Genomics Reporting Implementation Guide
1.1.0 - Ballot

This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

Example Bundle: Example - Multiple Oncology Variant Report Example

Bundle oncology-report-example of type transaction

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

Request:

POST Organization
If-None-Exist = identifier=http://molit.eu/fhir/genomics/NamingSystem/organization|CEGAT

Resource Organization:

Generated Narrative

Texts

-
*

identifier: id: CEGAT

name: CEGAT

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

Request:

POST Patient
If-None-Exist = identifier=http://molit.eu/fhir/genomics/NamingSystem/cegat/patID|11111

Resource Patient:

Exception generating narrative: null

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

Request:

POST Specimen
If-None-Exist = identifier=http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID|UNKNOWN

Resource Specimen:

Generated Narrative

Texts

-
*

identifier: id: UNKNOWN

type: Tumor

subject: Generated Summary: type: transaction

Collections

-MethodBodySite
*BiopsieC16.0

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

Request:

POST Observation

Resource Observation:

Generated Narrative

Texts

-
*

category: Laboratory

code: Genetic variant assessment

subject: Generated Summary: type: transaction

performer: Generated Summary: type: transaction

value: Present

method: Sequencing

specimen:

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: c.3140A>G

component

code: DNA change type

value: substitution

component

code: Amino acid change (pHGVS)

value: p.H1047R

component

code: Molecular Consequence

value: missense_variant

component

code: Transcript reference sequence [ID]

value: NM_006218.3

component

code: Genomic ref allele [ID]

value: A

component

code: Sample VAF

value: 0.2188 relative frequency of a particular allele in the specimen

component

code: Allelic read depth

value: 64.0 reads per base pair

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

Request:

POST Observation

Resource Observation:

Generated Narrative

Texts

-
*

category: Laboratory

code: Genetic variant assessment

subject: Generated Summary: type: transaction

performer: Generated Summary: type: transaction

value: Present

method: Sequencing

specimen:

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: c.34G>T

component

code: DNA change type

value: substitution

component

code: Amino acid change (pHGVS)

value: p.G12C

component

code: Molecular Consequence

value: missense_variant

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

component

code: Allelic read depth

value: 145.0 reads per base pair

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

Request:

POST Observation

Resource Observation:

Generated Narrative

Texts

-
*

category: Laboratory

code: Genetic variant assessment

subject: Generated Summary: type: transaction

performer: Generated Summary: type: transaction

value: Present

method: Sequencing

specimen:

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: c.1394G>A

component

code: DNA change type

value: substitution

component

code: Amino acid change (pHGVS)

value: p.R465H

component

code: Molecular Consequence

value: missense_variant

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

component

code: Allelic read depth

value: 57.0 reads per base pair

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

Request:

POST Observation

Resource Observation:

Generated Narrative

Texts

-
*

category: Laboratory

code: Genetic variant assessment

subject: Generated Summary: type: transaction

performer: Generated Summary: type: transaction

value: Present

method: Sequencing

specimen:

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: c.7900_7901delCA

component

code: DNA change type

value: deletion

component

code: Amino acid change (pHGVS)

value: p.Q2634Afs*20

component

code: Molecular Consequence

value: frameshift

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

component

code: Allelic read depth

value: 117.0 reads per base pair

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

Request:

POST Observation

Resource Observation:

Generated Narrative

Texts

-
*

category: Laboratory

code: Genetic variant assessment

subject: Generated Summary: type: transaction

performer: Generated Summary: type: transaction

value: Present

method: Sequencing

specimen:

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: c.333G>T

component

code: DNA change type

value: substitution

component

code: Amino acid change (pHGVS)

value: p.K111N

component

code: Molecular Consequence

value: missense_variant

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

component

code: Allelic read depth

value: 68.0 reads per base pair

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

Request:

POST Observation

Resource Observation:

Generated Narrative

Texts

-
*

category: Laboratory

code: Genetic variant assessment

subject: Generated Summary: type: transaction

performer: Generated Summary: type: transaction

value: Present

method: Sequencing

specimen:

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: c.3960C>T

component

code: DNA change type

value: substitution

component

code: Amino acid change (pHGVS)

value: p.=

component

code: Molecular Consequence

value: synonymous_variant

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

component

code: Allelic read depth

value: 134.0 reads per base pair

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

Request:

POST Observation

Resource Observation:

Generated Narrative

Texts

-
*

category: Laboratory

code: Genetic variant assessment

subject: Generated Summary: type: transaction

performer: Generated Summary: type: transaction

value: Present

method: Sequencing

specimen:

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: c.9_32del

component

code: DNA change type

value: deletion

component

code: Amino acid change (pHGVS)

value: p.A4_P11del

component

code: Molecular Consequence

value: inframe_variant

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

component

code: Allelic read depth

value: 112.0 reads per base pair

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

Request:

POST Observation

Resource Observation:

Generated Narrative

Texts

-
*

category: Laboratory

code: Genetic variant assessment

subject: Generated Summary: type: transaction

performer: Generated Summary: type: transaction

value: Present

method: Sequencing

specimen:

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: c.2086C>T

component

code: DNA change type

value: substitution

component

code: Amino acid change (pHGVS)

value: p.R696C

component

code: Molecular Consequence

value: missense_variant

component

code: Transcript reference sequence [ID]

value: NM_004260.3

component

code: Genomic ref allele [ID]

value: G

component

code: Sample VAF

value: 0.2568 relative frequency of a particular allele in the specimen

component

code: Allelic read depth

value: 148.0 reads per base pair

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

Request:

POST Observation

Resource Observation:

Generated Narrative

Texts

-
*

category: Laboratory

code: Genetic variant assessment

subject: Generated Summary: type: transaction

performer: Generated Summary: type: transaction

value: Present

method: Sequencing

specimen:

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: c.4964G>A

component

code: DNA change type

value: substitution

component

code: Amino acid change (pHGVS)

value: p.R1655H

component

code: Molecular Consequence

value: missense_variant

component

code: Transcript reference sequence [ID]

value: NM_000540.2

component

code: Genomic ref allele [ID]

value: G

component

code: Sample VAF

value: 0.2151 relative frequency of a particular allele in the specimen

component

code: Allelic read depth

value: 93.0 reads per base pair

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

Request:

POST Observation

Resource Observation:

Generated Narrative

Texts

-
*

category: Laboratory

code: Genetic variant assessment

subject: Generated Summary: type: transaction

performer: Generated Summary: type: transaction

value: Present

method: Sequencing

specimen:

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: c.12118G>A

component

code: DNA change type

value: substitution

component

code: Amino acid change (pHGVS)

value: p.A4040T

component

code: Molecular Consequence

value: missense_variant

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

component

code: Allelic read depth

value: 60.0 reads per base pair

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

Request:

POST Observation

Resource Observation:

Generated Narrative

Texts

-
*

category: Laboratory

code: Genetic variant assessment

subject: Generated Summary: type: transaction

performer: Generated Summary: type: transaction

value: Present

method: Sequencing

specimen:

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: c.1290C>A

component

code: DNA change type

value: substitution

component

code: Amino acid change (pHGVS)

value: p.N430K

component

code: Molecular Consequence

value: missense_variant

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

component

code: Allelic read depth

value: 53.0 reads per base pair

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

Request:

POST Observation

Resource Observation:

Generated Narrative

Texts

-
*

category: Laboratory

code: Genetic variant assessment

subject: Generated Summary: type: transaction

performer: Generated Summary: type: transaction

value: Present

method: Sequencing

specimen:

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: c.2372C>T

component

code: DNA change type

value: substitution

component

code: Amino acid change (pHGVS)

value: p.A791V

component

code: Molecular Consequence

value: missense_variant

component

code: Transcript reference sequence [ID]

value: NM_001128849.1

component

code: Genomic ref allele [ID]

value: C

component

code: Sample VAF

value: 0.1938 relative frequency of a particular allele in the specimen

component

code: Allelic read depth

value: 160.0 reads per base pair

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

Request:

POST DiagnosticReport

Resource DiagnosticReport:

Exception generating narrative: null