GenomeX Data Exchange FHIR IG
0.2.0 - draft

GenomeX Data Exchange FHIR IG, published by MITRE. This guide is not an authorized publication; it is the continuous build for version 0.2.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/CodeX-HL7-FHIR-Accelerator/GenomeX-DataExchange/ and changes regularly. See the Directory of published versions

Example Bundle: HereditaryCancerTestingBundleCollectionNegative

Generated Narrative: Bundle HereditaryCancerTestingBundleCollectionNegative

Bundle HereditaryCancerTestingBundleCollectionNegative of type collection


Entry 1 - fullUrl = http://hapi-fhir-server:8080/fhir/Bundle/PatientFemale

Resource Patient:

Generated Narrative: Patient PatientFemale

version: 1; Last updated: 2024-09-25 00:02:13+0000;

Information Source: #mzuK1EHcvMPipAda

Jenny M (official) Female, DoB: 1988-02-12 ( Patient ID: 7fb905f171204b94b8ee33d33cb624e6 (use: official, ))


Active:true
Contact DetailUS (home)

Entry 2 - fullUrl = http://hapi-fhir-server:8080/fhir/Bundle/SpecimenBloodFemale

Resource Specimen:

Generated Narrative: Specimen SpecimenBloodFemale

identifier: http://www.somesystemabc.net/identifiers/specimens/07007253-BLD

status: Available

type: Blood specimen (specimen)

subject: Jenny M (official) Female, DoB: 1988-02-12 ( Patient ID: 7fb905f171204b94b8ee33d33cb624e6 (use: official, ))

receivedTime: 2023-07-06 17:06:06+0500

Collections

-Collected[x]
*2023-07-03 07:03:03+0500

Entry 3 - fullUrl = http://hapi-fhir-server:8080/fhir/Bundle/HereditaryCancerTestingGenomicStudyAnalysis

Resource Procedure:

Generated Narrative: Procedure HereditaryCancerTestingGenomicStudyAnalysis

Genomic Study Analysis Regions

  • description: protein-coding and exon-splicing regions
  • studied: BRCA2
  • studied: APC
  • studied: ATM
  • studied: AXIN2
  • studied: BAP1
  • studied: BARD1
  • studied: BMPR1A
  • studied: BRCA1
  • studied: BRIP1
  • studied: CDH1
  • studied: CDK4
  • studied: CDKN2A
  • studied: CHEK2
  • studied: CTNNA1
  • studied: FH
  • studied: FLCN
  • studied: HOXB13
  • studied: MEN1
  • studied: MET
  • studied: MLH1
  • studied: MSH2
  • studied: MSH3
  • studied: MSH6
  • studied: MMAYH
  • studied: NTHL1
  • studied: PALB2
  • studied: PMS2
  • studied: PTEN
  • studied: RAD51C
  • studied: RAD51D
  • studied: SDHA
  • studied: SDHB
  • studied: SDHC
  • studied: SDHD
  • studied: SMAD4
  • studied: STK11
  • studied: TP53
  • studied: TSC1
  • studied: TSC2
  • studied: VHL
  • studied: EGFR
  • studied: EPCAM
  • studied: GREM1
  • studied: MITF
  • studied: POLE
  • studied: POLD1
  • studied: RET
  • studied: TERT

Genomic Study Analysis Method Type: Sequence analysis of the entire coding region

Genomic Study Analysis Genome Build: GRCh38

Genomic Study Analysis Specimen: Specimen: identifier = http://www.somesystemabc.net/identifiers/specimens#07007253-BLD; status = available; type = Blood specimen (specimen); receivedTime = 2023-07-06 17:06:06+0500

Genomic Study Analysis Focus: Jenny M (official) Female, DoB: 1988-02-12 ( Patient ID: 7fb905f171204b94b8ee33d33cb624e6 (use: official, ))

Genomic Study Analysis Output

status: Completed

category: Laboratory

subject: Jenny M (official) Female, DoB: 1988-02-12 ( Patient ID: 7fb905f171204b94b8ee33d33cb624e6 (use: official, ))

note: Genes Analyzed: Sequencing (seq) and large rearrangement analyses were performed for all coding exons in the following genes, unless otherwise indicated: APC, ATM, AXIN2, BAP1, BARD1, BMPR1A, BRCA1, BRCA2, BRIP1, CDH1, CDK4, CDKN2A, CHEK2, CTNNA1, FH, FLCN, HOXB13 (seq only), MEN1, MET, MLH1, MSH2, MSH3 (excluding repetitive portions of exon 1), MSH6, MMAYH, NTHL1, PALB2, PMS2, PTEN, RAD51C, RAD51D, SDHA, SDHB, SDHC, SDHD, SMAD4, STK11, TP53, TSC1, TSC2, VHL. Limited promoter regions may also be analyzed for large rearrangements., Sequencing (seq) and/or large rearrangement (LR) analyses were performed only for the gene portions indicated in parenthesis for the following genes: EGFR (exons 18-21, seq and LR), EPCAM (exons 8-9, LR only), GREM1 (exon 1 and upstream regulatory regions, LR only), MITF (c.952, seq only), POLE (exonuclease domain, seq only), POLD1 (exonuclease domain, seq only), RET (exons 5, 8, 10, 11, 13-16 seq and LR), TERT (promoter c.DNA -1 to -70, seq only). Other genes not analyzed with this test may also be associated with cancer., Indication for Testing: It is our understanding that this individual was identified for testing due to a personal or family history suggestive of a hereditary predisposition for cancer., Associated Cancer Risks and Clinical Management: The "HereditaryCancerTesting Management Tool" associated with this report provides a summary of cancer risk and professional society medical management guidelines that may be useful in developing a plan for this patient based on any clinically significant test results and/or reported personal/family history. In some cases, a HereditaryCancerTesting Management Tool cannot be provided, such as when the result has a special interpretation or includes a mutation with unusual characteristics., Analysis Description: The Technical Specifications summary (myriad.com/technical-specifications) describes the analysis, method, performance, nomenclature, and interpretive criteria of this test. Current testing technologies are unable to definitively determine whether a variant is germline or somatic in origin, which may significantly impact risk estimates and medical management; therefore, these results should be correlated with this patient's personal and family history. The interpretation of this test may also be impacted if the patient has a hematologic malignancy or an allogeneic bone marrow transplant.


Entry 4 - fullUrl = http://hapi-fhir-server:8080/fhir/Bundle/PractitionerOrderingProvider

Resource Practitioner:

Generated Narrative: Practitioner PractitionerOrderingProvider

active: true

name: Laura Salma

address: 123 Main St. San Francisco CA 94080


Entry 5 - fullUrl = http://hapi-fhir-server:8080/fhir/Bundle/PractitionerPathologist

Resource Practitioner:

Generated Narrative: Practitioner PractitionerPathologist

identifier: United States National Provider Identifier/9123456789

active: true

name: Pauline Pathologist

gender: Female

address: 456 Laboratory Drive, Anytown, MA, 12345, USA

Qualifications

-Code
*Doctor of Medicine - MD

Entry 6 - fullUrl = http://hapi-fhir-server:8080/fhir/Bundle/HereditaryCancerTestingGenomicStudy

Resource Procedure:

Generated Narrative: Procedure HereditaryCancerTestingGenomicStudy

Genomic Study Analysis Extension: Procedure: extension = ,Sequence analysis of the entire coding region,GRCh38,->Specimen: identifier = http://www.somesystemabc.net/identifiers/specimens#07007253-BLD; status = available; type = Blood specimen (specimen); receivedTime = 2023-07-06 17:06:06+0500,->Jenny M (official) Female, DoB: 1988-02-12 ( Patient ID: 7fb905f171204b94b8ee33d33cb624e6 (use: official, )),; status = completed; category = Laboratory; performed[x] = 2023-02-02 01:01:10-0600; note = Genes Analyzed: Sequencing (seq) and large rearrangement analyses were performed for all coding exons in the following genes, unless otherwise indicated: APC, ATM, AXIN2, BAP1, BARD1, BMPR1A, BRCA1, BRCA2, BRIP1, CDH1, CDK4, CDKN2A, CHEK2, CTNNA1, FH, FLCN, HOXB13 (seq only), MEN1, MET, MLH1, MSH2, MSH3 (excluding repetitive portions of exon 1), MSH6, MMAYH, NTHL1, PALB2, PMS2, PTEN, RAD51C, RAD51D, SDHA, SDHB, SDHC, SDHD, SMAD4, STK11, TP53, TSC1, TSC2, VHL. Limited promoter regions may also be analyzed for large rearrangements.,Sequencing (seq) and/or large rearrangement (LR) analyses were performed only for the gene portions indicated in parenthesis for the following genes: EGFR (exons 18-21, seq and LR), EPCAM (exons 8-9, LR only), GREM1 (exon 1 and upstream regulatory regions, LR only), MITF (c.952, seq only), POLE (exonuclease domain, seq only), POLD1 (exonuclease domain, seq only), RET (exons 5, 8, 10, 11, 13-16 seq and LR), TERT (promoter c.DNA -1 to -70, seq only). Other genes not analyzed with this test may also be associated with cancer.,Indication for Testing: It is our understanding that this individual was identified for testing due to a personal or family history suggestive of a hereditary predisposition for cancer.,Associated Cancer Risks and Clinical Management: The "HereditaryCancerTesting Management Tool" associated with this report provides a summary of cancer risk and professional society medical management guidelines that may be useful in developing a plan for this patient based on any clinically significant test results and/or reported personal/family history. In some cases, a HereditaryCancerTesting Management Tool cannot be provided, such as when the result has a special interpretation or includes a mutation with unusual characteristics.,Analysis Description: The Technical Specifications summary (myriad.com/technical-specifications) describes the analysis, method, performance, nomenclature, and interpretive criteria of this test. Current testing technologies are unable to definitively determine whether a variant is germline or somatic in origin, which may significantly impact risk estimates and medical management; therefore, these results should be correlated with this patient's personal and family history. The interpretation of this test may also be impacted if the patient has a hematologic malignancy or an allogeneic bone marrow transplant.

status: Completed

category: Laboratory

code: HereditaryCancerTesting™ Hereditary Cancer Test

subject: Jenny M (official) Female, DoB: 1988-02-12 ( Patient ID: 7fb905f171204b94b8ee33d33cb624e6 (use: official, ))

note: Details About Non-Clinically Significant Variants: All individuals carry DNA changes (i.e., variants), and most variants do not increase an individual's risk of cancer or other diseases. When identified, variants of uncertain significance (VUS) are reported. Likely benign variants (Favor Polymorphisms) and benign variants (Polymorphisms) are not reported and available data indicate that these variants most likely do not cause increased cancer risk. Present evidence does not suggest that non-clinically significant variant findings be used to modify patient medical management beyond what is indicated by the personal and family history and any other clinically significant findings., Variant Classification: Organization's myVisionTM Variant Classification Program performs ongoing evaluations of variant classifications. In certain cases, healthcare providers may be contacted for more clinical information or to arrange family testing to aid in variant classification. When new evidence about a variant is identified and determined to result in clinical significance and management change, that information will automatically be made available to the healthcare provider through an amended report.


Entry 7 - fullUrl = http://hapi-fhir-server:8080/fhir/Bundle/HereditaryCancerTestingServiceRequest

Resource ServiceRequest:

Generated Narrative: ServiceRequest HereditaryCancerTestingServiceRequest

identifier: Laboratory Accession ID/1234567890

status: Active

intent: Plan

code: No display for ServiceRequest.code (concept: )

subject: Jenny M (official) Female, DoB: 1988-02-12 ( Patient ID: 7fb905f171204b94b8ee33d33cb624e6 (use: official, ))

requester: Practitioner Laura Salma

specimen: Specimen: identifier = http://www.somesystemabc.net/identifiers/specimens#07007253-BLD; status = available; type = Blood specimen (specimen); receivedTime = 2023-07-06 17:06:06+0500


Entry 8 - fullUrl = http://hapi-fhir-server:8080/fhir/Bundle/HereditaryCancerTestingOverInterNegative

Resource Observation:

Generated Narrative: Observation HereditaryCancerTestingOverInterNegative

status: Final

category: Laboratory

code: Discrete variation analysis overall interpretation

subject: Jenny M (official) Female, DoB: 1988-02-12 ( Patient ID: 7fb905f171204b94b8ee33d33cb624e6 (use: official, ))

value: Negative

specimen: Specimen: identifier = http://www.somesystemabc.net/identifiers/specimens#07007253-BLD; status = available; type = Blood specimen (specimen); receivedTime = 2023-07-06 17:06:06+0500

component

code: Conclusion Text

value: Organization HRD Status: NEGATIVE

component

code: Genetic Result: Negative - No Clinically Significant Mutation Identified

value: Note: "CLINICALLY SIGNIFICANT", as defined in this report, is a genetic change that is associated with the potential to alter medical intervention.

component

code: Breast Cancer Risk Assessment Tool (assessment scale)

value: Breast Cancer RiskScore®: Remaining Lifetime Risk 10.9%

component

code: Clinical History Analysis: No additional management guidelines identified based on the clinical history provded

value: Other clinical factors may influence the individualized management. This analysis may be incomplete if details about cancer diagnoses, ages, family relationships or other factors were omitted or ambiguous. If this patient also has a clinically significant mutation, the recommendations based on the clinical history analysis should be considered in light of the possibility that this mutation explains all or some of the cancer history in the family.


Entry 9 - fullUrl = http://hapi-fhir-server:8080/fhir/Bundle/PractitionerLabDirector

Resource Practitioner:

Generated Narrative: Practitioner PractitionerLabDirector

identifier: National provider identifier/1750369955 (use: official, )

active: true

name: PractitionerJane Smith

gender: Female

address: Address 123 Boston MA 12345

Qualifications

-Code
*Laboratory Director

Entry 10 - fullUrl = http://hapi-fhir-server:8080/fhir/Bundle/HereditaryCancerTestingVarNegative

Resource Observation:

Generated Narrative: Observation HereditaryCancerTestingVarNegative

basedOn: ServiceRequest

partOf: Procedure Structural variation detection

status: Final

category: Laboratory, Genetics

code: Where testing scenarios are intended to assess the presence or absence of a known set of DNA variants (e.g. tumor profiling using genotyping technology), then the Genetic Variant Assessment is used in conjunction with answer list supports structured communication of these findings. Of note, 'No Call' is different from 'Absent', because 'No Call' did not result in the determination of the marker's presents or absents. This may be due to test failure or specimen specific context which renders the test ineffective.

subject: Jenny M (official) Female, DoB: 1988-02-12 ( Patient ID: 7fb905f171204b94b8ee33d33cb624e6 (use: official, ))

effective: 2021-12-03

performer: Practitioner Pauline Pathologist

value: Variant Assess: Indeterminate

method: Usually refers to high-throughput, next-generation sequencing methods, although can also refer to traditional capillary-based Sanger sequencing. Advantages: a lot of data at little cost. Disadvantages: short read length; high error rates. Next-Gen Sequencing is currently the most popular method for generating genetic data in general, and for detecting both single-nucleotide and structural variation.

component

code: Conclusion Text

value: Details About Non-Clinically Significant Variants:</b> All individuals carry DNA changes (i.e., variants), and most variants do not increase an individual's risk of cancer or other diseases. When identified, variants of uncertain significance (VUS) are reported. Likely benign variants (Favor Polymorphisms) and benign variants (Polymorphisms) are not reported and available data indicate that these variants most likely do not cause increased cancer risk. Present evidence does not suggest that non-clinically significant variant findings be used to modify patient medical management beyond what is indicated by the personal and family history and any other clinically significant findings.

interpretation: An absence finding of the specified component / analyte, organism or clinical sign based on the established threshold of the performed test or procedure.

component

code: Gene studied [ID]

value: STK11

component

code: Genomic source class [Type]

value: Germline


Entry 11 - fullUrl = http://hapi-fhir-server:8080/fhir/Bundle/Organization

Resource Organization:

Generated Narrative: Organization Organization

identifier: Clinical Laboratory Improvement Amendments/12A4567890 (use: official, )

type: Healthcare Provider

name: Generic Laboratories, Inc.

contact

telecom: ph: (800) 876-5309, fax: (781) 876-5305, http://www.genericlaboratoriesinc.com, info@genericlaboratoriesinc.com

address: 321 Laboratory Court, Anytown, MA, 12345, USA


Entry 12 - fullUrl = http://hapi-fhir-server:8080/fhir/Bundle/HereditaryCancerTestingRecommendedFollowupNegative

Resource Task:

Generated Narrative: Task HereditaryCancerTestingRecommendedFollowupNegative

status: Requested

intent: Proposal

code: THIS PLACEHOLDER LOINC CODE IS FOR: 'Genetic counseling recommended'

for: Jenny M (official) Female, DoB: 1988-02-12 ( Patient ID: 7fb905f171204b94b8ee33d33cb624e6 (use: official, ))


Entry 13 - fullUrl = http://hapi-fhir-server:8080/fhir/Bundle/HereditaryCancerTestingGenRiskAssessNegative

Resource RiskAssessment:

Generated Narrative: RiskAssessment HereditaryCancerTestingGenRiskAssessNegative

status: Final

method: BRCAPRO

subject: Jenny M (official) Female, DoB: 1988-02-12 ( Patient ID: 7fb905f171204b94b8ee33d33cb624e6 (use: official, ))

occurrence: 2021-12-03 01:01:01+0000

basis: Observation Discrete variation analysis overall interpretation

prediction

outcome: Prostate

probability: 0.16

when: ?-70

prediction

outcome: Male Breast

probability: 0.012

when: ?-70

prediction

outcome: Pancreatic

when: ?-70

rationale: Elevated risk


Entry 14 - fullUrl = http://hapi-fhir-server:8080/fhir/Bundle/HereditaryCancerTestingQuestionnaireResponseNegative

Resource QuestionnaireResponse:

Generated Narrative: QuestionnaireResponse HereditaryCancerTestingQuestionnaireResponseNegative

LinkIDTextDefinitionAnswerdoco
.. HereditaryCancerTestingQuestionnaireResponseNegativeQuestionnaire:None specified
... 1General questions
.... 1.1Woman's age60
.... 1.2AncestryWhite/Non-Hispanic
.... 1.3Height5 ft 7 in
.... 1.4Weight175 lbs
... 2Menopause
.... 2.1Age of menarche13
.... 2.2Patient's menopausal statusPre-menopausal
... 3Children
.... 3.1Age of first live birth27
... 4Hormone replacement therapy
.... 4.1Hormone replacement therapy (HRT)No
... 5Biopsy
.... 5.1Breast biopsyNo Benign Disease
... 6Number of patient's female relatives
.... 6.1Daughters1
.... 6.2Sisters2
.... 6.3Maternal Aunts2
.... 6.4Paternal Aunts2

doco Documentation for this format

Entry 15 - fullUrl = http://hapi-fhir-server:8080/fhir/Bundle/HereditaryCancerTestingDiagnosticReportNegative

Resource DiagnosticReport:

Generated Narrative: DiagnosticReport HereditaryCancerTestingDiagnosticReportNegative

Genetic analysis report (Genetics)

SubjectJenny M (official) Female, DoB: 1988-02-12 ( Patient ID: 7fb905f171204b94b8ee33d33cb624e6 (use: official, ))
When For2023-06-28 06:08:08+0500
Reported2023-05-27 00:00:00-0500
Performer Organization Generic Laboratories, Inc.
Identifier Accession ID/TST-175-442

Report Details

CodeValueFlagsWhen For
Where testing scenarios are intended to assess the presence or absence of a known set of DNA variants (e.g. tumor profiling using genotyping technology), then the Genetic Variant Assessment is used in conjunction with answer list supports structured communication of these findings. Of note, 'No Call' is different from 'Absent', because 'No Call' did not result in the determination of the marker's presents or absents. This may be due to test failure or specimen specific context which renders the test ineffective.Variant Assess: IndeterminateFinal2021-12-03
Discrete variation analysis overall interpretationNegativeFinal