Retrieve count or list of patients having diagnostic implications.

Retrieve count or list of patients having molecular consequences.

Retrieve count or list of patients having specified genotypes/haplotypes.

Retrieve count or list of patients having specified variants.

Retrieve count or list of patients having structural intersecting variants in specified regions.

Retrieve count or list of patients having structural subsuming variants in specified regions.

Retrieve count or list of patients having therapeutic implications.

Retrieve metadata about sequencing studies performed on a subject.

Retrieves genetic diagnostic implications for variants.

Retrieve haplotypes/genotypes for specified genes.

Retrieves molecular consequences of a DNA variant.

See if specified haplotypes/genotypes are present.

Determine if specified simple variants are present.

Determine if structural variants are present that overlap range(s).

Determine if structural variants are present that fully subsume a range.

Retrieves genetic therapeutic implications for variants/haplotypes/genotypes.

Determine if simple variants are present that overlap range(s).

Base profile that defines characteristics shared by all genetic observations.

Properties common to genetic findings whose results are expressed as computable discrete elements (e.g. genotypes, haplotypes, variants, etc.).

Properties common to genomic implications expressed as computable discrete elements.

Observation stating a linkage between one or more genotype/haplotype/variation Observations and evidence for or against a particular disease, condition, or cancer diagnosis.

Task proposing a follow-up that is recommended based on the implications of genomic findings.

A profile of DocumentReference used to represent a genomics file.

Genomic profile of DiagnosticReport.

A genomic study is a set of analyses performed to analyze and generate genomic data.

A genomic study analysis is a component of a genomic study.

Assertion of a particular genotype on the basis of one or more variants or haplotypes.

Assertion of a particular haplotype on the basis of one or more variants.

Task proposing medication recommendations based on the implications of genomic findings.

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.

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).

Indicates whether two entities are in Cis (same strand) or Trans (opposite strand) relationship to each other.

Profile with properties for observations that convey the potential impact of genomic characteristics on a medication or non-medicinal therapy.

Details about a set of changes in the tested sample compared to a reference sequence.

Annotation DataType with added CodeableConcept extension element

Codifies the content of an Annotation

Adds codified notes to a report to capture additional content

RiskAssessment delivered as part of a genomics report or observation

Defines the change type for a genomic analysis

Genomic Study Analysis Device

Used to transmit the one or more analysis per GenomimcStudy

Defines a focus for a genomic analysis

Defines the genome build for a genomic analysis

Genomic Study Analysis Input

Defines a method type for a genomic analysis

Metrics about the sequencing analysis that was performed

Genomic Study Analysis Output

Defines a protocol that was performed for a genomic analysis

Defines the regions studied, regions called, and regions deemed uncallable (generally due to low coverage)

Defines a specimen for a genomic analysis

Defines a title for a genomic analysis

Used to reference a GenomicStudy profile

Used to reference to the referrer of the study

Used to reference a specific medication that was assessed (e.g. a FHIR Medication or a FHIR MedicationKnowledge).

References a proposed action that is recommended based on the results of the diagnostic report.

Use the RelatedArtifact at the Observation.component element (not valid in the R4 extension)

Use to group and order repeat expansion motifs.

Used to reference a specific therapy that was assessed (e.g. a FHIR ResearchStudy, a FHIR CarePlan, or a FHIR PlanDefinition).

Value Set for specific types of coded annotations

Value Set for specific transmission patterns of a condition in a pedigree

DNA Change Type of a variant.

Example sources of values for Evidence Level

The effect of a variant on downstream biological products or pathways.

Value Set for terms that describe a predicted ramification based on the presence of associated molecular finding(s).

Backport of http://hl7.org/fhir/ValueSet/genomicstudy-changetype

Backport of http://hl7.org/fhir/ValueSet/genomicstudy-dataformat

Backport of http://hl7.org/fhir/ValueSet/genomicstudy-methodtype

Backport of http://hl7.org/fhir/ValueSet/genomicstudy-status

Backport of http://hl7.org/fhir/ValueSet/genomicstudy-type

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.

This value set includes high/low codes for Observation Interpretations

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)

This value set is drawn from the Molecular Biomarker Ontology code system, which provides codes that characterize a molecular biomarker.

Value Set for terms that can be used as Biomarkers.

The calculated or observed effect of a variant on its downstream transcript and, if applicable, ensuing protein sequence.

Value Set for specific types of relationships

Value Set for codes yet to be defined in LOINC

A code that classifies the confidence for calling this variant.

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.

Code System for specific types of coded annotations

Backport of http://hl7.org/fhir/genomicstudy-changetype

Backport of http://hl7.org/fhir/genomicstudy-dataformat

Backport of http://hl7.org/fhir/genomicstudy-methodtype

Backport of http://hl7.org/fhir/genomicstudy-status

Backport of http://hl7.org/fhir/genomicstudy-type

This (experimental) code system provides for a draft categorization of biomarkers along several axes. Based on ballot feedback, the committee anticipates significant revisions.

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.

Code System for specific types of relationships

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.

A code that represents the confidence of a true positive variant call.

Mapping from http://loinc.org ValueSet for DNA Change Type to http://sequenceontology.org codes

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

Example Molecular Consequence ATR frameshift

Example DiagnosticImplication - ATR likely pathogenic

Example for ATR insertion

Example of a Diagnostic Implication for Familial hypercholesterolemia

Example for Patient. Supports references to subject for multiple genomics reporting profile conforming instances.

CNVAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.

Example Molecular Consequence EGFR L858R missense_variant

Example DiagnosticImplication - EGFR pathogenic

Example of EGFR-L858R Therapeutic Implication for drug treatment 1

Example of EGFR-L858R Therapeutic Implication for drug treatment 2

Example for EGFR L858R

Example for germline CNV

Example for germline DEL

Example for germline INV

Organization (lab) example

Example Org

Patient example

ServiceRequest (order) example

Example for somatic CNV

Example for somatic DEL

Example for somatic INV

Specimen example

Example Output of ‘FindPopulationSpecificVariants’ Operation, based on ‘AND’ logic

Example Output of ‘FindPopulationSpecificVariants’ Operation, based on ‘OR’ logic

Example Output of ‘FindPopulationDxImplications’ Operation

Example Output of ‘FindPopulationMolecConseq’ Operation

Example Output of ‘FindPopulationSpecificHaplotypes’ Operation

Example Output of ‘FindPopulationStructuralIntersectingVariants’ Operation

Example Output of ‘FindPopulationStructuralSubsumingVariants’ Operation

Example Output of ‘FindPopulationTxImplications’ Operation

Example Output of ‘FindStudyMetadata’ Operation

Example Output of ‘FindSubjectDxImplications’ Operation

Example Output of ‘FindSubjectHaplotypes’ Operation

Example Output of ‘FindSubjectMolecConseq’ Operation

Example Output of ‘FindSubjectSpecificHaplotypes’ Operation

Example Output of ‘FindSubjectSpecificVariants’ Operation

Example Output of ‘FindSubjectStructuralIntersectingVariants’ Operation

Example Output of ‘FindSubjectStructuralSubsumingVariants’ Operation

Example Output of ‘FindSubjectTxImplications’ Operation

Example Output of ‘Find Subject Variants’ Operation

Example for Genomic Data File FullGenome-GRCh38

Polygenic Risk Score example

Example of a Report carrying a Genotype, Therapeutic Implication, and Medication Recommendation

Example for Service Request

Example for Genomic Specimen

Example for Genomic Specimen from Buccal Swab

Example of a Genotype. A complete haplotype set defines a genotype. In this example the gneotype is dervied from observations of the underlying haplotypes.

Example of a Genotype, Medication Recommendation, and MedicationStatement

Example of a Genotype using Pharmvar Haplotypes

Generic grouping of Therapeutic Implication observations

Generic grouping of Genotype observations

Generic grouping of Regions Studied and Variant observations

Example for HER2 by immune stain

Example for HER2 by immunoassay

Example for Patient. Supports references to subject for multiple genomics reporting profile conforming instances.

Example for HLA-A-haplotype1

Example for HLA-A-haplotype2

Example for HLA-B-haplotype1

Example for HLA-B-haplotype2

Example for HLA-C-haplotype1

Example for HLA-C-haplotype2

Example of a Haplotype using PharmVar

Example of a Haplotype using PharmVar

Example of a Haplotype as part of a Haplotype Set (1 of 2). A complete haplotype set defines a genotype.

Example of a Haplotype as part of a Haplotype Set (2 of 2). A complete haplotype set defines a genotype.

Basic example for karyotype Variant expressed in ISCN

Basic example of a Diagnostic Implication for CML

Normal example for karyotype Variant expressed in ISCN

Example DiagnosticImplication - MSH2 deletion Hereditary cancer-predisposing syndrome

Example Molecular Consequence MSH2 frameshift

Example for MSH2 deletion

Example for MSI

Example of a Medication Recommendation

MedicationStatement for Warfarin

Example for MSI

Repeat Expansion Variant with multiple motifs

Example DiagnosticImplication - NOTCH1 uncertain significance

Example Molecular Consequence NOTCH1 missense_variant

Example for NOTCH1 uncertain

Example DiagnosticImplication - NTHL1 SNV Hereditary cancer-predisposing syndrome

Example Molecular Consequence NTHL1 SNV variant with nonsense codon

Example for NTHL1 SNV

Example for PD-L1

Example of PGX sequencing panel

Example of PGX Sequence analysis

Example of a Report carrying multiple Therapeutic Implications, Genotypes, and Variants

Example of a Report carrying multiple Therapeutic Implications, Genotypes, and Variants

Example of a Medication Recommendation for alternatives to clopidogrel

Example of a Medication Recommendation for alternatives to voriconazole

Example of a Medication Recommendation for decreasing dosage for citalopram

Example of a Medication Recommendation for decreasing dosage for escitalopram

Example of a Medication Recommendation for decreasing dosage for amitriptyline

Example of a Genotype from eMERGE

Example of a Genotype from eMERGE

Example of a Genotype from eMERGE

Example variant 1011

Example variant 1012

Example variant 1013

Example variant 1014

Example variant 1015

Example variant 1016

Example variant 1017

Example variant 1018

Example variant 1019

Example variant 1020

Example variant 1021

Example of a Diagnostic Implication for Diabetes Type 2 with a polygenic risk score.

Example Molecular Consequence ROS1 Fusion

Example DiagnosticImplication - ROS1 disease

Example of ROS1 Fusion Therapeutic Implication for drug treatment

Example of ROS1 Fusion Therapeutic Implication for Clinical Trial

Example for ROS1 Fusion but as typically reported in PDF, without necessarily declaring a particular fusion partner

Repeat Expansion Variant

Example Variant

Example Molecular Consequence STAG2 frameshift

Example DiagnosticImplication - STAG2 likely pathogenic

Example for STAG2 insertion

Example for sequence phase relation.

Very simple producure representing a genomic study’s protocol

SimpleVariantAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.

Example of high TMB Therapeutic Implication for drug treatment

Example for Tumor Mutation Burden

Example of a Therapeutic Implication for Carbamazepine

Example of a Therapeutic Implication for Clinical Trial

Example of a Therapeutic Implication for Carbamazepine

Example for Tumor Mutation Burden

Example of a Therapeutic Implication from eMERGE

Example of a Therapeutic Implication from eMERGE

Example of a Therapeutic Implication from eMERGE

Example of a Therapeutic Implication from eMERGE

Example of a Therapeutic Implication from eMERGE

Example of a Therapeutic Implication from eMERGE

Representing a BED file that represents uncallable regions

Example for Somatic Variant and Clinical Trial

Example for Variant NM_004448.4(ERBB2):c.2264_2278del

Example for Variant given by HGVS

Example for genomic Variant given by VCF columns

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.

Example for Genomic Data File WES-UncallableRegions-GRCh38

Example DiagnosticImplication - ZFHX3 uncertain significance

Example Molecular Consequence ZFHX3 missense_variant

Example for ZFHX3 uncertain

Example for Tumor Normal Genomics Study Analysis

Example for just Tumor RNA Genomic Study Analysis

Example of a HLA bundle

Example bundle containing CYP2C19 report and variants

Example bundle showing a variety of profiles.

Example bundle showing a variety of profiles, including how groupings of Observations might be delivered.

Example bundle with compound heterozygous variant, where the specific changes are represented without HGVS.

Example bundle with compound heterozygous variant, where the specific changes are represented with HGVS.

Example of an oncology report, TMB, variants, and implications.

Example oncology bundle including report, variants, and other resources.

Example bundle with an oncology report with SNVs, TMB, MSI, and therapy matches.

Example bundle with an oncology report with SNVs, TMB, MSI, and therapy matches, including some groupings of observations

Example bundle with a PGx report and a variety of observations.

Example Sequence Phase Relation showing a report with two variants in cis

Child of a trio

Father of a trio

Mother of a trio

Example GenomicReport including an HLA glstring

Example PGx Service Request

A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline

A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline

A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline

A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline

Example patient

Example of Molecular genetic test

Example of lung specimen obtained by biopsy

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: A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline.

GenomicStudy example of a trio analysis

GenomicStudy Analysis example of a trio analysis

Genotype example: Sequence-based typing of HLA-A

Example Haplotype Sequence-based typing of HLA-A

Example of solid tumor whole exome sequencing panel

Example of Sequence analysis of the entire coding region

Example of Deletion/duplication analysis

Example Molecular Consequence that includes Loss of Function prediction

Example Molecular Consequence

Example Molecular Consequence

Example Molecular Consequence

Example for normal specimen

Example DiagnosticImplication - Pathogenic for CF

Example of an ordering provider

Example of a pathologist

Example of a Pathology lab

Example practitioner

Example ServiceRequest for genomics

Somatic example Patient

Example somatic GenomicReport

Example for Somatic Testing Request

Example for somatic genetic study

Example for Genomic Data File somaticVCFfile

Example HLA specimen

Example of a supervisor

Triodenovo Software

Example for tumor specimen

Variant with molecular consequences