Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

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