Genomics Reporting Implementation Guide
2.0.0 - trial-use

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

Artifacts Summary

This page provides a list of the FHIR artifacts defined as part of this implementation guide.

Behavior: Operation Definitions

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.

Structures: Abstract Profiles

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.

Structures: Resource Profiles

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.

Structures: Data Type Profiles

These define constraints on FHIR data types for systems conforming to this implementation guide

Coded Annotation

Annotation DataType with added CodeableConcept extension element

Structures: Extension Definitions

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).

Terminology: Value Sets

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.

Terminology: Code Systems

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.

Terminology: Concept Maps

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

Example: Example Instances

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