f-0e76bc5dc9c2

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)

> effective: 2023-03-05

> performer: Organization CEGAT

> value: Present

> method: Sequencing

> specimen: Identifier: `http://example.org/genomics/NamingSystem/cegat/tissueID`/UNKNOWN

> > component

> > code: Genomic source class

> > value: Somatic

> > component

> > code: Gene studied [ID]

> > value: IRS2

> > component

> > code: Human reference sequence assembly version

> > value: GRCh37

> > component

> > code: DNA change (c.HGVS)

> > value: NM_003749.2:c.3960C>T

> > component

> > code: DNA change type

> > value: substitution

> > component

> > code: Transcript reference sequence [ID]

> > value: NM_003749.2

> > component

> > code: Genomic ref allele [ID]

> > value: G

> > component

> > code: Sample VAF

> > value: 0.1343 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1')

> > component

> > code: Allelic read depth

> > value: 134 reads per base pair (Details: UCUM code1 = '1')

Request:

    POST Observation

Entry 10 - fullUrl = urn:uuid:41bebbe5-e06f-4867-aa22-7c06db69dbd1

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)

> effective: 2023-03-05

> performer: Organization CEGAT

> value: Present

> method: Sequencing

> specimen: Identifier: `http://example.org/genomics/NamingSystem/cegat/tissueID`/UNKNOWN

> > component

> > code: Genomic source class

> > value: Somatic

> > component

> > code: Gene studied [ID]

> > value: CDKN2A

> > component

> > code: Human reference sequence assembly version

> > value: GRCh37

> > component

> > code: DNA change (c.HGVS)

> > value: NM_000077.4:c.9_32del

> > component

> > code: DNA change type

> > value: deletion

> > component

> > code: Amino acid change (pHGVS)

> > value: NP_000068.1:p.Ala4_Pro11del

> > component

> > code: Transcript reference sequence [ID]

> > value: NM_000077.4

> > component

> > code: Genomic ref allele [ID]

> > value: AGGCTCCATGCTGCTCCCCGCCGCC

> > component

> > code: Sample VAF

> > value: 0.0536 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1')

> > component

> > code: Allelic read depth

> > value: 112 reads per base pair (Details: UCUM code1 = '1')

Request:

    POST Observation

Entry 11 - fullUrl = urn:uuid:1642f190-e2c6-4999-8040-b9b2a70618bf

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)

> effective: 2023-03-05

> performer: Organization CEGAT

> value: Present

> method: Sequencing

> specimen: Identifier: `http://example.org/genomics/NamingSystem/cegat/tissueID`/UNKNOWN

> > component

> > code: Genomic source class

> > value: Somatic

> > component

> > code: Gene studied [ID]

> > value: RECQL4

> > component

> > code: Human reference sequence assembly version

> > value: GRCh37

> > component

> > code: DNA change (c.HGVS)

> > value: NM_004260.4:c.2086C>T

> > component

> > code: DNA change type

> > value: substitution

> > component

> > code: Amino acid change (pHGVS)

> > value: NP_004251.4:p.Arg696Cys

> > component

> > code: Transcript reference sequence [ID]

> > value: NM_004260.4

> > component

> > code: Genomic ref allele [ID]

> > value: G

> > component

> > code: Sample VAF

> > value: 0.2568 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1')

> > component

> > code: Allelic read depth

> > value: 148 reads per base pair (Details: UCUM code1 = '1')

Request:

    POST Observation

Entry 12 - fullUrl = urn:uuid:c3587931-242f-4129-93f9-be24500c8f29

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)

> effective: 2023-03-05

> performer: Organization CEGAT

> value: Present

> method: Sequencing

> specimen: Identifier: `http://example.org/genomics/NamingSystem/cegat/tissueID`/UNKNOWN

> > component

> > code: Genomic source class

> > value: Somatic

> > component

> > code: Gene studied [ID]

> > value: RYR1

> > component

> > code: Human reference sequence assembly version

> > value: GRCh37

> > component

> > code: DNA change (c.HGVS)

> > value: NM_000540.3:c.4964G>A

> > component

> > code: DNA change type

> > value: substitution

> > component

> > code: Amino acid change (pHGVS)

> > value: NP_000531.2:p.Arg1655Leu

> > component

> > code: Transcript reference sequence [ID]

> > value: NM_000540.3

> > component

> > code: Genomic ref allele [ID]

> > value: G

> > component

> > code: Sample VAF

> > value: 0.2151 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1')

> > component

> > code: Allelic read depth

> > value: 93 reads per base pair (Details: UCUM code1 = '1')

Request:

    POST Observation

Entry 13 - fullUrl = urn:uuid:41695fc0-1fd5-4cc8-95e6-82b2848a5cb6

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)

> effective: 2023-03-05

> performer: Organization CEGAT

> value: Present

> method: Sequencing

> specimen: Identifier: `http://example.org/genomics/NamingSystem/cegat/tissueID`/UNKNOWN

> > component

> > code: Genomic source class

> > value: Somatic

> > component

> > code: Gene studied [ID]

> > value: SACS

> > component

> > code: Human reference sequence assembly version

> > value: GRCh37

> > component

> > code: DNA change (c.HGVS)

> > value: NM_014363.5:c.12118G>A

> > component

> > code: DNA change type

> > value: substitution

> > component

> > code: Transcript reference sequence [ID]

> > value: NM_014363.5

> > component

> > code: Genomic ref allele [ID]

> > value: C

> > component

> > code: Sample VAF

> > value: 0.3333 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1')

> > component

> > code: Allelic read depth

> > value: 60 reads per base pair (Details: UCUM code1 = '1')

Request:

    POST Observation

Entry 14 - fullUrl = urn:uuid:58eb14f6-4059-4168-86a9-155ae61d30e2

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)

> effective: 2023-03-05

> performer: Organization CEGAT

> value: Present

> method: Sequencing

> specimen: Identifier: `http://example.org/genomics/NamingSystem/cegat/tissueID`/UNKNOWN

> > component

> > code: Genomic source class

> > value: Somatic

> > component

> > code: Gene studied [ID]

> > value: SLIT2

> > component

> > code: Human reference sequence assembly version

> > value: GRCh37

> > component

> > code: DNA change (c.HGVS)

> > value: NM_004787.3:c.1290C>A

> > component

> > code: DNA change type

> > value: substitution

> > component

> > code: Transcript reference sequence [ID]

> > value: NM_004787.3

> > component

> > code: Genomic ref allele [ID]

> > value: C

> > component

> > code: Sample VAF

> > value: 0.2642 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1')

> > component

> > code: Allelic read depth

> > value: 53 reads per base pair (Details: UCUM code1 = '1')

Request:

    POST Observation

Entry 15 - fullUrl = urn:uuid:1a71e80f-b044-4a91-80e1-eadbe5a53dca

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)

> effective: 2023-03-05

> performer: Organization CEGAT

> value: Present

> method: Sequencing

> specimen: Identifier: `http://example.org/genomics/NamingSystem/cegat/tissueID`/UNKNOWN

> > component

> > code: Genomic source class

> > value: Somatic

> > component

> > code: Gene studied [ID]

> > value: SMARCA4

> > component

> > code: Human reference sequence assembly version

> > value: GRCh37

> > component

> > code: DNA change (c.HGVS)

> > value: NM_003072.5:c.2372C>T

> > component

> > code: DNA change type

> > value: substitution

> > component

> > code: Amino acid change (pHGVS)

> > value: NP_003063.2:p.Ala791Val

> > component

> > code: Transcript reference sequence [ID]

> > value: NM_003072.5

> > component

> > code: Genomic ref allele [ID]

> > value: C

> > component

> > code: Sample VAF

> > value: 0.1938 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1')

> > component

> > code: Allelic read depth

> > value: 160 reads per base pair (Details: UCUM code1 = '1')

Request:

    POST Observation

Entry 16 - fullUrl = urn:uuid:6a80003f-822d-489e-8286-1f1dcba56dfa

Resource DiagnosticReport:

> Profile: Genomic Report

> ## Genetic analysis report (Genetics)

> Subject | Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)
> Reported | 2019-09-15 11:35:05-0400
> Performer | Organization CEGAT
> Identifier | `http://example.org/genomics/NamingSystem/cegat/reportID`/42867

> Report Details

> Code | Value | Flags | When For
> Genetic variant assessment | Present | Final | 2023-03-05
> Genetic variant assessment | Present | Final | 2023-03-05
> Genetic variant assessment | Present | Final | 2023-03-05
> Genetic variant assessment | Present | Final | 2023-03-05
> Genetic variant assessment | Present | Final | 2023-03-05
> Genetic variant assessment | Present | Final | 2023-03-05
> Genetic variant assessment | Present | Final | 2023-03-05
> Genetic variant assessment | Present | Final | 2023-03-05
> Genetic variant assessment | Present | Final | 2023-03-05
> Genetic variant assessment | Present | Final | 2023-03-05
> Genetic variant assessment | Present | Final | 2023-03-05
> Genetic variant assessment | Present | Final | 2023-03-05

Request:

    POST DiagnosticReport