Use this operation to retrieve variants with precise endpoints from a specified genomic region for a specified patient. If the range in question has been studied, the operation returns a FHIR Parameters resource containing variants overlapping the region. If the patient or the specified region has not been studied, the operation returns a 404 error.

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.

Base profile that defines characteristics shared by all genetic observations.

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 describing the follow-up that is recommended

A profile of DocumentReference used to represent a genomics file.

Genomics profile of DiagnosticReport.

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.

Microsatellite Instability (MSI) is the condition of genetic hypermutability (predisposition to mutation) that results from impaired DNA mismatch repair (MMR).

Task proposing medication recommendations based on genetic results.

Provides a coarse overall interpretation of the genomic results reported.

The Region Studied profile is used to assert actual regions studied for the performed test(s). Intended coverage areas may differ from actual coverage areas (e.g. due to technical limitations during test performance).

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

The total number of mutations (changes) found in the DNA of cancer cells. Knowing the tumor mutational burden may help plan the best treatment. For example, tumors that have a high number of mutations appear to be more likely to respond to certain types of immunotherapy. Tumor mutational burden is being used as a type of biomarker.

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

Captures citations, evidence and other supporting documentation for the observation or report.

Used to transmit the contents of or links to files that were produced as part of the testing process. Examples are VCF, BAM, CRAM, and other similar files.

RiskAssessment delivered as part of a genomics report or observation

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.

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).

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.

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 includes high/low codes for Observation Interpretations

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.

By which parent the variant was inherited in the patient, if known.

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

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 currently ‘TBD’ codes. The CG WG plans to request formal LOINC codes to replace these codes as these concepts are validated.

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

Example of a Diagnostic Implication for Familial hypercholesterolemia

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

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

Polygenic Risk Score example

Example for Genomic Specimen

Example for Genomic Specimen from Buccal Swab

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

Example for Service Request

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 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.

Example of a Medication Recommendation

MedicationStatement for Warfarin

Example for MSI

Example for Overall Interpretation.

Example for Overall Interpretation.

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.

eMERGE PGx CYP2C19

eMERGE PGx CYP2C9

eMERGE PGx VKORC1

Example Variant

Example for sequence phase relation.

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

Example of what a VCF as a DocumentRefence would look like.

Example for Somatic Variant and Clinical Trial

Example for Variant given by HGVS

Example for genomic Variant given by VCF columns

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

Example GenomicsReport including an HLA glstring

Example PGx Service Request

Genotype example: Sequence-based typing of HLA-A

Example Haplotype Sequence-based typing of HLA-A

Example DiagnosticImplication - Pathogenic for CF

Example ServiceRequest for genomics

Example HLA specimen