Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT 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

Generated Narrative: 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:

Generated Narrative: Organization Inline-Instance-for-oncology-report-example-1

identifier: http://molit.eu/fhir/genomics/NamingSystem/organization/CEGAT

name: CEGAT

Request:

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

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

Resource Patient:

Generated Narrative: Patient Inline-Instance-for-oncology-report-example-2

Anonymous Patient (no stated gender), DoB Unknown ( http://molit.eu/fhir/genomics/NamingSystem/cegat/patID#11111)

Request:

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

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

Resource Specimen:

Generated Narrative: Specimen Inline-Instance-for-oncology-report-example-3

identifier: http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID/UNKNOWN

type: Tumor

subject: Bundle: type = transaction

Collections

-MethodBodySite
*BiopsyNo display for Specimen.collection.bodySite
  • concept: Malignant neoplasm of cardia

Request:

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

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

Resource Observation:

Generated Narrative: Observation Inline-Instance-for-oncology-report-example-4

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Bundle: type = transaction

effective: 2023-03-05

performer: Bundle: type = transaction

value: Present

method: Sequencing

specimen: Identifier: http://molit.eu/fhir/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:

Generated Narrative: Observation Inline-Instance-for-oncology-report-example-5

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Bundle: type = transaction

effective: 2023-03-05

performer: Bundle: type = transaction

value: Present

method: Sequencing

specimen: Identifier: http://molit.eu/fhir/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:

Generated Narrative: Observation Inline-Instance-for-oncology-report-example-6

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Bundle: type = transaction

effective: 2023-03-05

performer: Bundle: type = transaction

value: Present

method: Sequencing

specimen: Identifier: http://molit.eu/fhir/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:

Generated Narrative: Observation Inline-Instance-for-oncology-report-example-7

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Bundle: type = transaction

effective: 2023-03-05

performer: Bundle: type = transaction

value: Present

method: Sequencing

specimen: Identifier: http://molit.eu/fhir/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:

Generated Narrative: Observation Inline-Instance-for-oncology-report-example-8

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Bundle: type = transaction

effective: 2023-03-05

performer: Bundle: type = transaction

value: Present

method: Sequencing

specimen: Identifier: http://molit.eu/fhir/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:

Generated Narrative: Observation Inline-Instance-for-oncology-report-example-9

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Bundle: type = transaction

effective: 2023-03-05

performer: Bundle: type = transaction

value: Present

method: Sequencing

specimen: Identifier: http://molit.eu/fhir/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:

Generated Narrative: Observation Inline-Instance-for-oncology-report-example-10

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Bundle: type = transaction

effective: 2023-03-05

performer: Bundle: type = transaction

value: Present

method: Sequencing

specimen: Identifier: http://molit.eu/fhir/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:

Generated Narrative: Observation Inline-Instance-for-oncology-report-example-11

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Bundle: type = transaction

effective: 2023-03-05

performer: Bundle: type = transaction

value: Present

method: Sequencing

specimen: Identifier: http://molit.eu/fhir/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:

Generated Narrative: Observation Inline-Instance-for-oncology-report-example-12

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Bundle: type = transaction

effective: 2023-03-05

performer: Bundle: type = transaction

value: Present

method: Sequencing

specimen: Identifier: http://molit.eu/fhir/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:

Generated Narrative: Observation Inline-Instance-for-oncology-report-example-13

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Bundle: type = transaction

effective: 2023-03-05

performer: Bundle: type = transaction

value: Present

method: Sequencing

specimen: Identifier: http://molit.eu/fhir/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:

Generated Narrative: Observation Inline-Instance-for-oncology-report-example-14

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Bundle: type = transaction

effective: 2023-03-05

performer: Bundle: type = transaction

value: Present

method: Sequencing

specimen: Identifier: http://molit.eu/fhir/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:

Generated Narrative: Observation Inline-Instance-for-oncology-report-example-15

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Bundle: type = transaction

effective: 2023-03-05

performer: Bundle: type = transaction

value: Present

method: Sequencing

specimen: Identifier: http://molit.eu/fhir/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:

Generated Narrative: DiagnosticReport Inline-Instance-for-oncology-report-example-16

Genetic analysis report (Genetics)

SubjectNot done yet
Reported2019-09-15 11:35:05-0400
Performer Bundle: type = transaction
Identifier http://molit.eu/fhir/genomics/NamingSystem/cegat/reportID/42867

Report Details

CodeValue

Request:

POST DiagnosticReport