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-cibuild 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. That is, 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.
Genomic Study	Procedure	Procedure	A genomic study is a set of analyses performed to analyze and generate genomic data.
Genomic Study Analysis	Procedure	Procedure	A genomic study analysis is a component of a genomic study.
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
Genomic Study Analysis Change Type	Defines the types of alterations detectable by a given genomic analysis
Genomic Study Analysis Device	Genomic Study Analysis Device
Genomic Study Analysis Extension	Used to transmit the one or more analysis per GenomimcStudy
Genomic Study Analysis Focus	Defines a focus for a genomic analysis
Genomic Study Analysis Genome Build	Defines the genome build for a genomic analysis
Genomic Study Analysis Input	Genomic Study Analysis Input
Genomic Study Analysis Method Type	Defines a method type for a genomic analysis
Genomic Study Analysis Metrics	Metrics about the sequencing analysis that was performed
Genomic Study Analysis Output	Genomic Study Analysis Output
Genomic Study Analysis Protocol Performed	Defines a protocol that was performed for a genomic analysis
Genomic Study Analysis Regions	Defines the regions studied, regions called, and regions deemed uncallable (generally due to low coverage)
Genomic Study Analysis Source Class	The genomic class of the specimen being analyzed: Germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome.
Genomic Study Analysis Specimen	Defines a specimen for a genomic analysis
Genomic Study Analysis Title	Defines a title for a genomic analysis
Genomic Study Reference	Used to reference a GenomicStudy profile
Genomic Study Referrer Extension	Used to reference to the referrer of the study
Knowledgebase Ancestry Group	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
Genomic Study Change Type CodeSystem	Backport of http://hl7.org/fhir/genomicstudy-changetype
Genomic Study Data Format CodeSystem	Backport of http://hl7.org/fhir/genomicstudy-dataformat
Genomic Study Method Type CodeSystem	Backport of http://hl7.org/fhir/genomicstudy-methodtype
Genomic Study Status CodeSystem	Backport of http://hl7.org/fhir/genomicstudy-status
Genomic Study Type CodeSystem	Backport of http://hl7.org/fhir/genomicstudy-type
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).
Genomic Study Change Type ValueSet	Backport of http://hl7.org/fhir/ValueSet/genomicstudy-changetype
Genomic Study Data Format ValueSet	Backport of http://hl7.org/fhir/ValueSet/genomicstudy-dataformat
Genomic Study Method Type ValueSet	Backport of http://hl7.org/fhir/ValueSet/genomicstudy-methodtype
Genomic Study Status ValueSet	Backport of http://hl7.org/fhir/ValueSet/genomicstudy-status
Genomic Study Type ValueSet	Backport of http://hl7.org/fhir/ValueSet/genomicstudy-type
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
Genomic Study Status Map	Mapping from Procedure's EventStatus (http://hl7.org/fhir/ValueSet/event-status) ValueSet for 'status' to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/genomicstudy-status-vs codes

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	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.

Diagnostic Implication Examples

Example	Description
AnnotationExample	Example of a Diagnostic Implication for Familial hypercholesterolemia
ATR-insertion-significance	Example DiagnosticImplication - ATR likely pathogenic
diagnosticImplication-interact-smn1-smn2	Diagnostic Implication for SMN1/SMN2 CNV example
EGFR-L858R-significance	Example DiagnosticImplication - EGFR pathogenic
ISCN-CMLImplication	Basic example of a Diagnostic Implication for CML
MSH2-del-disease	Example DiagnosticImplication - MSH2 deletion Hereditary cancer-predisposing syndrome
NOTCH1-significance	Example DiagnosticImplication - NOTCH1 uncertain significance
NTHL1-snv-disease	Example DiagnosticImplication - NTHL1 SNV Hereditary cancer-predisposing syndrome
obs-idh-ex	Example DiagnosticImplication - Pathogenic for CF
PolyGenicDiagnosticImpExample	Example of a Diagnostic Implication for Diabetes Type 2 with a polygenic risk score.
ROS1-Fusion-disease	Example DiagnosticImplication - ROS1 disease
STAG2-insertion-significance	Example DiagnosticImplication - STAG2 likely pathogenic
ZFHX3-significance	Example DiagnosticImplication - ZFHX3 uncertain significance

Followup Recommendation Examples

Example	Description
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

Genomic Annotation Examples

Example	Description
pop-allele-freq	Example genomic annotation showing a population allele frequency

Genomic Data File Examples

Example	Description
CNVAnalysis-called	CNVAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.
FullGenome-GRCh38	Example for Genomic Data File FullGenome-GRCh38
genomicFileFatherBAM	A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline
genomicFileMotherBAM	A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline
genomicFileProbandBAM	A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline
genomicFileProbandVCF	A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline
genomicVCFfile-cnv	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	genomicVCFfile_simple: A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline.
SimpleVariantAnalysis-called	SimpleVariantAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.
somaticVCFfile	Example for Genomic Data File somaticVCFfile
UncallableRegions	Representing a BED file that represents uncallable regions
WES-FullSequencedRegion-GRCh38	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	Example for Genomic Data File WES-UncallableRegions-GRCh38

Genomic Report Examples

Example	Description
diagnosticreport-hla-glstring-r4	Example GenomicReport including an HLA glstring
GenomicReportExample01	Example of a Report carrying a Genotype, Therapeutic Implication, and Medication Recommendation
PGxGenomicReportEMERGE	Example of a Report carrying multiple Therapeutic Implications, Genotypes, and Variants
PGxGenomicReportEMERGE-withGrouping	Example of a Report carrying multiple Therapeutic Implications, Genotypes, and Variants
somaticReport	Example somatic GenomicReport

Genomic Study Examples

Example	Description
genomicstudy-trio2	GenomicStudy example of a trio analysis
lungMass	Example of solid tumor whole exome sequencing panel
PGXGenomicStudy	Example of PGX sequencing panel
somaticStudy	Example for somatic genetic study

Genomic Study Analysis Examples

Example	Description
analysisTumorNormalDNA	Example for Tumor Normal Genomics Study Analysis
analysisTumorRNA	Example for just Tumor RNA Genomic Study Analysis
genomicstudyanalysis-trio2	GenomicStudy Analysis example of a trio analysis
lungMass-analysis1	Example of Sequence analysis of the entire coding region
lungMass-analysis2	Example of Deletion/duplication analysis
PGXGenomicStudyAnalysis	Example of PGX Sequence analysis

Genotype Examples

Example	Description
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.
genotype-hla-a-glstring-r4	Genotype example: Sequence-based typing of HLA-A
GenotypeExample1	Example of a Genotype, Medication Recommendation, and MedicationStatement
GenotypeExamplePharmVar	Example of a Genotype using Pharmvar Haplotypes
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

Haplotype Examples

Example	Description
haplotype-hla-a-1-r4	Example Haplotype Sequence-based typing of HLA-A
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.
HLA-A-haplotype1	Example for HLA-A-haplotype1
HLA-A-haplotype2	Example for HLA-A-haplotype2
HLA-B-haplotype1	Example for HLA-B-haplotype1
HLA-B-haplotype2	Example for HLA-B-haplotype2
HLA-C-haplotype1	Example for HLA-C-haplotype1
HLA-C-haplotype2	Example for HLA-C-haplotype2

Medication Recommendation Examples

Example	Description
MedicationRecommendationExample1	Example of a Medication Recommendation

Molecular Biomarker Examples

Example	Description
HER2byImmuneStainExample	Example for HER2 by immune stain
HER2byImmunoassayExample	Example for HER2 by immunoassay
MicrosatelliteInstabilityExample01	Example for MSI
MSIExample	Example for MSI
PDL1Example	Example for PD-L1
TMBExample	Example for Tumor Mutation Burden
TumorMutationBurdenExample01	Example for Tumor Mutation Burden

Molecular Consequence Examples

Example	Description
ATR-insertion-molc	Example Molecular Consequence ATR frameshift
EGFR-L858R-molc	Example Molecular Consequence EGFR L858R missense_variant
molec-conseq1	Example Molecular Consequence that includes Loss of Function prediction
molec-conseq2	Example Molecular Consequence
molec-conseq3	Example Molecular Consequence
molec-conseq4	Example Molecular Consequence
MSH2-del-molc	Example Molecular Consequence MSH2 frameshift
NOTCH1-uncertain-molc	Example Molecular Consequence NOTCH1 missense_variant
NTHL1-snv-molc	Example Molecular Consequence NTHL1 SNV variant with nonsense codon
ROS1-Fusion	Example Molecular Consequence ROS1 Fusion
STAG2-insertion-molc	Example Molecular Consequence STAG2 frameshift
ZFHX3-uncertain-molc	Example Molecular Consequence ZFHX3 missense_variant

Sequence Phase Relationship Examples

Example	Description
SequencePhaseRelationExample1	Example for sequence phase relation.

Therapeutic Implication Examples

Example	Description
EGFR-L858R-therapuDrug1	Example of EGFR-L858R Therapeutic Implication for drug treatment 1
EGFR-L858R-therapuDrug2	Example of EGFR-L858R Therapeutic Implication for drug treatment 2
ROS1-Fusion-therapuDrug	Example of ROS1 Fusion Therapeutic Implication for drug treatment
ROS1-Fusion-therapuTrial	Example of ROS1 Fusion Therapeutic Implication for Clinical Trial
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
therapuDrug1-interact-smn1-smn2	Antisense Oligonucelotide example of Therapeutic Implication for SMN1/SMN2 CNV example
therapuDrug2-interact-smn1-smn2	Transgene example of Therapeutic Implication for SMN1/SMN2 CNV example
therapuDrug3-interact-smn1-smn2	Small molecule example of Therapeutic Implication for SMN1/SMN2 CNV example
TMB-therapuDrug	Example of high TMB Therapeutic Implication for drug treatment
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

Variant Examples

Example	Description
ATR-insertion-var	Example for ATR insertion
EGFR-L858R-var	Example for EGFR L858R
ExampleGermlineCNV	Example for germline CNV
ExampleGermlineDEL	Example for germline DEL
ExampleGermlineINV	Example for germline INV
ExampleSomaticCNV	Example for somatic CNV
ExampleSomaticDEL	Example for somatic DEL
ExampleSomaticINV	Example for somatic INV
ISCN-CMLExample	Basic example for karyotype Variant expressed in ISCN
ISCN-NormalExample	Normal example for karyotype Variant expressed in ISCN
MSH2-del-var	Example for MSH2 deletion
MultipleRepeatExpansions	Repeat Expansion Variant with multiple motifs
NOTCH1-uncertain-var	Example for NOTCH1 uncertain
NTHL1-snv-var	Example for NTHL1 SNV
obs1-interact-smn1-smn2	SMN1 CNV companion for SMN1/SMN2 CNV example
obs2-interact-smn1-smn2	SMN2 CNV companion for SMN1/SMN2 CNV example
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
RepeatExpansion	Repeat Expansion Variant
ROS1-Fusion-var	Example for ROS1 Fusion but as typically reported in PDF, without necessarily declaring a particular fusion partner
SNVexample	Example Variant
STAG2-insertion-var	Example for STAG2 insertion
Variant-Somatic-Clinical-Trial	Example for Somatic Variant and Clinical Trial
variant-with-molec-consequences	Variant with molecular consequences
VariantExample	Example for Variant NM_004448.4(ERBB2):c.2264_2278del
VariantExample1	Example for Variant given by HGVS
VariantExample2	Example for genomic Variant given by VCF columns
ZFHX3-uncertain-var	Example for ZFHX3 uncertain

No Profile Examples

Example	Resource	Description
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.
denovoChild	Patient	Child of a trio
denovoFather	Patient	Father of a trio
denovoMother	Patient	Mother of a trio
eMERGEServiceRequest	ServiceRequest	Example PGx Service Request
ExampleLab	Organization	Organization (lab) example
ExampleOrg	Organization	Example Org
ExamplePatient	Patient	Patient example
ExampleServiceRequest	ServiceRequest	ServiceRequest (order) example
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
genomicPatient	Patient	Example patient
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
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
HG00403	Patient	Example for Patient. Supports references to subject for multiple genomics reporting profile conforming instances.
MedicationStatementWarfarin	MedicationStatement	MedicationStatement for Warfarin
normalSpecimen	Specimen	Example for normal specimen
orderingPractitioner	Practitioner	Example of an ordering provider
pathologistPractitioner	Practitioner	Example of a pathologist
performingOrganization	Organization	Example of a Pathology lab
practitioner02	Practitioner	Example practitioner
SequencingProcedure	Procedure	Very simple producure representing a genomic study's protocol
servicerequest-hla-a-r4	ServiceRequest	Example ServiceRequest for genomics
somaticPatient	Patient	Somatic example Patient
somaticServiceRequest	ServiceRequest	Example for Somatic Testing Request
specimen-hla-r4	Specimen	Example HLA specimen
supervisorPractitioner	Practitioner	Example of a supervisor
triodenovo-software	Device	Triodenovo Software
tumorSpecimen	Specimen	Example for tumor specimen