Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions
Bundle bundle-oncology-report-example of type transaction
Entry 1 - fullUrl = 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: Organization
Resource Organization "Inline-Instance-for-oncology-report-example-1"
identifier: id: CEGAT
name: CEGAT
Entry 2 - fullUrl = 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:
null, DoB: ( id: 11111)
Entry 3 - fullUrl = 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:
Resource Specimen "Inline-Instance-for-oncology-report-example-3"
identifier: id: UNKNOWN
type: Tumor (specimenType#TUMOR)
subject: See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)
Collections
Method BodySite Biopsy () Malignant neoplasm of cardia (International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM)#C16.0)
Entry 4 - fullUrl = urn:uuid:dac358c3-403a-4dbb-b478-4259aed882ae
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncology-report-example-4"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)
effective: 2023-03-05
performer: See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
specimen: id: UNKNOWN
component
code: Genomic source class (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: PIK3CA (HUGO Gene Nomenclature Committee Genes#HGNC:8975)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)
component
code: DNA change (c.HGVS) (LOINC#48004-6)
value: NM_006218.4:c.3140A>G (Human Genome Variation Society nomenclature#NM_006218.4:c.3140A>G)
component
code: DNA change type (LOINC#48019-4)
value: substitution (sequenceontology.org#SO:1000002)
component
code: Amino acid change (pHGVS) (LOINC#48005-3)
value: NP_006209.2:p.His1047Arg (Human Genome Variation Society nomenclature#NP_006209.2:p.His1047Arg)
component
code: Transcript reference sequence [ID] (LOINC#51958-7)
value: NM_006218.4 (Gene Reference Sequence Collection#NM_006218.3)
component
code: Genomic ref allele [ID] (LOINC#69547-8)
value: A
component
code: Sample VAF (LOINC#81258-6)
value: 0.2188 relative frequency of a particular allele in the specimen (Details: UCUM code 1 = '1')
component
code: Allelic read depth (LOINC#82121-5)
value: 64 reads per base pair (Details: UCUM code 1 = '1')
Entry 5 - fullUrl = urn:uuid:1d773d66-cec7-44a2-b92a-46d00adeae00
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncology-report-example-5"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)
effective: 2023-03-05
performer: See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
specimen: id: UNKNOWN
component
code: Genomic source class (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: NRAS (HUGO Gene Nomenclature Committee Genes#HGNC:7989)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)
component
code: DNA change (c.HGVS) (LOINC#48004-6)
value: NM_002524.4:c.34G>T (Human Genome Variation Society nomenclature#NM_002524.4:c.34G>T)
component
code: DNA change type (LOINC#48019-4)
value: substitution (sequenceontology.org#SO:1000002)
component
code: Transcript reference sequence [ID] (LOINC#51958-7)
value: NM_002524.4 (Gene Reference Sequence Collection#NM_002524.4)
component
code: Genomic ref allele [ID] (LOINC#69547-8)
value: C
component
code: Sample VAF (LOINC#81258-6)
value: 0.1793 relative frequency of a particular allele in the specimen (Details: UCUM code 1 = '1')
component
code: Allelic read depth (LOINC#82121-5)
value: 145 reads per base pair (Details: UCUM code 1 = '1')
Entry 6 - fullUrl = urn:uuid:842d9ab9-d940-4f0c-adf9-e5c528f5c0e5
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncology-report-example-6"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)
effective: 2023-03-05
performer: See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
specimen: id: UNKNOWN
component
code: Genomic source class (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: FBXW7 (HUGO Gene Nomenclature Committee Genes#HGNC:16712)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)
component
code: DNA change (c.HGVS) (LOINC#48004-6)
value: NM_001349798.2:c.1394G>A (Human Genome Variation Society nomenclature#NM_001349798.2:c.1394G>A)
component
code: DNA change type (LOINC#48019-4)
value: substitution (sequenceontology.org#SO:1000002)
component
code: Amino acid change (pHGVS) (LOINC#48005-3)
value: NP_001336727.1:p.Arg465His (Human Genome Variation Society nomenclature#NP_001336727.1:p.Arg465His)
component
code: Transcript reference sequence [ID] (LOINC#51958-7)
value: NM_001349798.2 (Gene Reference Sequence Collection#NM_001349798.2)
component
code: Genomic ref allele [ID] (LOINC#69547-8)
value: C
component
code: Sample VAF (LOINC#81258-6)
value: 0.1053 relative frequency of a particular allele in the specimen (Details: UCUM code 1 = '1')
component
code: Allelic read depth (LOINC#82121-5)
value: 57 reads per base pair (Details: UCUM code 1 = '1')
Entry 7 - fullUrl = urn:uuid:9a9f9a4a-52e3-4738-bd0b-a25374bbf358
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncology-report-example-7"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)
effective: 2023-03-05
performer: See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
specimen: id: UNKNOWN
component
code: Genomic source class (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: KMT2D (HUGO Gene Nomenclature Committee Genes#HGNC:7133)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)
component
code: DNA change (c.HGVS) (LOINC#48004-6)
value: NM_003482.3:c.7900_7901delCA (Human Genome Variation Society nomenclature#NM_003482.3:c.7900_7901delCA)
component
code: DNA change type (LOINC#48019-4)
value: deletion (sequenceontology.org#SO:0000159)
component
code: Transcript reference sequence [ID] (LOINC#51958-7)
value: NM_003482.3 (Gene Reference Sequence Collection#NM_003482.3)
component
code: Genomic ref allele [ID] (LOINC#69547-8)
value: CTG
component
code: Sample VAF (LOINC#81258-6)
value: 0.188 relative frequency of a particular allele in the specimen (Details: UCUM code 1 = '1')
component
code: Allelic read depth (LOINC#82121-5)
value: 117 reads per base pair (Details: UCUM code 1 = '1')
Entry 8 - fullUrl = urn:uuid:58828523-8893-45fc-973b-16290366c5e5
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncology-report-example-8"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)
effective: 2023-03-05
performer: See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
specimen: id: UNKNOWN
component
code: Genomic source class (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: PIK3CA (HUGO Gene Nomenclature Committee Genes#HGNC:8975)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)
component
code: DNA change (c.HGVS) (LOINC#48004-6)
value: NM_006218.3:c.333G>T (Human Genome Variation Society nomenclature#NM_006218.3:c.333G>T)
component
code: DNA change type (LOINC#48019-4)
value: substitution (sequenceontology.org#SO:1000002)
component
code: Transcript reference sequence [ID] (LOINC#51958-7)
value: NM_006218.3 (Gene Reference Sequence Collection#NM_006218.3)
component
code: Genomic ref allele [ID] (LOINC#69547-8)
value: G
component
code: Sample VAF (LOINC#81258-6)
value: 0.1471 relative frequency of a particular allele in the specimen (Details: UCUM code 1 = '1')
component
code: Allelic read depth (LOINC#82121-5)
value: 68 reads per base pair (Details: UCUM code 1 = '1')
Entry 9 - fullUrl = urn:uuid:2c28b23f-3e9f-4c03-8c8f-0e76bc5dc9c2
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncology-report-example-9"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)
effective: 2023-03-05
performer: See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
specimen: id: UNKNOWN
component
code: Genomic source class (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: IRS2 (HUGO Gene Nomenclature Committee Genes#HGNC:6126)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)
component
code: DNA change (c.HGVS) (LOINC#48004-6)
value: NM_003749.2:c.3960C>T (Human Genome Variation Society nomenclature#NM_003749.2:c.3960C>T)
component
code: DNA change type (LOINC#48019-4)
value: substitution (sequenceontology.org#SO:1000002)
component
code: Transcript reference sequence [ID] (LOINC#51958-7)
value: NM_003749.2 (Gene Reference Sequence Collection#NM_003749.2)
component
code: Genomic ref allele [ID] (LOINC#69547-8)
value: G
component
code: Sample VAF (LOINC#81258-6)
value: 0.1343 relative frequency of a particular allele in the specimen (Details: UCUM code 1 = '1')
component
code: Allelic read depth (LOINC#82121-5)
value: 134 reads per base pair (Details: UCUM code 1 = '1')
Entry 10 - fullUrl = urn:uuid:41bebbe5-e06f-4867-aa22-7c06db69dbd1
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncology-report-example-10"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)
effective: 2023-03-05
performer: See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
specimen: id: UNKNOWN
component
code: Genomic source class (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: CDKN2A (HUGO Gene Nomenclature Committee Genes#HGNC:1787)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)
component
code: DNA change (c.HGVS) (LOINC#48004-6)
value: NM_000077.4:c.9_32del (Human Genome Variation Society nomenclature#NM_000077.4:c.9_32del)
component
code: DNA change type (LOINC#48019-4)
value: deletion (sequenceontology.org#SO:0000159)
component
code: Amino acid change (pHGVS) (LOINC#48005-3)
value: NP_000068.1:p.Ala4_Pro11del (Human Genome Variation Society nomenclature#NP_000068.1:p.Ala4_Pro11del)
component
code: Transcript reference sequence [ID] (LOINC#51958-7)
value: NM_000077.4 (Gene Reference Sequence Collection#NM_000077.4)
component
code: Genomic ref allele [ID] (LOINC#69547-8)
value: AGGCTCCATGCTGCTCCCCGCCGCC
component
code: Sample VAF (LOINC#81258-6)
value: 0.0536 relative frequency of a particular allele in the specimen (Details: UCUM code 1 = '1')
component
code: Allelic read depth (LOINC#82121-5)
value: 112 reads per base pair (Details: UCUM code 1 = '1')
Entry 11 - fullUrl = urn:uuid:1642f190-e2c6-4999-8040-b9b2a70618bf
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncology-report-example-11"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)
effective: 2023-03-05
performer: See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
specimen: id: UNKNOWN
component
code: Genomic source class (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: RECQL4 (HUGO Gene Nomenclature Committee Genes#HGNC:9949)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)
component
code: DNA change (c.HGVS) (LOINC#48004-6)
value: NM_004260.4:c.2086C>T (Human Genome Variation Society nomenclature#NM_004260.4:c.2086C>T)
component
code: DNA change type (LOINC#48019-4)
value: substitution (sequenceontology.org#SO:1000002)
component
code: Amino acid change (pHGVS) (LOINC#48005-3)
value: NP_004251.4:p.Arg696Cys (Human Genome Variation Society nomenclature#NP_004251.4:p.Arg696Cys)
component
code: Transcript reference sequence [ID] (LOINC#51958-7)
value: NM_004260.4 (Gene Reference Sequence Collection#NM_004260.4)
component
code: Genomic ref allele [ID] (LOINC#69547-8)
value: G
component
code: Sample VAF (LOINC#81258-6)
value: 0.2568 relative frequency of a particular allele in the specimen (Details: UCUM code 1 = '1')
component
code: Allelic read depth (LOINC#82121-5)
value: 148 reads per base pair (Details: UCUM code 1 = '1')
Entry 12 - fullUrl = urn:uuid:c3587931-242f-4129-93f9-be24500c8f29
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncology-report-example-12"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)
effective: 2023-03-05
performer: See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
specimen: id: UNKNOWN
component
code: Genomic source class (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: RYR1 (HUGO Gene Nomenclature Committee Genes#HGNC:10483)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)
component
code: DNA change (c.HGVS) (LOINC#48004-6)
value: NM_000540.3:c.4964G>A (Human Genome Variation Society nomenclature#NM_000540.3:c.4964G>A)
component
code: DNA change type (LOINC#48019-4)
value: substitution (sequenceontology.org#SO:1000002)
component
code: Amino acid change (pHGVS) (LOINC#48005-3)
value: NP_000531.2:p.Arg1655Leu (Human Genome Variation Society nomenclature#NP_000531.2:p.Arg1655Leu)
component
code: Transcript reference sequence [ID] (LOINC#51958-7)
value: NM_000540.3 (Gene Reference Sequence Collection#NM_000540.2)
component
code: Genomic ref allele [ID] (LOINC#69547-8)
value: G
component
code: Sample VAF (LOINC#81258-6)
value: 0.2151 relative frequency of a particular allele in the specimen (Details: UCUM code 1 = '1')
component
code: Allelic read depth (LOINC#82121-5)
value: 93 reads per base pair (Details: UCUM code 1 = '1')
Entry 13 - fullUrl = urn:uuid:41695fc0-1fd5-4cc8-95e6-82b2848a5cb6
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncology-report-example-13"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)
effective: 2023-03-05
performer: See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
specimen: id: UNKNOWN
component
code: Genomic source class (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: SACS (HUGO Gene Nomenclature Committee Genes#HGNC:10519)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)
component
code: DNA change (c.HGVS) (LOINC#48004-6)
value: NM_014363.5:c.12118G>A (Human Genome Variation Society nomenclature#NM_014363.5:c.12118G>A)
component
code: DNA change type (LOINC#48019-4)
value: substitution (sequenceontology.org#SO:1000002)
component
code: Transcript reference sequence [ID] (LOINC#51958-7)
value: NM_014363.5 (Gene Reference Sequence Collection#NM_014363.5)
component
code: Genomic ref allele [ID] (LOINC#69547-8)
value: C
component
code: Sample VAF (LOINC#81258-6)
value: 0.3333 relative frequency of a particular allele in the specimen (Details: UCUM code 1 = '1')
component
code: Allelic read depth (LOINC#82121-5)
value: 60 reads per base pair (Details: UCUM code 1 = '1')
Entry 14 - fullUrl = urn:uuid:58eb14f6-4059-4168-86a9-155ae61d30e2
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncology-report-example-14"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)
effective: 2023-03-05
performer: See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
specimen: id: UNKNOWN
component
code: Genomic source class (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: SLIT2 (HUGO Gene Nomenclature Committee Genes#HGNC:11086)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)
component
code: DNA change (c.HGVS) (LOINC#48004-6)
value: NM_004787.3:c.1290C>A (Human Genome Variation Society nomenclature#NM_004787.3:c.1290C>A)
component
code: DNA change type (LOINC#48019-4)
value: substitution (sequenceontology.org#SO:1000002)
component
code: Transcript reference sequence [ID] (LOINC#51958-7)
value: NM_004787.3 (Gene Reference Sequence Collection#NM_004787.3)
component
code: Genomic ref allele [ID] (LOINC#69547-8)
value: C
component
code: Sample VAF (LOINC#81258-6)
value: 0.2642 relative frequency of a particular allele in the specimen (Details: UCUM code 1 = '1')
component
code: Allelic read depth (LOINC#82121-5)
value: 53 reads per base pair (Details: UCUM code 1 = '1')
Entry 15 - fullUrl = urn:uuid:1a71e80f-b044-4a91-80e1-eadbe5a53dca
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncology-report-example-15"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)
effective: 2023-03-05
performer: See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
specimen: id: UNKNOWN
component
code: Genomic source class (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: SMARCA4 (HUGO Gene Nomenclature Committee Genes#HGNC:11100)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)
component
code: DNA change (c.HGVS) (LOINC#48004-6)
value: NM_003072.5:c.2372C>T (Human Genome Variation Society nomenclature#NM_003072.5:c.2372C>T)
component
code: DNA change type (LOINC#48019-4)
value: substitution (sequenceontology.org#SO:1000002)
component
code: Amino acid change (pHGVS) (LOINC#48005-3)
value: NP_003063.2:p.Ala791Val (Human Genome Variation Society nomenclature#NP_003063.2:p.Ala791Val)
component
code: Transcript reference sequence [ID] (LOINC#51958-7)
value: NM_003072.5 (Gene Reference Sequence Collection#NM_003072.5)
component
code: Genomic ref allele [ID] (LOINC#69547-8)
value: C
component
code: Sample VAF (LOINC#81258-6)
value: 0.1938 relative frequency of a particular allele in the specimen (Details: UCUM code 1 = '1')
component
code: Allelic read depth (LOINC#82121-5)
value: 160 reads per base pair (Details: UCUM code 1 = '1')
Entry 16 - fullUrl = urn:uuid:6a80003f-822d-489e-8286-1f1dcba56dfa
Request:
POST DiagnosticReport
Resource DiagnosticReport:
Genetic analysis report (Genetics)
Subject Not done yet Reported 2019-09-15 11:35:05-0400 Identifier: id: 42867 Report Details
Code Value When For Genetic variant assessment Present 2023-03-05 Genetic variant assessment Present 2023-03-05 Genetic variant assessment Present 2023-03-05 Genetic variant assessment Present 2023-03-05 Genetic variant assessment Present 2023-03-05 Genetic variant assessment Present 2023-03-05 Genetic variant assessment Present 2023-03-05 Genetic variant assessment Present 2023-03-05 Genetic variant assessment Present 2023-03-05 Genetic variant assessment Present 2023-03-05 Genetic variant assessment Present 2023-03-05 Genetic variant assessment Present 2023-03-05
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0-ballot based on FHIR 4.0.1. Generated 2023-12-18
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