The lab order or request that triggered the execution of the genomics test

Constraints on Specimen for use with clinical genomics reporting

Defines the overall genomic report

Provides a description of the region studied.

Organizes information within a genomic report

Provides a coarse overall interpretation of the genomic results reported.

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

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

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

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

Tumor mutational burden (TMB), also known as mutation load.

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

Profile with properties for observations that convey the potential impact of genomic characteristics on a diagnosis

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

Task describing what sort of change (if any) should be made in a patient’s medication based on an identified finding

Task describing the followup that is recommended

Base profile that defines characteristics shared by all genetic observations.

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

Abstract profile for observations linking a genomic finding to an external knowledgebase.

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

References a proposed action that is recommended based on the results of the report or observations

Additional information relevant to interpreting/understanding the report

Code System for codes yet to be defined in LOINC

Code System for specific types of relationships

High/Low codes for Observation.interpretation

Value Set for HGVS

Value Set for HGNC (genes and gene groups)

Value Set for codes yet to be defined in LOINC

DNA change type for variants

Changes in structural features of a sequence due to the observed variant.

Value Set for specific types of relationships

origins of variants

Mapping LOINC answers to SequenceOntology

Retrieves variants from a specified genomic region

Example Org

Test instance of TherapeuticImplication

Test instance of Genotype

Test instance of TaskMedChg

Test instance of GenomicsReport

Test instance of Sequence Phase Relationship

Test instance of Overall Interpretation

Test instance of TMB

Test instance of MSI

Test instance of Service Request

Test instance of Variant given by Clinvar ID

Test instance of Variant given by VCF columns

Test instance a patient

Test instance a specimen

Test instance of PGx Genotype given by star allele

Test instance of PGx Genotype given by star allele

Test instance of PGx Genotype given by rs ID and allele

Test instance of PGx overall report interpretation

Test instance of PGx Observation grouper consisting of Implications from the lab

Test instance of PGx Observation grouper consisting of genotypes from the lab

Test instance of PGx Observation grouper consisting of variants and regions studied from the lab

Test instance of PGx Diagnostic report based on eMERGE panel

Test instance of PGx variant defined by VCF column data

Test instance of PGx variant defined by VCF column data

Test instance of PGx variant defined by VCF column data

Test instance of PGx variant defined by VCF column data

Test instance of PGx variant defined by HGVS nomenclature

Test instance of PGx variant defined by VCF column data

Test instance of PGx variant defined by VCF column data

Test instance of PGx variant defined by VCF column data

Test instance of PGx variant defined by HGVS nomenclature

Test instance of PGx variant defined by VCF column data

Test instance of PGx variant defined by VCF column data

Test instance of region studied report for one gene

Test instance of region studied report for one gene

Test instance of region studied report for one gene

Test instance of observation stating therapeutic implication from guideline

Test instance of observation stating therapeutic implication from guideline

Test instance of observation stating therapeutic implication from guideline

Test instance of observation stating therapeutic implication from guideline

Test instance of observation stating therapeutic implication from guideline

Test instance of observation stating therapeutic implication from guideline

Test instance of service request for PGx test

Test instance showing data from the CG v2 spec

Compound Heterozygote Variant Example

Compound Heterozygote Variant example, using position, reference, and alternate allele instead of HGVS.

SNV example

ACMG annotation

Inherited Disease Pathogenicity

Pharmacogenomic Report Example instances

CYP2C19 report from 1000 Genomes

Phase relation on CYP2C19 report

Full Bundle HLA Typing Example

DiagnosticReport HLA Typing Example

HLA-A genoyping Example: HLA-A03:01:01:01+HLA-A30:01:01

HLA-A allele observaation: HLA-A*03:01:01:01

Specimen example: Buccal swab for HLA typing

ServiceRequest example: High-resolution HLA-A genotyping

Oncology Example Report with 12 reported variants

Small example report with 1 reported variant and somatic diagnostic implication

Full Bundle Oncology Example

Extension reference to RiskAssessment resource

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

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

A set of terms that describe the transmission pattern of a condition in a pedigree.

For clopidogrel, individuals with this diplotype are expected to have significantly reduced platelet inhibition, increased residual platelet aggregation and increased risk for adverse cardiovascular events in response to clopidogrel. Alternative antiplatelet therapy (if no contraindication) is recommended. Refer to current guidelines for dosage and recommendations at https://cpicpgx.org/guidelines/guideline- for-clopidogrel-and-cyp2c19/

voriconazole - An alternative agent that is not dependent on CYP2C19 metabolism such as isavuconazole, liposomal amphotericin B, or posaconazole is recommended as primary therapy in lieu of voriconazole. A lower than standard dosage of voriconazole with careful therapeutic drug monitoring is another alternative. Refer to current guidelines for dosage and recommendations at https://cpicpgx.org/guidelines/guideline-for-voriconazole-and-cyp2c19/.

For citalopram, a 50% reduction in starting dose is recommended with therapeutic drug monitoring to guide dose adjustment or select an alternate drug not predominantly metabolized by CYP2C19. Refer to current guidelines for dosage and recommendations at https://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/. If CYP2D6 genotyping is available, refer to the current guidelines for dosing recommendations.

For escitalopram, a 50% reduction in starting dose is recommended with therapeutic drug monitoring to guide dose adjustment or select an alternate drug not predominantly metabolized by CYP2C19. Refer to current guidelines for dosage and recommendations at https://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/. If CYP2D6 genotyping is available, refer to the current guidelines for dosing recommendations.

For amitriptyline, a 50% reduction in starting dose is recommended with therapeutic drug monitoring to guide dose adjustment. Refer to current guidelines for dosage and recommendations at https://cpicpgx.org/guidelines/guideline-for- tricyclic-antidepressants-and-cyp2d6-and-cyp2c19/. If CYP2D6 genotyping is available, refer to the current guidelines for dosing recommendations.