This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v3.0.0: STU 3) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions
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 69548-6 Present 2019-04-01 69548-6 Present 2019-04-01 69548-6 Present 2019-04-01 69548-6 Present 2019-04-01 69548-6 Present 2019-04-01 69548-6 Present 2019-04-01 69548-6 Present 2019-04-01 69548-6 Present 2019-04-01 Diagnostic Implication 2019-04-01 Diagnostic Implication 2019-04-01 Diagnostic Implication 2019-04-01 69548-6 Present 2019-04-01 69548-6 Absent 2019-04-01 94076-7 57.1 1/1000000{Base} 2019-04-01 81695-9 MSI-H 2019-04-01 Therapeutic Implication 2019-04-01 Therapeutic Implication 2019-04-01 Therapeutic Implication 2019-04-01 Therapeutic Implication 2019-04-01 Therapeutic Implication 2019-04-01
Entry 3 - fullUrl = http://example.org/fhir/ServiceRequest/gx-order-tumornormal-gensop-inc
Resource ServiceRequest:
Generated Narrative: ServiceRequest
Resource ServiceRequest "gx-order-tumornormal-gensop-inc"
identifier: Filler Identifier: 22howe
status: COMPLETED
intent: ORDER
code: xT - 648 gene panel (www.gensop.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"
name: Test Pathologist, MD
Entry 5 - fullUrl = http://example.org/fhir/Specimen/gx-genomic-specimen-tumornormal-tumor
Resource Specimen:
Resource Specimen "gx-genomic-specimen-tumornormal-tumor"
Profile: Human Specimen Profile
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#44029006)
Entry 6 - fullUrl = http://example.org/fhir/Specimen/gx-genomic-specimen-tumornormal-normal
Resource Specimen:
Resource Specimen "gx-genomic-specimen-tumornormal-normal"
Profile: Human Specimen Profile
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
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: 69548-6 (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: 48018-6 (LOINC#48018-6)
value: BAP1 (HUGO Gene Nomenclature Committee Genes#HGNC:950; gene#3815)
component
code: 51958-7 (LOINC#51958-7)
value: NM_004656.4 (Gene Reference Sequence Collection#NM_004656)
component
code: 48004-6 (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: 48005-3 (LOINC#48005-3)
value: NP_004647.1:p.(Gln590Ter) (Human Genome Variation Society nomenclature#NP_004647.1:p.(Gln590Ter))
component
code: 48002-0 (LOINC#48002-0)
value: Somatic (LOINC#LA6684-0)
component
code: 81258-6 (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: 62374-4 (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
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: 69548-6 (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: 48018-6 (LOINC#48018-6)
value: CDKN2A (HUGO Gene Nomenclature Committee Genes#HGNC:1787; gene#1029)
component
code: 48002-0 (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: 62374-4 (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
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: 69548-6 (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: 48018-6 (LOINC#48018-6)
value: CDKN2B (HUGO Gene Nomenclature Committee Genes#HGNC:1788; gene#1030)
component
code: 48002-0 (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: 62374-4 (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
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: 69548-6 (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: 48018-6 (LOINC#48018-6)
value: KDM5D (HUGO Gene Nomenclature Committee Genes#HGNC:11115; gene#8284)
component
code: 48002-0 (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: 62374-4 (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
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: 69548-6 (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: 48018-6 (LOINC#48018-6)
value: MTAP (HUGO Gene Nomenclature Committee Genes#HGNC:7413; gene#4507)
component
code: 48002-0 (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: 62374-4 (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
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: 69548-6 (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: 48018-6 (LOINC#48018-6)
value: MYCN (HUGO Gene Nomenclature Committee Genes#HGNC:7559; gene#4613)
component
code: 48002-0 (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: 62374-4 (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
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: 69548-6 (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: 48018-6 (LOINC#48018-6)
value: POF1B (HUGO Gene Nomenclature Committee Genes#HGNC:13711; gene#79983)
component
code: 48002-0 (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: 51958-7 (LOINC#51958-7)
value: NM_004656 (Gene Reference Sequence Collection#NM_004656)
component
code: 48004-6 (LOINC#48004-6)
value: NM_001307940.2:c.430C>T (Human Genome Variation Society nomenclature#NM_001307940.2:c.430C>T)
component
code: 48005-3 (LOINC#48005-3)
value: NP_001294869.1:p.(Pro144Ser) (Human Genome Variation Society nomenclature#NP_001294869.1:p.(Pro144Ser))
component
code: 81258-6 (LOINC#81258-6)
value: 78.6 % (Details: UCUM code % = '%')
component
code: 62374-4 (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
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: 69548-6 (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: 48018-6 (LOINC#48018-6)
value: POLRMT (gene#5442)
component
code: 48002-0 (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: 51958-7 (LOINC#51958-7)
value: NM_005035 (Gene Reference Sequence Collection#NM_004656)
component
code: 48004-6 (LOINC#48004-6)
value: NM_005035.4:c.598G>A (Human Genome Variation Society nomenclature#NM_005035.4:c.598G>A)
component
code: 48005-3 (LOINC#48005-3)
value: NP_005026.3:p.(Gly200Arg) (Human Genome Variation Society nomenclature#NP_005026.3:p.(Gly200Arg))
component
code: 81258-6 (LOINC#81258-6)
value: 75.6 % (Details: UCUM code % = '%')
component
code: 62374-4 (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
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
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
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
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
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
derivedFrom: See above (Observation/gx-genomic-variant-somatic-pof1b)
Components
Code Value[x] 53037-8 (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
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
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
derivedFrom: See above (Observation/gx-genomic-variant-somatic-polrmt)
Components
Code Value[x] 53037-8 (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
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: 69548-6 (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
component
code: 48018-6 (LOINC#48018-6)
value: MET (HUGO Gene Nomenclature Committee Genes#HGNC:7029; gene#4233)
component
code: 48018-6 (LOINC#48018-6)
value: ALK (HUGO Gene Nomenclature Committee Genes#HGNC:427; gene#238)
component
code: 48019-4 (LOINC#48019-4)
value: complex chromosomal rearrangement (#SO:0002062)
component
code: 48002-0 (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
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: 69548-6 (LOINC#69548-6)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
value: Absent (LOINC#LA9634-2)
method: Sequencing (LOINC#LA26398-0)
component
code: 48018-6 (LOINC#48018-6)
value: NRAS (HUGO Gene Nomenclature Committee Genes#HGNC:6342)
component
code: 48018-6 (LOINC#48018-6)
value: KIT (HUGO Gene Nomenclature Committee Genes#HGNC:7989)
component
code: 48018-6 (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
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: 94076-7 (LOINC#94076-7)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
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
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
derivedFrom: See above (Observation/gx-genomic-variant-fusion-met-alk)
component
code: 51963-7 (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
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
derivedFrom: See above (Observation/gx-genomic-variant-fusion-met-alk)
component
code: 51963-7 (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
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
derivedFrom: See above (Observation/gx-genomic-variant-fusion-met-alk)
component
code: 51963-7 (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
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
derivedFrom: See above (Observation/gx-genomic-variant-fusion-met-alk)
component
code: 51963-7 (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
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Therapeutic Implication (To Be Determined Codes#therapeutic-implication)
subject: See above (Patient/gx-cancer-patient-adam-anyperson)
effective: 2019-04-01
performer: Practitioner/us-core-practitioner-owen-oncologist " ONCOLOGIST"
derivedFrom: See above (Observation/gx-genomic-variant-fusion-met-alk)
component
code: 51963-7 (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)