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
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 Detail US (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-BLDstatus: Available
type: Blood specimen (specimen)
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
- type: VCF
- file: DocumentReference/HereditaryCancerTestingVCF
status: Completed
category: Laboratory
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
status: Completed
category: Laboratory
code: HereditaryCancerTesting™ Hereditary Cancer Test
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: )
requester: Practitioner Laura Salma
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
value: Negative
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.
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'
Entry 13 - fullUrl = http://hapi-fhir-server:8080/fhir/Bundle/HereditaryCancerTestingGenRiskAssessNegative
Resource RiskAssessment:
Generated Narrative: RiskAssessment HereditaryCancerTestingGenRiskAssessNegative
status: Final
method: BRCAPRO
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
LinkID Text Definition Answer HereditaryCancerTestingQuestionnaireResponseNegative Questionnaire:None specified 1 General questions 1.1 Woman's age 60 1.2 Ancestry White/Non-Hispanic 1.3 Height 5 ft 7 in 1.4 Weight 175 lbs 2 Menopause 2.1 Age of menarche 13 2.2 Patient's menopausal status Pre-menopausal 3 Children 3.1 Age of first live birth 27 4 Hormone replacement therapy 4.1 Hormone replacement therapy (HRT) No 5 Biopsy 5.1 Breast biopsy No Benign Disease 6 Number of patient's female relatives 6.1 Daughters 1 6.2 Sisters 2 6.3 Maternal Aunts 2 6.4 Paternal Aunts 2
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)
Subject Jenny M (official) Female, DoB: 1988-02-12 ( Patient ID: 7fb905f171204b94b8ee33d33cb624e6 (use: official, )) When For 2023-06-28 06:08:08+0500 Reported 2023-05-27 00:00:00-0500 Performer Organization Generic Laboratories, Inc. Identifier Accession ID/TST-175-442 Report Details