Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. 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/genomics-reporting/ and changes regularly. See the Directory of published versions

Artifact List

Page standards status: Informative

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

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.

Profile	Base	Type	Description
Genomic Base	Observation	Observation	Base profile that defines characteristics shared by all genetic observations.
Genomic Finding	GenomicBase	Observation	Properties common to genetic findings whose results are expressed as computable discrete elements (e.g. genotypes, haplotypes, variants, etc.).
Genomic Implication	GenomicBase	Observation	Properties common to genomic implications expressed as computable discrete elements.

Resource Profiles

These define constraints on FHIR resources for systems conforming to this implementation guide.

Profile	Base	Type	Description
Diagnostic Implication	GenomicImplication	Observation	Observation stating a diagnostic annotation (e.g. disease risk) on one or more genotype/haplotype/variant/biomarker observations.
Followup Recommendation	Task	Task	Task proposing a follow-up that is recommended based on the implications of genomic findings.
Genomic Annotation	GenomicImplication	Observation	Profile for communicating miscellaneous genomic annotations that are neither Diagnostic Implications, Therapeutic Implications, nor Molecular Consequences.
Genomic Data File	DocumentReference	DocumentReference	A profile of DocumentReference used to represent a genomics file.
Genomic Report	DiagnosticReport	DiagnosticReport	Genomic profile of DiagnosticReport.
Genotype	GenomicFinding	Observation	Assertion of a particular genotype on the basis of one or more variants or haplotypes.
Haplotype	GenomicFinding	Observation	Assertion of a particular haplotype on the basis of one or more variants.
Medication Recommendation	Task	Task	Task proposing medication recommendations based on the implications of genomic findings.
Molecular Biomarker	Observation	Observation	This profile is used to represent laboratory measurements of human inherent substances such as gene products, antigens and antibodies, and complex chemicals that result from post-translational processing of multi-gene products.
Molecular Consequence	GenomicImplication	Observation	Profile for communicating the calculated or observed effect of a DNA variant, generally on its downstream transcript and, if applicable, ensuing protein sequence. Molecular consequences may also apply to DNA, such as intergenic regions where there are no transcripts (e.g. 'regulatory_region_variant'). Component 'feature-consequence' categorizes the structural implications of a variant (e.g. the variant disrupts a regulatory region, the variant is an inframe insertion), whereas component 'functional-effect' categorizes how the variant affects overall function (e.g. is predicted to result in loss of gene function).
Sequence Phase Relationship	GenomicFinding	Observation	Indicates whether two entities are in Cis (same strand) or Trans (opposite strand) relationship to each other.
Therapeutic Implication	GenomicImplication	Observation	Observation stating a therapeutic annotation (e.g. drug susceptibility, clinical trial eligibility) on one or more genotype/haplotype/variant/biomarker observations.
Variant	GenomicFinding	Observation	Details about a set of changes in the tested sample compared to a reference sequence.

Data Type Profiles

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

Data Type	Base	Description
Coded Annotation	Annotation	Annotation DataType with added CodeableConcept extension element

Extension Profiles

These define constraints on FHIR extensions for systems conforming to this implementation guide.

Extension	Description
Annotation Code	Codifies the content of an Annotation
Genomic Report Note	Adds codified notes to a report to capture additional content
Genomic Risk Assessment	RiskAssessment delivered as part of a genomics report or observation
KnowledgebaseAncestryGroup	Used to identify the sample ancestry group using terms obtained from the knowledgebase
Medication Assessed reference to a FHIR resource	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.
Repeat Motif Order	Use to group and order repeat expansion motifs.
Therapy Assessed reference to a FHIR resource	Used to reference a specific therapy that was assessed (e.g. a FHIR ResearchStudy, a FHIR CarePlan, or a FHIR PlanDefinition).

Code Systems

These define code systems that are used by systems conforming to this implementation guide.

Code System	Description
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
Knowledge Base Codes	This example code systems provides examples on how to properly display the knowledge base version number. Version numbers should always be followed by the letter v and calendar dates are displayed Month Day Year. For clarity the month SHALL be written in full.
Molecular Biomarker Ontology Codes	This (experimental) code system provides for a draft categorization of biomarkers along several axes. Based on ballot feedback, the committee anticipates significant revisions.
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 'TBD' codes, meaning they are important concepts but codes have not been identifed in available code systems. The CG WG anticpates these codes maturing over time. We may remove some codes as we refine the concepts, or identify suitable replacement codes from other code systems. As we approach normative and these concepts are validated, for codes that remain, we plan to request formal LOINC codes to replace these temporary codes.
Variant Confidence Status Codes	A code that represents the confidence of a true positive variant call.

Value Sets

These define value sets that are used by systems conforming to this implementation guide.

Value Set	Description
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 Value Set	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)
Knowledge Base Version Codes	Value set for example terms to display the knowledge base version used to calculate and/or obtain data
Molecular Biomarker Categories	This value set is drawn from the Molecular Biomarker Ontology code system, which provides codes that characterize a molecular biomarker.
Molecular Biomarker Codes	Value Set for terms that can be used as Biomarkers.
Molecular Consequence Value Set	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.

Concept Maps

These define mappings between code systems used by systems conforming to this implementation guide.

Concept Map	Description
DNA Change Type Map	LOINC and SequenceOntology mappings for DNA change type

Operation Definitions

These define operations that are used by systems conforming to this implementation guide.

Operation	Description
Find Population Diagnostic Implications	Retrieve count or list of patients having diagnostic implications.
Find Population Molecular Consequences	Retrieve count or list of patients having molecular consequences.
Find Population Specific Haplotypes	Retrieve count or list of patients having specified genotypes/haplotypes.
Find Population Specific Variants	Retrieve count or list of patients having specified variants.
Find Population Structural Intersecting Variants	Retrieve count or list of patients having structural intersecting variants in specified regions.
Find Population Structural Subsuming Variants	Retrieve count or list of patients having structural subsuming variants in specified regions.
Find Population Treatment Implications	Retrieve count or list of patients having therapeutic implications.
Find Study Metadata	Retrieve metadata about sequencing studies performed on a subject.
Find Subject Diagnostic Implications	Retrieves genetic diagnostic implications for variants.
Find Subject Haplotypes	Retrieve haplotypes/genotypes for specified genes.
Find Subject Molecular Consequences	Retrieves molecular consequences of a DNA variant.
Find Subject Specific Haplotypes	See if specified haplotypes/genotypes are present.
Find Subject Specific Variants	Determine if specified simple variants are present.
Find Subject Structural Intersecting Variants	Determine if structural variants are present that overlap range(s).
Find Subject Structural Subsuming Variants	Determine if structural variants are present that fully subsume a range.
Find Subject Treatment Implications	Retrieves genetic therapeutic implications for variants/haplotypes/genotypes.
Find Subject Variants	Determine if simple variants are present that overlap range(s).

Parameters

These define example parameters for operations used by systems conforming to this implementation guide.

Parameters Example	Description
FindALLPopulationSpecificVariantsOutput	Example Output of 'FindPopulationSpecificVariants' Operation, based on 'AND' logic
FindANYPopulationSpecificVariantsOutput	Example Output of 'FindPopulationSpecificVariants' Operation, based on 'OR' logic
FindPopulationDxImplicationsOutput	Example Output of 'FindPopulationDxImplications' Operation
FindPopulationMolecConseqOutput	Example Output of 'FindPopulationMolecConseq' Operation
FindPopulationSpecificHaplotypesOutput	Example Output of 'FindPopulationSpecificHaplotypes' Operation
FindPopulationStructuralIntersectingVariantsOutput	Example Output of 'FindPopulationStructuralIntersectingVariants' Operation
FindPopulationStructuralSubsumingVariantsOutput	Example Output of 'FindPopulationStructuralSubsumingVariants' Operation
FindPopulationTxImplicationsOutput	Example Output of 'FindPopulationTxImplications' Operation
FindStudyMetadataOutput	Example Output of 'FindStudyMetadata' Operation
FindSubjectDxImplicationsOutput	Example Output of 'FindSubjectDxImplications' Operation
FindSubjectHaplotypesOutput	Example Output of 'FindSubjectHaplotypes' Operation
FindSubjectMolecConseqOutput	Example Output of 'FindSubjectMolecConseq' Operation
FindSubjectSpecificHaplotypesOutput	Example Output of 'FindSubjectSpecificHaplotypes' Operation
FindSubjectSpecificVariantsOutput	Example Output of 'FindSubjectSpecificVariants' Operation
FindSubjectStructuralIntersectingVariantsOutput	Example Output of 'FindSubjectStructuralIntersectingVariants' Operation
FindSubjectStructuralSubsumingVariantsOutput	Example Output of 'FindSubjectStructuralSubsumingVariants' Operation
FindSubjectTxImplicationsOutput	Example Output of 'FindSubjectTxImplications' Operation
FindSubjectVariantsOutput	Example Output of 'Find Subject Variants' Operation

Example Instances

These are example instances that show what data produced and consumed by systems conforming with this implementation guide might look like.

Example	Type Of Resource	Example Of Profile	Description
AnnotationExample	Observation	Diagnostic Implication	Example of a Diagnostic Implication for Familial hypercholesterolemia
ATR-insertion-molc	Observation	Molecular Consequence	Example Molecular Consequence ATR frameshift
ATR-insertion-significance	Observation	Diagnostic Implication	Example DiagnosticImplication - ATR likely pathogenic
ATR-insertion-var	Observation	Variant	Example for ATR insertion
bundle-CG-IG-HLA-FullBundle-01	Bundle		Example of a HLA bundle
bundle-cgexample	Bundle		Example bundle showing a variety of profiles.
bundle-cgexample-withGrouping	Bundle		Example bundle showing a variety of profiles, including how groupings of Observations might be delivered.
bundle-complexVariant-nonHGVS	Bundle		Example bundle with compound heterozygous variant, where the specific changes are represented without HGVS.
bundle-compound-heterozygote	Bundle		Example bundle with compound heterozygous variant, where the specific changes are represented with HGVS.
bundle-CYP2C19	Bundle		Example bundle containing CYP2C19 report and variants
bundle-oncology-diagnostic	Bundle		Example of an oncology report, TMB, variants, and implications.
bundle-oncology-report-example	Bundle		Example oncology bundle including report, variants, and other resources.
bundle-oncologyexamples-r4	Bundle		Example bundle with an oncology report with SNVs, TMB, MSI, and therapy matches.
bundle-oncologyexamples-r4-withGrouping	Bundle		Example bundle with an oncology report with SNVs, TMB, MSI, and therapy matches, including some groupings of observations
bundle-pgxexample	Bundle		Example bundle with a PGx report and a variety of observations.
bundle-sequence-phase-relation-CYP2C19	Bundle		Example Sequence Phase Relation showing a report with two variants in cis
CGPatientExample01	Patient		Example for Patient. Supports references to subject for multiple genomics reporting profile conforming instances.
CNVAnalysis-called	DocumentReference	Genomic Data File	CNVAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.
denovoChild	Patient		Child of a trio
denovoFather	Patient		Father of a trio
denovoMother	Patient		Mother of a trio
diagnosticImplication-interact-smn1-smn2	Observation	Diagnostic Implication	Diagnostic Implication for SMN1/SMN2 CNV example
diagnosticreport-hla-glstring-r4	DiagnosticReport	Genomic Report	Example GenomicReport including an HLA glstring
EGFR-L858R-molc	Observation	Molecular Consequence	Example Molecular Consequence EGFR L858R missense_variant
EGFR-L858R-significance	Observation	Diagnostic Implication	Example DiagnosticImplication - EGFR pathogenic
EGFR-L858R-therapuDrug1	Observation	Therapeutic Implication	Example of EGFR-L858R Therapeutic Implication for drug treatment 1
EGFR-L858R-therapuDrug2	Observation	Therapeutic Implication	Example of EGFR-L858R Therapeutic Implication for drug treatment 2
EGFR-L858R-var	Observation	Variant	Example for EGFR L858R
eMERGEServiceRequest	ServiceRequest		Example PGx Service Request
ExampleGermlineCNV	Observation	Variant	Example for germline CNV
ExampleGermlineDEL	Observation	Variant	Example for germline DEL
ExampleGermlineINV	Observation	Variant	Example for germline INV
ExampleLab	Organization		Organization (lab) example
ExampleOrg	Organization		Example Org
ExamplePatient	Patient		Patient example
ExampleServiceRequest	ServiceRequest		ServiceRequest (order) example
ExampleSomaticCNV	Observation	Variant	Example for somatic CNV
ExampleSomaticDEL	Observation	Variant	Example for somatic DEL
ExampleSomaticINV	Observation	Variant	Example for somatic INV
ExampleSpecimen	Specimen		Specimen example
FindALLPopulationSpecificVariantsOutput	Parameters		Example Output of 'FindPopulationSpecificVariants' Operation, based on 'AND' logic
FindANYPopulationSpecificVariantsOutput	Parameters		Example Output of 'FindPopulationSpecificVariants' Operation, based on 'OR' logic
FindPopulationDxImplicationsOutput	Parameters		Example Output of 'FindPopulationDxImplications' Operation
FindPopulationMolecConseqOutput	Parameters		Example Output of 'FindPopulationMolecConseq' Operation
FindPopulationSpecificHaplotypesOutput	Parameters		Example Output of 'FindPopulationSpecificHaplotypes' Operation
FindPopulationStructuralIntersectingVariantsOutput	Parameters		Example Output of 'FindPopulationStructuralIntersectingVariants' Operation
FindPopulationStructuralSubsumingVariantsOutput	Parameters		Example Output of 'FindPopulationStructuralSubsumingVariants' Operation
FindPopulationTxImplicationsOutput	Parameters		Example Output of 'FindPopulationTxImplications' Operation
FindStudyMetadataOutput	Parameters		Example Output of 'FindStudyMetadata' Operation
FindSubjectDxImplicationsOutput	Parameters		Example Output of 'FindSubjectDxImplications' Operation
FindSubjectHaplotypesOutput	Parameters		Example Output of 'FindSubjectHaplotypes' Operation
FindSubjectMolecConseqOutput	Parameters		Example Output of 'FindSubjectMolecConseq' Operation
FindSubjectSpecificHaplotypesOutput	Parameters		Example Output of 'FindSubjectSpecificHaplotypes' Operation
FindSubjectSpecificVariantsOutput	Parameters		Example Output of 'FindSubjectSpecificVariants' Operation
FindSubjectStructuralIntersectingVariantsOutput	Parameters		Example Output of 'FindSubjectStructuralIntersectingVariants' Operation
FindSubjectStructuralSubsumingVariantsOutput	Parameters		Example Output of 'FindSubjectStructuralSubsumingVariants' Operation
FindSubjectTxImplicationsOutput	Parameters		Example Output of 'FindSubjectTxImplications' Operation
FindSubjectVariantsOutput	Parameters		Example Output of 'Find Subject Variants' Operation
FullGenome-GRCh38	DocumentReference	Genomic Data File	Example for Genomic Data File FullGenome-GRCh38
genomicFileFatherBAM	DocumentReference	Genomic Data File	A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline
genomicFileMotherBAM	DocumentReference	Genomic Data File	A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline
genomicFileProbandBAM	DocumentReference	Genomic Data File	A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline
genomicFileProbandVCF	DocumentReference	Genomic Data File	A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline
genomicPatient	Patient		Example patient
GenomicReportExample01	DiagnosticReport	Genomic Report	Example of a Report carrying a Genotype, Therapeutic Implication, and Medication Recommendation
genomicServiceRequest	ServiceRequest		Example of Molecular genetic test
GenomicServiceRequestExample01	ServiceRequest		Example for Service Request
genomicSpecimen	Specimen		Example of lung specimen obtained by biopsy
GenomicSpecimenExample01	Specimen		Example for Genomic Specimen
GenomicSpecimenExample02	Specimen		Example for Genomic Specimen from Buccal Swab
genomicstudy-trio2	GenomicStudy		GenomicStudy example of a trio analysis
genomicVCFfile-cnv	DocumentReference	Genomic Data File	genomicVCFfile_cnv: A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline.
genomicVCFfile-simple	DocumentReference	Genomic Data File	genomicVCFfile_simple: A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline.
Genotype-Clinical-Trial-Example-using-haplotypes	Observation	Genotype	Example of a Genotype. A complete haplotype set defines a genotype. In this example the gneotype is dervied from observations of the underlying haplotypes.
genotype-hla-a-glstring-r4	Observation	Genotype	Genotype example: Sequence-based typing of HLA-A
GenotypeExample1	Observation	Genotype	Example of a Genotype, Medication Recommendation, and MedicationStatement
GenotypeExamplePharmVar	Observation	Genotype	Example of a Genotype using Pharmvar Haplotypes
GenRiskDiabetesT2	RiskAssessment		Polygenic Risk Score example
GrouperEx01	Observation		Generic grouping of Therapeutic Implication observations
GrouperEx02	Observation		Generic grouping of Genotype observations
GrouperEx03	Observation		Generic grouping of Regions Studied and Variant observations
haplotype-hla-a-1-r4	Observation	Haplotype	Example Haplotype Sequence-based typing of HLA-A
HaplotypeExamplePharmVar01	Observation	Haplotype	Example of a Haplotype using PharmVar
HaplotypeExamplePharmVar02	Observation	Haplotype	Example of a Haplotype using PharmVar
HaplotypeSet-Clinical-Trial-Example-1of2	Observation	Haplotype	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	Observation	Haplotype	Example of a Haplotype as part of a Haplotype Set (2 of 2). A complete haplotype set defines a genotype.
HER2byImmuneStainExample	Observation	Molecular Biomarker	Example for HER2 by immune stain
HER2byImmunoassayExample	Observation	Molecular Biomarker	Example for HER2 by immunoassay
HG00403	Patient		Example for Patient. Supports references to subject for multiple genomics reporting profile conforming instances.
HLA-A-haplotype1	Observation	Haplotype	Example for HLA-A-haplotype1
HLA-A-haplotype2	Observation	Haplotype	Example for HLA-A-haplotype2
HLA-B-haplotype1	Observation	Haplotype	Example for HLA-B-haplotype1
HLA-B-haplotype2	Observation	Haplotype	Example for HLA-B-haplotype2
HLA-C-haplotype1	Observation	Haplotype	Example for HLA-C-haplotype1
HLA-C-haplotype2	Observation	Haplotype	Example for HLA-C-haplotype2
ISCN-CMLExample	Observation	Variant	Basic example for karyotype Variant expressed in ISCN
ISCN-CMLImplication	Observation	Diagnostic Implication	Basic example of a Diagnostic Implication for CML
ISCN-NormalExample	Observation	Variant	Normal example for karyotype Variant expressed in ISCN
lungMass	GenomicStudy		Example of solid tumor whole exome sequencing panel
MedicationRecommendationExample1	Task	Medication Recommendation	Example of a Medication Recommendation
MedicationStatementWarfarin	MedicationStatement		MedicationStatement for Warfarin
MicrosatelliteInstabilityExample01	Observation	Molecular Biomarker	Example for MSI
molec-conseq1	Observation	Molecular Consequence	Example Molecular Consequence that includes Loss of Function prediction
molec-conseq2	Observation	Molecular Consequence	Example Molecular Consequence
molec-conseq3	Observation	Molecular Consequence	Example Molecular Consequence
molec-conseq4	Observation	Molecular Consequence	Example Molecular Consequence
MSH2-del-disease	Observation	Diagnostic Implication	Example DiagnosticImplication - MSH2 deletion Hereditary cancer-predisposing syndrome
MSH2-del-molc	Observation	Molecular Consequence	Example Molecular Consequence MSH2 frameshift
MSH2-del-var	Observation	Variant	Example for MSH2 deletion
MSIExample	Observation	Molecular Biomarker	Example for MSI
MultipleRepeatExpansions	Observation	Variant	Repeat Expansion Variant with multiple motifs
normalSpecimen	Specimen		Example for normal specimen
NOTCH1-significance	Observation	Diagnostic Implication	Example DiagnosticImplication - NOTCH1 uncertain significance
NOTCH1-uncertain-molc	Observation	Molecular Consequence	Example Molecular Consequence NOTCH1 missense_variant
NOTCH1-uncertain-var	Observation	Variant	Example for NOTCH1 uncertain
NTHL1-snv-disease	Observation	Diagnostic Implication	Example DiagnosticImplication - NTHL1 SNV Hereditary cancer-predisposing syndrome
NTHL1-snv-molc	Observation	Molecular Consequence	Example Molecular Consequence NTHL1 SNV variant with nonsense codon
NTHL1-snv-var	Observation	Variant	Example for NTHL1 SNV
obs-idh-ex	Observation	Diagnostic Implication	Example DiagnosticImplication - Pathogenic for CF
obs1-interact-smn1-smn2	Observation	Variant	SMN1 CNV companion for SMN1/SMN2 CNV example
obs2-interact-smn1-smn2	Observation	Variant	SMN2 CNV companion for SMN1/SMN2 CNV example
orderingPractitioner	Practitioner		Example of an ordering provider
pathologistPractitioner	Practitioner		Example of a pathologist
PDL1Example	Observation	Molecular Biomarker	Example for PD-L1
performingOrganization	Organization		Example of a Pathology lab
Pgx-geno-1001	Observation	Genotype	Example of a Genotype from eMERGE
Pgx-geno-1002	Observation	Genotype	Example of a Genotype from eMERGE
Pgx-geno-1003	Observation	Genotype	Example of a Genotype from eMERGE
Pgx-var-1011	Observation	Variant	Example variant 1011
Pgx-var-1012	Observation	Variant	Example variant 1012
Pgx-var-1013	Observation	Variant	Example variant 1013
Pgx-var-1014	Observation	Variant	Example variant 1014
Pgx-var-1015	Observation	Variant	Example variant 1015
Pgx-var-1016	Observation	Variant	Example variant 1016
Pgx-var-1017	Observation	Variant	Example variant 1017
Pgx-var-1018	Observation	Variant	Example variant 1018
Pgx-var-1019	Observation	Variant	Example variant 1019
Pgx-var-1020	Observation	Variant	Example variant 1020
Pgx-var-1021	Observation	Variant	Example variant 1021
PGxGenomicReportEMERGE	DiagnosticReport	Genomic Report	Example of a Report carrying multiple Therapeutic Implications, Genotypes, and Variants
PGxGenomicReportEMERGE-withGrouping	DiagnosticReport	Genomic Report	Example of a Report carrying multiple Therapeutic Implications, Genotypes, and Variants
PGXGenomicStudy	GenomicStudy		Example of PGX sequencing panel
PGxRecEx01	Task	Followup Recommendation	Example of a Medication Recommendation for alternatives to clopidogrel
PGxRecEx02	Task	Followup Recommendation	Example of a Medication Recommendation for alternatives to voriconazole
PGxRecEx03	Task	Followup Recommendation	Example of a Medication Recommendation for decreasing dosage for citalopram
PGxRecEx04	Task	Followup Recommendation	Example of a Medication Recommendation for decreasing dosage for escitalopram
PGxRecEx05	Task	Followup Recommendation	Example of a Medication Recommendation for decreasing dosage for amitriptyline
PolyGenicDiagnosticImpExample	Observation	Diagnostic Implication	Example of a Diagnostic Implication for Diabetes Type 2 with a polygenic risk score.
pop-allele-freq	Observation	Genomic Annotation	Example genomic annotation showing a population allele frequency
practitioner02	Practitioner		Example practitioner
RepeatExpansion	Observation	Variant	Repeat Expansion Variant
ROS1-Fusion	Observation	Molecular Consequence	Example Molecular Consequence ROS1 Fusion
ROS1-Fusion-disease	Observation	Diagnostic Implication	Example DiagnosticImplication - ROS1 disease
ROS1-Fusion-therapuDrug	Observation	Therapeutic Implication	Example of ROS1 Fusion Therapeutic Implication for drug treatment
ROS1-Fusion-therapuTrial	Observation	Therapeutic Implication	Example of ROS1 Fusion Therapeutic Implication for Clinical Trial
ROS1-Fusion-var	Observation	Variant	Example for ROS1 Fusion but as typically reported in PDF, without necessarily declaring a particular fusion partner
SequencePhaseRelationExample1	Observation	Sequence Phase Relationship	Example for sequence phase relation.
SequencingProcedure	Procedure		Very simple producure representing a genomic study's protocol
servicerequest-hla-a-r4	ServiceRequest		Example ServiceRequest for genomics
SimpleVariantAnalysis-called	DocumentReference	Genomic Data File	SimpleVariantAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.
SNVexample	Observation	Variant	Example Variant
somaticPatient	Patient		Somatic example Patient
somaticReport	DiagnosticReport	Genomic Report	Example somatic GenomicReport
somaticServiceRequest	ServiceRequest		Example for Somatic Testing Request
somaticStudy	GenomicStudy		Example for somatic genetic study
somaticVCFfile	DocumentReference	Genomic Data File	Example for Genomic Data File somaticVCFfile
specimen-hla-r4	Specimen		Example HLA specimen
STAG2-insertion-molc	Observation	Molecular Consequence	Example Molecular Consequence STAG2 frameshift
STAG2-insertion-significance	Observation	Diagnostic Implication	Example DiagnosticImplication - STAG2 likely pathogenic
STAG2-insertion-var	Observation	Variant	Example for STAG2 insertion
supervisorPractitioner	Practitioner		Example of a supervisor
Therapeutic-Implication-Clinical-Trial-2	Observation	Therapeutic Implication	Example of a Therapeutic Implication for Carbamazepine
Therapeutic-Implication-Clinical-Trial-Somatic	Observation	Therapeutic Implication	Example of a Therapeutic Implication for Clinical Trial
TherapeuticImplicationExample1	Observation	Therapeutic Implication	Example of a Therapeutic Implication for Carbamazepine
therapuDrug1-interact-smn1-smn2	Observation	Therapeutic Implication	Antisense Oligonucelotide example of Therapeutic Implication for SMN1/SMN2 CNV example
therapuDrug2-interact-smn1-smn2	Observation	Therapeutic Implication	Transgene example of Therapeutic Implication for SMN1/SMN2 CNV example
therapuDrug3-interact-smn1-smn2	Observation	Therapeutic Implication	Small molecule example of Therapeutic Implication for SMN1/SMN2 CNV example
TMB-therapuDrug	Observation	Therapeutic Implication	Example of high TMB Therapeutic Implication for drug treatment
TMBExample	Observation	Molecular Biomarker	Example for Tumor Mutation Burden
triodenovo-software	Device		Triodenovo Software
TumorMutationBurdenExample01	Observation	Molecular Biomarker	Example for Tumor Mutation Burden
tumorSpecimen	Specimen		Example for tumor specimen
TxImp01	Observation	Therapeutic Implication	Example of a Therapeutic Implication from eMERGE
TxImp02	Observation	Therapeutic Implication	Example of a Therapeutic Implication from eMERGE
TxImp03	Observation	Therapeutic Implication	Example of a Therapeutic Implication from eMERGE
TxImp04	Observation	Therapeutic Implication	Example of a Therapeutic Implication from eMERGE
TxImp05	Observation	Therapeutic Implication	Example of a Therapeutic Implication from eMERGE
TxImp06	Observation	Therapeutic Implication	Example of a Therapeutic Implication from eMERGE
UncallableRegions	DocumentReference	Genomic Data File	Representing a BED file that represents uncallable regions
Variant-Somatic-Clinical-Trial	Observation	Variant	Example for Somatic Variant and Clinical Trial
variant-with-molec-consequences	Observation	Variant	Variant with molecular consequences
VariantExample	Observation	Variant	Example for Variant NM_004448.4(ERBB2):c.2264_2278del
VariantExample1	Observation	Variant	Example for Variant given by HGVS
VariantExample2	Observation	Variant	Example for genomic Variant given by VCF columns
WES-FullSequencedRegion-GRCh38	DocumentReference	Genomic Data File	WES_FullSequencedRegion_GRCh38: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.
WES-UncallableRegions-GRCh38	DocumentReference	Genomic Data File	Example for Genomic Data File WES-UncallableRegions-GRCh38
ZFHX3-significance	Observation	Diagnostic Implication	Example DiagnosticImplication - ZFHX3 uncertain significance
ZFHX3-uncertain-molc	Observation	Molecular Consequence	Example Molecular Consequence ZFHX3 missense_variant
ZFHX3-uncertain-var	Observation	Variant	Example for ZFHX3 uncertain