HL7.FHIR.US.MCODE\gx-genomic-bundle-adam-anyperson

This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.1.0. For a full list of available versions, see the Directory of published versions

Example Bundle: gx-genomic-bundle-adam-anyperson

Bundle gx-genomic-bundle-adam-anyperson of type collection

Entry 1 - fullUrl = http://example.org/fhir/Patient/gx-cancer-patient-adam-anyperson

Resource Patient:

Adam Anyperson Male, DoB: 1990-01-01 ( Medical Record Number: 123456789)

Entry 2 - fullUrl = http://example.org/fhir/DiagnosticReport/gx-genomics-report-adam-anyperson

Resource DiagnosticReport:

Genetic analysis report (Genetics)
Subject Adam Anyperson male, DoB: 1990-01-01 ( Medical Record Number: 123456789)
When For 2022-02-15 19:28:58+0500
Report Details
Code Value When For
Genetic variant assessment Present
Genetic variant assessment Present 2019-04-01
Genetic variant assessment Present 2019-04-01
Genetic variant assessment Present 2019-04-01
Genetic variant assessment Present 2019-04-01
Genetic variant assessment Present 2019-04-01
Genetic variant assessment Present 2019-04-01
Genetic variant assessment Present 2019-04-01
Diagnostic Implication 2019-04-01
Diagnostic Implication 2019-04-01
Diagnostic Implication 2019-04-01
Genetic variant assessment Present 2019-04-01
Genetic variant assessment Absent 2019-04-01
Mutations/Megabase [# Ratio] in Tumor 57.1 1/1000000{Base}
Microsatellite instability [Interpretation] in Cancer specimen Qualitative MSI-H
Therapeutic Implication
Therapeutic Implication
Therapeutic Implication
Therapeutic Implication
Therapeutic Implication

Entry 3 - fullUrl = http://example.org/fhir/ServiceRequest/gx-order-tumornormal-tempus-inc

Resource ServiceRequest:

Generated Narrative: ServiceRequest
Resource ServiceRequest "gx-order-tumornormal-tempus-inc"
Texts
- Div
* <div/>
identifier: Filler Identifier: 22howe
status: COMPLETED
intent: ORDER
code: xT - 648 gene panel (www.tempus.com#XT.V4)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)

Entry 4 - fullUrl = http://example.org/fhir/Practitioner/gx-practitioner-test-pathologist

Resource Practitioner:

Generated Narrative: Practitioner
Resource Practitioner "gx-practitioner-test-pathologist"
Texts
- Div
* <div/>
name: Test Pathologist, MD

Entry 5 - fullUrl = http://example.org/fhir/Specimen/gx-genomic-specimen-tumornormal-tumor

Resource Specimen:

Generated Narrative: Specimen
Resource Specimen "gx-genomic-specimen-tumornormal-tumor"
Profile: Human Specimen Profile
Texts
- Div
* <div/>
status: AVAILABLE
type: Tumor (specimenType#TUMOR)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
receivedTime: 2021-02-09 21:30:50+0500
Collections
- Collected[x] BodySite
* 2021-02-06 17:15:00+0500 Left lung structure (body structure) (SNOMED CT[Intl]#44029006)

Entry 6 - fullUrl = http://example.org/fhir/Specimen/gx-genomic-specimen-tumornormal-normal

Resource Specimen:

Generated Narrative: Specimen
Resource Specimen "gx-genomic-specimen-tumornormal-normal"
Profile: Human Specimen Profile
Texts
- Div
* <div/>
status: AVAILABLE
type: Whole Blood (specimenType#BLD)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
receivedTime: 2021-02-09 21:30:50+0500
Collections
- Collected[x]
* 2021-02-06 17:15:00+0500

Entry 7 - fullUrl = http://example.org/fhir/Observation/gx-genomic-variant-somatic-bap1-indel

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-variant-somatic-bap1-indel"
Profile: Genomic Variant Profile
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: BAP1 (HUGO Gene Nomenclature Committee Genes#HGNC:950; gene#3815)
component
code: Transcript reference sequence [ID] (LOINC#51958-7)
value: NM_004656.4 (Gene Reference Sequence Collection#NM_004656)
component
code: DNA change (c.HGVS) (LOINC#48004-6)
value: NC_000003.11(NM_004656.4):c.1768C>T (Human Genome Variation Society nomenclature#NM_004656.4:c.1768C>T)
component
code: Amino acid change (pHGVS) (LOINC#48005-3)
value: NP_004647.1:p.(Gln590Ter) (Human Genome Variation Society nomenclature#NP_004647.1:p.(Gln590Ter))
component
code: Genomic source class [Type] (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Sample variant allelic frequency [NFr] (LOINC#81258-6)
value: 57.4 % (Details: UCUM code % = '%')
component
code: Molecular Consequence (To Be Determined Codes#molecular-consequence)
value: stop_gained (#SO:0001587)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)

Entry 8 - fullUrl = http://example.org/fhir/Observation/gx-genomic-variant-somatic-cdkn2a-cnv

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-variant-somatic-cdkn2a-cnv"
Profile: Genomic Variant Profile
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: CDKN2A (HUGO Gene Nomenclature Committee Genes#HGNC:1787; gene#1029)
component
code: Genomic source class [Type] (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Molecular Consequence (To Be Determined Codes#molecular-consequence)
value: copy_number_loss (#SO:0001743)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)

Entry 9 - fullUrl = http://example.org/fhir/Observation/gx-genomic-variant-somatic-cdkn2b-cnv

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-variant-somatic-cdkn2b-cnv"
Profile: Genomic Variant Profile
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: CDKN2B (HUGO Gene Nomenclature Committee Genes#HGNC:1788; gene#1030)
component
code: Genomic source class [Type] (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Molecular Consequence (To Be Determined Codes#molecular-consequence)
value: copy_number_loss (#SO:0001743)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)

Entry 10 - fullUrl = http://example.org/fhir/Observation/gx-genomic-variant-somatic-kdm5d

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-variant-somatic-kdm5d"
Profile: Genomic Variant Profile
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: KDM5D (HUGO Gene Nomenclature Committee Genes#HGNC:11115; gene#8284)
component
code: Genomic source class [Type] (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Molecular Consequence (To Be Determined Codes#molecular-consequence)
value: copy_number_loss (#SO:0001743)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)

Entry 11 - fullUrl = http://example.org/fhir/Observation/gx-genomic-variant-somatic-mtap

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-variant-somatic-mtap"
Profile: Genomic Variant Profile
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: MTAP (HUGO Gene Nomenclature Committee Genes#HGNC:7413; gene#4507)
component
code: Genomic source class [Type] (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Molecular Consequence (To Be Determined Codes#molecular-consequence)
value: copy_number_loss (#SO:0001743)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)

Entry 12 - fullUrl = http://example.org/fhir/Observation/gx-genomic-variant-somatic-mycn

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-variant-somatic-mycn"
Profile: Genomic Variant Profile
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: MYCN (HUGO Gene Nomenclature Committee Genes#HGNC:7559; gene#4613)
component
code: Genomic source class [Type] (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Molecular Consequence (To Be Determined Codes#molecular-consequence)
value: copy_number_gain (#SO:0001742)
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)

Entry 13 - fullUrl = http://example.org/fhir/Observation/gx-genomic-variant-somatic-pof1b

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-variant-somatic-pof1b"
Profile: Genomic Variant Profile
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: POF1B (HUGO Gene Nomenclature Committee Genes#HGNC:13711; gene#79983)
component
code: Genomic source class [Type] (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Molecular Consequence (To Be Determined Codes#molecular-consequence)
value: missense_variant (#SO:0001583)
component
code: Transcript reference sequence [ID] (LOINC#51958-7)
value: NM_004656 (Gene Reference Sequence Collection#NM_004656)
component
code: DNA change (c.HGVS) (LOINC#48004-6)
value: NM_001307940.2:c.430C>T (Human Genome Variation Society nomenclature#NM_001307940.2:c.430C>T)
component
code: Amino acid change (pHGVS) (LOINC#48005-3)
value: NP_001294869.1:p.(Pro144Ser) (Human Genome Variation Society nomenclature#NP_001294869.1:p.(Pro144Ser))
component
code: Sample variant allelic frequency [NFr] (LOINC#81258-6)
value: 78.6 % (Details: UCUM code % = '%')
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)

Entry 14 - fullUrl = http://example.org/fhir/Observation/gx-genomic-variant-somatic-polrmt

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-variant-somatic-polrmt"
Profile: Genomic Variant Profile
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: POLRMT (gene#5442)
component
code: Genomic source class [Type] (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: Molecular Consequence (To Be Determined Codes#molecular-consequence)
value: missense_variant (#SO:0001583)
component
code: Transcript reference sequence [ID] (LOINC#51958-7)
value: NM_005035 (Gene Reference Sequence Collection#NM_004656)
component
code: DNA change (c.HGVS) (LOINC#48004-6)
value: NM_005035.4:c.598G>A (Human Genome Variation Society nomenclature#NM_005035.4:c.598G>A)
component
code: Amino acid change (pHGVS) (LOINC#48005-3)
value: NP_005026.3:p.(Gly200Arg) (Human Genome Variation Society nomenclature#NP_005026.3:p.(Gly200Arg))
component
code: Sample variant allelic frequency [NFr] (LOINC#81258-6)
value: 75.6 % (Details: UCUM code % = '%')
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)

Entry 15 - fullUrl = http://example.org/fhir/Observation/gx-genomic-diagnostic-implication-bap1

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-diagnostic-implication-bap1"
Profile: Diagnostic Implication
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Diagnostic Implication (To Be Determined Codes#diagnostic-implication)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
derivedFrom: See above (Observation/gx-genomic-variant-somatic-bap1-indel)
Components
- Code Value[x]
* Functional Effect (To Be Determined Codes#functional-effect) loss of function variant (#SO:0002054)

Entry 16 - fullUrl = http://example.org/fhir/Observation/gx-genomic-diagnostic-implication-pof1b

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-diagnostic-implication-pof1b"
Profile: Diagnostic Implication
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Diagnostic Implication (To Be Determined Codes#diagnostic-implication)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
derivedFrom: See above (Observation/gx-genomic-variant-somatic-pof1b)
Components
- Code Value[x]
* Genetic variation clinical significance [Imp] (LOINC#53037-8) Uncertain significance (LOINC#LA26333-7)

Entry 17 - fullUrl = http://example.org/fhir/Observation/gx-genomic-diagnostic-implication-polrmt

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-diagnostic-implication-polrmt"
Profile: Diagnostic Implication
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Diagnostic Implication (To Be Determined Codes#diagnostic-implication)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
derivedFrom: See above (Observation/gx-genomic-variant-somatic-polrmt)
Components
- Code Value[x]
* Genetic variation clinical significance [Imp] (LOINC#53037-8) Uncertain significance (LOINC#LA26333-7)

Entry 18 - fullUrl = http://example.org/fhir/Observation/gx-genomic-variant-fusion-met-alk

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-variant-fusion-met-alk"
Profile: Genomic Variant Profile
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: MET (HUGO Gene Nomenclature Committee Genes#HGNC:7029; gene#4233)
component
code: Gene studied [ID] (LOINC#48018-6)
value: ALK (HUGO Gene Nomenclature Committee Genes#HGNC:427; gene#238)
component
code: DNA Change Type (LOINC#48019-4)
value: complex chromosomal rearrangement (#SO:0002062)
component
code: Genomic source class [Type] (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)

Entry 19 - fullUrl = http://example.org/fhir/Observation/gx-genomic-variant-pertinent-negative-nras-kit-braf

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-variant-pertinent-negative-nras-kit-braf"
Profile: Genomic Variant Profile
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Genetic variant assessment (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
value: Absent (LOINC#LA9634-2)
method: Sequencing (LOINC#LA26398-0)
component
code: Gene studied [ID] (LOINC#48018-6)
value: NRAS (HUGO Gene Nomenclature Committee Genes#HGNC:6342)
component
code: Gene studied [ID] (LOINC#48018-6)
value: KIT (HUGO Gene Nomenclature Committee Genes#HGNC:7989)
component
code: Gene studied [ID] (LOINC#48018-6)
value: BRAF (HUGO Gene Nomenclature Committee Genes#HGNC:1097)

Entry 20 - fullUrl = http://example.org/fhir/Observation/gx-genomic-tmb

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-tmb"
Profile: Tumor Mutation Burden
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Mutations/Megabase [# Ratio] in Tumor (LOINC#94076-7)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
value: 57.1 1/1000000{Base} (Details: UCUM code 1/1000000{Base} = '1/1000000{Base}')

Entry 21 - fullUrl = http://example.org/fhir/Observation/gx-genomic-therapeutic-implication-alectinib

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-therapeutic-implication-alectinib"
Profile: Therapeutic Implication
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
derivedFrom: See above (Observation/gx-genomic-variant-fusion-met-alk)
component
code: Medication assessed [ID] (LOINC#51963-7)
value: alectinib (RxNorm#1727455)
component
code: Predicted Therapeutic Implication (To Be Determined Codes#predicted-therapeutic-implication)
value: Presumed responsive (LOINC#LA9661-5)

Entry 22 - fullUrl = http://example.org/fhir/Observation/gx-genomic-therapeutic-implication-brigatinib

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-therapeutic-implication-brigatinib"
Profile: Therapeutic Implication
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
derivedFrom: See above (Observation/gx-genomic-variant-fusion-met-alk)
component
code: Medication assessed [ID] (LOINC#51963-7)
value: brigatinib (RxNorm#1921217)
component
code: Predicted Therapeutic Implication (To Be Determined Codes#predicted-therapeutic-implication)
value: Presumed responsive (LOINC#LA9661-5)

Entry 23 - fullUrl = http://example.org/fhir/Observation/gx-genomic-therapeutic-implication-ceritinib

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-therapeutic-implication-ceritinib"
Profile: Therapeutic Implication
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
derivedFrom: See above (Observation/gx-genomic-variant-fusion-met-alk)
component
code: Medication assessed [ID] (LOINC#51963-7)
value: ceritinib (RxNorm#1535457)
component
code: Predicted Therapeutic Implication (To Be Determined Codes#predicted-therapeutic-implication)
value: Presumed responsive (LOINC#LA9661-5)

Entry 24 - fullUrl = http://example.org/fhir/Observation/gx-genomic-therapeutic-implication-crizotinib

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-therapeutic-implication-crizotinib"
Profile: Therapeutic Implication
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
derivedFrom: See above (Observation/gx-genomic-variant-fusion-met-alk)
component
code: Medication assessed [ID] (LOINC#51963-7)
value: crizotinib (RxNorm#1148495)
component
code: Predicted Therapeutic Implication (To Be Determined Codes#predicted-therapeutic-implication)
value: Presumed responsive (LOINC#LA9661-5)

Entry 25 - fullUrl = http://example.org/fhir/Observation/gx-genomic-therapeutic-implication-lorlatinib

Resource Observation:

Generated Narrative: Observation
Resource Observation "gx-genomic-therapeutic-implication-lorlatinib"
Profile: Therapeutic Implication
Texts
- Div
* <div/>
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
derivedFrom: See above (Observation/gx-genomic-variant-fusion-met-alk)
component
code: Medication assessed [ID] (LOINC#51963-7)
value: lorlatinib (RxNorm#2103164)
component
code: Predicted Therapeutic Implication (To Be Determined Codes#predicted-therapeutic-implication)
value: Presumed responsive (LOINC#LA9661-5)