minimal Common Oncology Data Elements (mCODE) Implementation Guide
4.0.0-ballot - STU4 Ballot United States of America flag

minimal Common Oncology Data Elements (mCODE) Implementation Guide, published by HL7 International / Clinical Interoperability Council. This guide is not an authorized publication; it is the continuous build for version 4.0.0-ballot built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/fhir-mCODE-ig/ and changes regularly. See the Directory of published versions

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

Generated Narrative: 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:

Generated Narrative: Patient gx-cancer-patient-adam-anyperson

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

Other Id:Patient external identifier/22ea1d1b-03a5-47d6-81e0-b9b4cbb15ccf (use: usual, )
Contact Detail987 Main St Anytown 12345 US
US Core Birth Sex ExtensionM

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

Resource DiagnosticReport:

Generated Narrative: DiagnosticReport gx-genomics-report-adam-anyperson

Genetic analysis report (Genetics)

SubjectAdam Anyperson Male, DoB: 1990-01-01 ( Medical Record Number: 123456789)
When For2022-02-15 19:28:58+0500
Performer Organization Gensop Labs, Inc.

Report Details

CodeValueFlagsWhen For
Genetic variant assessmentPresentFinal2019-04-01
Genetic variant assessmentPresentFinal2019-04-01
Genetic variant assessmentPresentFinal2019-04-01
Genetic variant assessmentPresentFinal2019-04-01
Genetic variant assessmentPresentFinal2019-04-01
Genetic variant assessmentPresentFinal2019-04-01
Genetic variant assessmentPresentFinal2019-04-01
Genetic variant assessmentPresentFinal2019-04-01
Diagnostic ImplicationFinal2019-04-01
Diagnostic ImplicationFinal2019-04-01
Diagnostic ImplicationFinal2019-04-01
Genetic variant assessmentPresentFinal2019-04-01
Genetic variant assessmentAbsentFinal2019-04-01
Mutations/Megabase [# Ratio] in Tumor57.1 1/1000000{Base} (Details: UCUM code1/1000000{Base} = '1/1000000{Base}')Final2019-04-01
Microsatellite instability [Interpretation] in Cancer specimen QualitativeMSI-HFinal2019-04-01
Therapeutic ImplicationFinal2019-04-01
Therapeutic ImplicationFinal2019-04-01
Therapeutic ImplicationFinal2019-04-01
Therapeutic ImplicationFinal2019-04-01
Therapeutic ImplicationFinal2019-04-01

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

Resource ServiceRequest:

Generated Narrative: ServiceRequest gx-order-tumornormal-gensop-inc

identifier: Filler Identifier/22howe

status: Completed

intent: Order

code: No display for ServiceRequest.code (concept: xT - 648 gene panel)

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

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

Resource Practitioner:

Generated Narrative: Practitioner gx-practitioner-test-pathologist

name: Test Pathologist, MD

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

Resource Specimen:

Generated Narrative: Specimen gx-genomic-specimen-tumornormal-tumor

status: Available

type: Tumor

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

receivedTime: 2021-02-09 21:30:50+0500

Collections

-Collected[x]BodySite
*2021-02-06 17:15:00+0500No display for Specimen.collection.bodySite (concept: Left lung structure (body structure))

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

Resource Specimen:

Generated Narrative: Specimen gx-genomic-specimen-tumornormal-normal

status: Available

type: Whole Blood

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

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 gx-genomic-variant-somatic-bap1-indel

status: Final

category: Laboratory

code: Genetic variant assessment

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

value: Present

method: Sequencing

component

code: Gene studied [ID]

value: BAP1

component

code: Transcript reference sequence [ID]

value: NM_004656.4

component

code: DNA change (c.HGVS)

value: NM_004656.4:c.1768C>T

component

code: Amino acid change (pHGVS)

value: NP_004647.1:p.(Gln590Ter)

component

code: Genomic source class [Type]

value: Somatic

component

code: Sample variant allelic frequency [NFr]

value: 57.4 % (Details: UCUM code% = '%')

component

code: Molecular Consequence

value: stop_gained

component

code: Human reference sequence assembly version

value: GRCh37

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

Resource Observation:

Generated Narrative: Observation gx-genomic-variant-somatic-cdkn2a-cnv

status: Final

category: Laboratory

code: Genetic variant assessment

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

value: Present

method: Sequencing

component

code: Gene studied [ID]

value: CDKN2A

component

code: Genomic source class [Type]

value: Somatic

component

code: Molecular Consequence

value: copy_number_loss

component

code: Human reference sequence assembly version

value: GRCh37

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

Resource Observation:

Generated Narrative: Observation gx-genomic-variant-somatic-cdkn2b-cnv

status: Final

category: Laboratory

code: Genetic variant assessment

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

value: Present

method: Sequencing

component

code: Gene studied [ID]

value: CDKN2B

component

code: Genomic source class [Type]

value: Somatic

component

code: Molecular Consequence

value: copy_number_loss

component

code: Human reference sequence assembly version

value: GRCh37

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

Resource Observation:

Generated Narrative: Observation gx-genomic-variant-somatic-kdm5d

status: Final

category: Laboratory

code: Genetic variant assessment

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

value: Present

method: Sequencing

component

code: Gene studied [ID]

value: KDM5D

component

code: Genomic source class [Type]

value: Somatic

component

code: Molecular Consequence

value: copy_number_loss

component

code: Human reference sequence assembly version

value: GRCh37

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

Resource Observation:

Generated Narrative: Observation gx-genomic-variant-somatic-mtap

status: Final

category: Laboratory

code: Genetic variant assessment

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

value: Present

method: Sequencing

component

code: Gene studied [ID]

value: MTAP

component

code: Genomic source class [Type]

value: Somatic

component

code: Molecular Consequence

value: copy_number_loss

component

code: Human reference sequence assembly version

value: GRCh37

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

Resource Observation:

Generated Narrative: Observation gx-genomic-variant-somatic-mycn

status: Final

category: Laboratory

code: Genetic variant assessment

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

value: Present

method: Sequencing

component

code: Gene studied [ID]

value: MYCN

component

code: Genomic source class [Type]

value: Somatic

component

code: Molecular Consequence

value: copy_number_gain

component

code: Human reference sequence assembly version

value: GRCh37

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

Resource Observation:

Generated Narrative: Observation gx-genomic-variant-somatic-pof1b

status: Final

category: Laboratory

code: Genetic variant assessment

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

value: Present

method: Sequencing

component

code: Gene studied [ID]

value: POF1B

component

code: Genomic source class [Type]

value: Somatic

component

code: Molecular Consequence

value: missense_variant

component

code: Transcript reference sequence [ID]

value: NM_004656

component

code: DNA change (c.HGVS)

value: NM_001307940.2:c.430C>T

component

code: Amino acid change (pHGVS)

value: NP_001294869.1:p.(Pro144Ser)

component

code: Sample variant allelic frequency [NFr]

value: 78.6 % (Details: UCUM code% = '%')

component

code: Human reference sequence assembly version

value: GRCh37

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

Resource Observation:

Generated Narrative: Observation gx-genomic-variant-somatic-polrmt

status: Final

category: Laboratory

code: Genetic variant assessment

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

value: Present

method: Sequencing

component

code: Gene studied [ID]

value: POLRMT

component

code: Genomic source class [Type]

value: Somatic

component

code: Molecular Consequence

value: missense_variant

component

code: Transcript reference sequence [ID]

value: NM_005035

component

code: DNA change (c.HGVS)

value: NM_005035.4:c.598G>A

component

code: Amino acid change (pHGVS)

value: NP_005026.3:p.(Gly200Arg)

component

code: Sample variant allelic frequency [NFr]

value: 75.6 % (Details: UCUM code% = '%')

component

code: Human reference sequence assembly version

value: GRCh37

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

Resource Observation:

Generated Narrative: Observation gx-genomic-diagnostic-implication-bap1

status: Final

category: Laboratory

code: Diagnostic Implication

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

derivedFrom: Observation Genetic variant assessment

Components

-CodeValue[x]
*Functional Effectloss of function variant

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

Resource Observation:

Generated Narrative: Observation gx-genomic-diagnostic-implication-pof1b

status: Final

category: Laboratory

code: Diagnostic Implication

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

derivedFrom: Observation Genetic variant assessment

Components

-CodeValue[x]
*Genetic variation clinical significance [Imp]Uncertain significance

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

Resource Observation:

Generated Narrative: Observation gx-genomic-diagnostic-implication-polrmt

status: Final

category: Laboratory

code: Diagnostic Implication

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

derivedFrom: Observation Genetic variant assessment

Components

-CodeValue[x]
*Genetic variation clinical significance [Imp]Uncertain significance

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

Resource Observation:

Generated Narrative: Observation gx-genomic-variant-fusion-met-alk

status: Final

category: Laboratory

code: Genetic variant assessment

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

value: Present

method: Sequencing

component

code: Gene studied [ID]

value: MET

component

code: Gene studied [ID]

value: ALK

component

code: DNA change type

value: complex chromosomal rearrangement

component

code: Genomic source class [Type]

value: Somatic

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

Resource Observation:

Generated Narrative: Observation gx-genomic-variant-pertinent-negative-nras-kit-braf

status: Final

category: Laboratory

code: Genetic variant assessment

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

value: Absent

method: Sequencing

component

code: Gene studied [ID]

value: NRAS

component

code: Gene studied [ID]

value: KIT

component

code: Gene studied [ID]

value: BRAF

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

Resource Observation:

Generated Narrative: Observation gx-genomic-tmb

status: Final

category: Laboratory

code: Mutations/Megabase [# Ratio] in Tumor

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

value: 57.1 1/1000000{Base} (Details: UCUM code1/1000000{Base} = '1/1000000{Base}')

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

Resource Observation:

Generated Narrative: Observation gx-genomic-therapeutic-implication-alectinib

status: Final

category: Laboratory

code: Therapeutic Implication

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

derivedFrom: Observation Genetic variant assessment

component

code: Medication assessed [ID]

value: alectinib

component

code: Predicted Therapeutic Implication

value: Presumed responsive

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

Resource Observation:

Generated Narrative: Observation gx-genomic-therapeutic-implication-brigatinib

status: Final

category: Laboratory

code: Therapeutic Implication

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

derivedFrom: Observation Genetic variant assessment

component

code: Medication assessed [ID]

value: brigatinib

component

code: Predicted Therapeutic Implication

value: Presumed responsive

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

Resource Observation:

Generated Narrative: Observation gx-genomic-therapeutic-implication-ceritinib

status: Final

category: Laboratory

code: Therapeutic Implication

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

derivedFrom: Observation Genetic variant assessment

component

code: Medication assessed [ID]

value: ceritinib

component

code: Predicted Therapeutic Implication

value: Presumed responsive

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

Resource Observation:

Generated Narrative: Observation gx-genomic-therapeutic-implication-crizotinib

status: Final

category: Laboratory

code: Therapeutic Implication

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

derivedFrom: Observation Genetic variant assessment

component

code: Medication assessed [ID]

value: crizotinib

component

code: Predicted Therapeutic Implication

value: Presumed responsive

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

Resource Observation:

Generated Narrative: Observation gx-genomic-therapeutic-implication-lorlatinib

status: Final

category: Laboratory

code: Therapeutic Implication

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

effective: 2019-04-01

performer: Practitioner Owen Oncologist

derivedFrom: Observation Genetic variant assessment

component

code: Medication assessed [ID]

value: lorlatinib

component

code: Predicted Therapeutic Implication

value: Presumed responsive