This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version. For a full list of available versions, see the Directory of published versions
Contents:
This page provides a list of the FHIR artifacts defined as part of this implementation guide.
These are custom operations that can be supported by and/or invoked by systems conforming to this implementation guide
Find Subject Variants |
Use this operation to retrieve variants with precise endpoints from a specified genomic region for a specified patient. If the range in question has been studied, the operation returns a FHIR Parameters resource containing variants overlapping the region. If the patient or the specified region has not been studied, the operation returns a 404 error. |
These are profiles on resources or data types that describe patterns used by other profiles, but cannot be instantiated directly. I.e. instances can conform to profiles based on these abstract profiles, but do not declare conformance to the abstract profiles themselves.
Genomics Finding |
Properties common to genetic findings whose results are expressed as computable discrete elements (e.g. genotypes, haplotypes, variants, etc.). |
Genomics Implication |
Properties common to genomic implications expressed as computable discrete elements. |
Genomics Base |
Base profile that defines characteristics shared by all genetic observations. |
These define constraints on FHIR resources for systems conforming to this implementation guide
Diagnostic Implication |
Observation stating a linkage between one or more genotype/haplotype/variation Observations and evidence for or against a particular disease, condition, or cancer diagnosis. |
Followup Recommendation |
Task describing the follow-up that is recommended |
Genomics DocumentReference |
A profile of DocumentReference used to represent a genomics file. |
Genomics Report |
Genomics profile of DiagnosticReport. |
Genotype |
Assertion of a particular genotype on the basis of one or more variants or haplotypes. |
Haplotype |
Assertion of a particular haplotype on the basis of one or more variants. |
Microsatellite Instability |
Microsatellite Instability (MSI) is the condition of genetic hypermutability (predisposition to mutation) that results from impaired DNA mismatch repair (MMR). |
Medication Recommendation |
Task proposing medication recommendations based on genetic results. |
Overall Interpretation |
Provides a coarse overall interpretation of the genomic results reported. |
Region Studied |
The Region Studied profile is used to assert actual regions studied for the performed test(s). Intended coverage areas may differ from actual coverage areas (e.g. due to technical limitations during test performance). |
Sequence Phase Relationship |
Indicates whether two entities are in Cis (same strand) or Trans (opposite strand) relationship to each other. |
Tumor Mutation Burden |
The total number of mutations (changes) found in the DNA of cancer cells. Knowing the tumor mutational burden may help plan the best treatment. For example, tumors that have a high number of mutations appear to be more likely to respond to certain types of immunotherapy. Tumor mutational burden is being used as a type of biomarker. |
Therapeutic Implication |
Profile with properties for observations that convey the potential impact of genomic characteristics on a medication or non-medicinal therapy. |
Variant |
Details about a set of changes in the tested sample compared to a reference sequence. |
These define constraints on FHIR data types for systems conforming to this implementation guide
Coded Annotation |
Annotation DataType with added CodeableConcept extension element |
These define constraints on FHIR data types for systems conforming to this implementation guide
Annotation Code |
Codifies the content of an Annotation |
Genomic Report Note |
Adds codified notes to a report to capture additional content |
Genomics Artifact |
Captures citations, evidence and other supporting documentation for the observation or report. |
Genomics File |
Used to transmit the contents of or links to files that were produced as part of the testing process. Examples are VCF, BAM, CRAM, and other similar files. |
Genomics Risk Assessment |
RiskAssessment delivered as part of a genomics report or observation |
Medication Assessed |
Used to reference a specific medication that was assessed (e.g. a FHIR Medication or a FHIR MedicationKnowledge). |
Recommended Action |
References a proposed action that is recommended based on the results of the diagnostic report. |
Therapy Assessed |
Used to reference a specific therapy that was assessed (e.g. a FHIR ResearchStudy, a FHIR CarePlan, or a FHIR PlanDefinition). |
These define sets of codes used by systems conforming to this implementation guide
Coded Annotation Types |
Value Set for specific types of coded annotations |
Condition Inheritance Patterns |
Value Set for specific transmission patterns of a condition in a pedigree |
DNA Change Type |
DNA Change Type of a variant. |
Evidence Level Examples |
Example sources of values for Evidence Level |
Functional Effect |
The effect of a variant on downstream biological products or pathways. |
Genetic Therapeutic Implications |
Value Set for terms that describe a predicted ramification based on the presence of associated molecular finding(s). |
HUGO Gene Nomenclature Committee Gene Names (HGNC) |
This value set includes all HGNC Codes, which includes multiple code systems. In this guide, Gene IDs from HGNC are used as CodeableConcepts, which must be sent with the HGNC gene ID including the prefix ‘HGNC:’ as the code and the HGNC ‘gene symbol’ as display. CAUTION: HGNC also indexes gene groups by numeric ID (without a prefix), and older systems may send HGNC gene IDs without the prefix, so care must be taken to confirm alignment. We have separately included the genegroup code system to draw attention to this ambiguity and potential error. |
Human Genome Variation Society (HGVS) Nomenclature |
HGVS-nomenclature is used to report and exchange information regarding variants found in DNA, RNA and protein sequences and serves as an international standard. (source: varnomen.hgvs.org) |
High Low codes |
This value set includes high/low codes for Observation Interpretations |
Molecular Consequence |
The calculated or observed effect of a variant on its downstream transcript and, if applicable, ensuing protein sequence. |
Sequence Phase Relationships |
Value Set for specific types of relationships |
To Be Determined Value Set |
Value Set for codes yet to be defined in LOINC |
Variant Confidence Status |
A code that classifies the confidence for calling this variant. |
Variant Inheritances |
By which parent the variant was inherited in the patient, if known. |
These define new code systems used by systems conforming to this implementation guide
ClinVar Evidence Level Example Codes |
ClinVar contains examples of evidence level concepts that are not conflated with clinical significance. These can be found on ClinVar https://www.ncbi.nlm.nih.gov/clinvar/docs/review_status/ . These examples are informational only, for copyright information contact the relevant source. |
Coded Annotation Type Codes |
Code System for specific types of coded annotations |
PharmGKB Evidence Level Example Codes |
PharmGKB contains examples of evidence level concepts that are not conflated with clinical significance. These can be found on PharmGKB https://www.pharmgkb.org/page/clinAnnLevels. These examples are informational only, for copyright information contact the relevant source. |
Sequence Phase Relationship Codes |
Code System for specific types of relationships |
To Be Determined Codes |
These codes are currently ‘TBD’ codes. The CG WG plans to request formal LOINC codes to replace these codes as these concepts are validated. |
Variant Confidence Status Codes |
A code that represents the confidence of a true positive variant call. |
These define transformations to convert between codes by systems conforming with this implementation guide
DNA Change Type Map |
Mapping from http://loinc.org ValueSet for DNA Change Type to http://sequenceontology.org codes |
These are example instances that show what data produced and consumed by systems conforming with this implementation guide might look like
AnnotationExample |
Example of a Diagnostic Implication for Familial hypercholesterolemia |
CGPatientExample01 |
Example for Patient. Supports references to subject for multiple genomics reporting profile conforming instances. |
ExampleGermlineCNV |
Example for germline CNV |
ExampleGermlineDEL |
Example for germline DEL |
ExampleGermlineINV |
Example for germline INV |
ExampleLab |
Organization (lab) example |
ExampleOrg |
Example Org |
ExamplePatient |
Patient example |
ExampleServiceRequest |
ServiceRequest (order) example |
ExampleSomaticCNV |
Example for somatic CNV |
ExampleSomaticDEL |
Example for somatic DEL |
ExampleSomaticINV |
Example for somatic INV |
ExampleSpecimen |
Specimen example |
GenRiskDiabetesT2 |
Polygenic Risk Score example |
GenomicSpecimenExample01 |
Example for Genomic Specimen |
GenomicSpecimenExample02 |
Example for Genomic Specimen from Buccal Swab |
GenomicsReportExample01 |
Example of a Report carrying a Genotype, Therapeutic Implication, and Medication Recommendation |
GenomicsServiceRequestExample01 |
Example for Service Request |
Genotype-Clinical-Trial-Example-using-haplotypes |
Example of a Genotype. A complete haplotype set defines a genotype. In this example the gneotype is dervied from observations of the underlying haplotypes. |
GenotypeExample1 |
Example of a Genotype, Medication Recommendation, and MedicationStatement |
GenotypeExamplePharmVar |
Example of a Genotype using Pharmvar Haplotypes |
GrouperEx01 |
Generic grouping of Therapeutic Implication observations |
GrouperEx02 |
Generic grouping of Genotype observations |
GrouperEx03 |
Generic grouping of Regions Studied and Variant observations |
HaplotypeExamplePharmVar01 |
Example of a Haplotype using PharmVar |
HaplotypeExamplePharmVar02 |
Example of a Haplotype using PharmVar |
HaplotypeSet-Clinical-Trial-Example-1of2 |
Example of a Haplotype as part of a Haplotype Set (1 of 2). A complete haplotype set defines a genotype. |
HaplotypeSet-Clinical-Trial-Example-2of2 |
Example of a Haplotype as part of a Haplotype Set (2 of 2). A complete haplotype set defines a genotype. |
MedicationRecommendationExample1 |
Example of a Medication Recommendation |
MedicationStatementWarfarin |
MedicationStatement for Warfarin |
MicrosatelliteInstabilityExample01 |
Example for MSI |
OverallInterpExample1 |
Example for Overall Interpretation. |
OverallInterpExample2 |
Example for Overall Interpretation. |
PGxGenomicsReportEMERGE |
Example of a Report carrying multiple Therapeutic Implications, Genotypes, and Variants |
PGxGenomicsReportEMERGE-withGrouping |
Example of a Report carrying multiple Therapeutic Implications, Genotypes, and Variants |
PGxRecEx01 |
Example of a Medication Recommendation for alternatives to clopidogrel |
PGxRecEx02 |
Example of a Medication Recommendation for alternatives to voriconazole |
PGxRecEx03 |
Example of a Medication Recommendation for decreasing dosage for citalopram |
PGxRecEx04 |
Example of a Medication Recommendation for decreasing dosage for escitalopram |
PGxRecEx05 |
Example of a Medication Recommendation for decreasing dosage for amitriptyline |
Pgx-geno-1001 |
Example of a Genotype from eMERGE |
Pgx-geno-1002 |
Example of a Genotype from eMERGE |
Pgx-geno-1003 |
Example of a Genotype from eMERGE |
Pgx-var-1011 |
Example variant 1011 |
Pgx-var-1012 |
Example variant 1012 |
Pgx-var-1013 |
Example variant 1013 |
Pgx-var-1014 |
Example variant 1014 |
Pgx-var-1015 |
Example variant 1015 |
Pgx-var-1016 |
Example variant 1016 |
Pgx-var-1017 |
Example variant 1017 |
Pgx-var-1018 |
Example variant 1018 |
Pgx-var-1019 |
Example variant 1019 |
Pgx-var-1020 |
Example variant 1020 |
Pgx-var-1021 |
Example variant 1021 |
PolyGenicDiagnosticImpExample |
Example of a Diagnostic Implication for Diabetes Type 2 with a polygenic risk score. |
RegionStudiedPGx1 |
eMERGE PGx CYP2C19 |
RegionStudiedPGx2 |
eMERGE PGx CYP2C9 |
RegionStudiedPGx3 |
eMERGE PGx VKORC1 |
SNVexample |
Example Variant |
SequencePhaseRelationExample1 |
Example for sequence phase relation. |
Therapeutic-Implication-Clinical-Trial-2 |
Example of a Therapeutic Implication for Carbamazepine |
Therapeutic-Implication-Clinical-Trial-Somatic |
Example of a Therapeutic Implication for Clinical Trial |
TherapeuticImplicationExample1 |
Example of a Therapeutic Implication for Carbamazepine |
TumorMutationBurdenExample01 |
Example for Tumor Mutation Burden |
TxImp01 |
Example of a Therapeutic Implication from eMERGE |
TxImp02 |
Example of a Therapeutic Implication from eMERGE |
TxImp03 |
Example of a Therapeutic Implication from eMERGE |
TxImp04 |
Example of a Therapeutic Implication from eMERGE |
TxImp05 |
Example of a Therapeutic Implication from eMERGE |
TxImp06 |
Example of a Therapeutic Implication from eMERGE |
VCFFile |
Example of what a VCF as a DocumentRefence would look like. |
Variant-Somatic-Clinical-Trial |
Example for Somatic Variant and Clinical Trial |
VariantExample1 |
Example for Variant given by HGVS |
VariantExample2 |
Example for genomic Variant given by VCF columns |
bundle-CG-IG-HLA-FullBundle-01 |
Example of a HLA bundle |
bundle-CYP2C19 |
Example bundle containing CYP2C19 report and variants |
bundle-cgexample |
Example bundle showing a variety of profiles. |
bundle-cgexample-withGrouping |
Example bundle showing a variety of profiles, including how groupings of Observations might be delivered. |
bundle-complexVariant-nonHGVS |
Example bundle with compound heterozygous variant, where the specific changes are represented without HGVS. |
bundle-compound-heterozygote |
Example bundle with compound heterozygous variant, where the specific changes are represented with HGVS. |
bundle-oncology-diagnostic |
Example of an oncology report, TMB, variants, and implications. |
bundle-oncology-report-example |
Example oncology bundle including report, variants, and other resources. |
bundle-oncologyexamples-r4 |
Example bundle with an oncology report with SNVs, TMB, MSI, and therapy matches. |
bundle-oncologyexamples-r4-withGrouping |
Example bundle with an oncology report with SNVs, TMB, MSI, and therapy matches, including some groupings of observations |
bundle-pgxexample |
Example bundle with a PGx report and a variety of observations. |
bundle-sequence-phase-relation-CYP2C19 |
Example Sequence Phase Relation showing a report with two variants in cis |
diagnosticreport-hla-glstring-r4 |
Example GenomicsReport including an HLA glstring |
eMERGEServiceRequest |
Example PGx Service Request |
genotype-hla-a-glstring-r4 |
Genotype example: Sequence-based typing of HLA-A |
haplotype-hla-a-1-r4 |
Example Haplotype Sequence-based typing of HLA-A |
obs-idh-ex |
Example DiagnosticImplication - Pathogenic for CF |
servicerequest-hla-a-r4 |
Example ServiceRequest for genomics |
specimen-hla-r4 |
Example HLA specimen |