Genomics Reporting Implementation Guide
3.0.0 - release International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 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

Artifacts Summary

This page provides a list of the FHIR artifacts defined as part of this implementation guide.

Behavior: Operation Definitions

These are custom operations that can be supported by and/or invoked by systems conforming to this implementation guide.

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).

Structures: Abstract Profiles

These are profiles on resources or data types that describe patterns used by other profiles, but cannot be instantiated directly. I.e. instances can conform to profiles based on these abstract profiles, but do not declare conformance to the abstract profiles themselves.

Genomic Base

Base profile that defines characteristics shared by all genetic observations.

Genomic Finding

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

Genomic Implication

Properties common to genomic implications expressed as computable discrete elements.

Structures: Resource Profiles

These define constraints on FHIR resources for systems conforming to this implementation guide.

Diagnostic Implication

Observation stating a diagnostic annotation (e.g. disease risk) on one or more genotype/haplotype/variant/biomarker observations.

Followup Recommendation

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

Genomic Data File

A profile of DocumentReference used to represent a genomics file.

Genomic Report

Genomic profile of DiagnosticReport.

Genomic Study

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

Genomic Study Analysis

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

Genotype

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

Haplotype

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

Medication Recommendation

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

Molecular Biomarker

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

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

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

Therapeutic Implication

Observation stating a therapeutic annotation (e.g. drug susceptibility, clinical trial eligibility) on one or more genotype/haplotype/variant/biomarker observations.

Variant

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

Structures: Data Type Profiles

These define constraints on FHIR data types for systems conforming to this implementation guide.

Coded Annotation

Annotation DataType with added CodeableConcept extension element

Structures: Extension Definitions

These define constraints on FHIR data types for systems conforming to this implementation guide.

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

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.

Related Artifact for Observation component

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

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).

Terminology: Value Sets

These define sets of codes used by systems conforming to this implementation guide.

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)

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.

Terminology: Code Systems

These define new code systems used by systems conforming to this implementation guide.

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

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.

Terminology: Concept Maps

These define transformations to convert between codes by systems conforming with this implementation guide.

DNA Change Type Map

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

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

Example: Example Instances

These are example instances that show what data produced and consumed by systems conforming with this implementation guide might look like.

ATR-insertion-molc

Example Molecular Consequence ATR frameshift

ATR-insertion-significance

Example DiagnosticImplication - ATR likely pathogenic

ATR-insertion-var

Example for ATR insertion

AnnotationExample

Example of a Diagnostic Implication for Familial hypercholesterolemia

CGPatientExample01

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

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.

EGFR-L858R-molc

Example Molecular Consequence EGFR L858R missense_variant

EGFR-L858R-significance

Example DiagnosticImplication - EGFR pathogenic

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

EGFR-L858R-var

Example for EGFR L858R

ExampleGermlineCNV

Example for germline CNV

ExampleGermlineDEL

Example for germline DEL

ExampleGermlineINV

Example for germline INV

ExampleLab

Organization (lab) example

ExampleOrg

Example Org

ExamplePatient

Patient example

ExampleServiceRequest

ServiceRequest (order) example

ExampleSomaticCNV

Example for somatic CNV

ExampleSomaticDEL

Example for somatic DEL

ExampleSomaticINV

Example for somatic INV

ExampleSpecimen

Specimen example

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

FullGenome-GRCh38

Example for Genomic Data File FullGenome-GRCh38

GenRiskDiabetesT2

Polygenic Risk Score example

GenomicReportExample01

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

GenomicServiceRequestExample01

Example for Service Request

GenomicSpecimenExample01

Example for Genomic Specimen

GenomicSpecimenExample02

Example for Genomic Specimen from Buccal Swab

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.

GenotypeExample1

Example of a Genotype, Medication Recommendation, and MedicationStatement

GenotypeExamplePharmVar

Example of a Genotype using Pharmvar Haplotypes

GrouperEx01

Generic grouping of Therapeutic Implication observations

GrouperEx02

Generic grouping of Genotype observations

GrouperEx03

Generic grouping of Regions Studied and Variant observations

HER2byImmuneStainExample

Example for HER2 by immune stain

HER2byImmunoassayExample

Example for HER2 by immunoassay

HG00403

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

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

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.

ISCN-CMLExample

Basic example for karyotype Variant expressed in ISCN

ISCN-CMLImplication

Basic example of a Diagnostic Implication for CML

ISCN-NormalExample

Normal example for karyotype Variant expressed in ISCN

MSH2-del-disease

Example DiagnosticImplication - MSH2 deletion Hereditary cancer-predisposing syndrome

MSH2-del-molc

Example Molecular Consequence MSH2 frameshift

MSH2-del-var

Example for MSH2 deletion

MSIExample

Example for MSI

MedicationRecommendationExample1

Example of a Medication Recommendation

MedicationStatementWarfarin

MedicationStatement for Warfarin

MicrosatelliteInstabilityExample01

Example for MSI

MultipleRepeatExpansions

Repeat Expansion Variant with multiple motifs

NOTCH1-significance

Example DiagnosticImplication - NOTCH1 uncertain significance

NOTCH1-uncertain-molc

Example Molecular Consequence NOTCH1 missense_variant

NOTCH1-uncertain-var

Example for NOTCH1 uncertain

NTHL1-snv-disease

Example DiagnosticImplication - NTHL1 SNV Hereditary cancer-predisposing syndrome

NTHL1-snv-molc

Example Molecular Consequence NTHL1 SNV variant with nonsense codon

NTHL1-snv-var

Example for NTHL1 SNV

PDL1Example

Example for PD-L1

PGXGenomicStudy

Example of PGX sequencing panel

PGXGenomicStudyAnalysis

Example of PGX Sequence analysis

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

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

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

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

PolyGenicDiagnosticImpExample

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

ROS1-Fusion

Example Molecular Consequence ROS1 Fusion

ROS1-Fusion-disease

Example DiagnosticImplication - ROS1 disease

ROS1-Fusion-therapuDrug

Example of ROS1 Fusion Therapeutic Implication for drug treatment

ROS1-Fusion-therapuTrial

Example of ROS1 Fusion Therapeutic Implication for Clinical Trial

ROS1-Fusion-var

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

RepeatExpansion

Repeat Expansion Variant

SNVexample

Example Variant

STAG2-insertion-molc

Example Molecular Consequence STAG2 frameshift

STAG2-insertion-significance

Example DiagnosticImplication - STAG2 likely pathogenic

STAG2-insertion-var

Example for STAG2 insertion

SequencePhaseRelationExample1

Example for sequence phase relation.

SequencingProcedure

Very simple producure representing a genomic study’s protocol

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.

TMB-therapuDrug

Example of high TMB Therapeutic Implication for drug treatment

TMBExample

Example for Tumor Mutation Burden

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

TumorMutationBurdenExample01

Example for Tumor Mutation Burden

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

UncallableRegions

Representing a BED file that represents uncallable regions

Variant-Somatic-Clinical-Trial

Example for Somatic Variant and Clinical Trial

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

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

ZFHX3-significance

Example DiagnosticImplication - ZFHX3 uncertain significance

ZFHX3-uncertain-molc

Example Molecular Consequence ZFHX3 missense_variant

ZFHX3-uncertain-var

Example for ZFHX3 uncertain

analysisTumorNormalDNA

Example for Tumor Normal Genomics Study Analysis

analysisTumorRNA

Example for just Tumor RNA Genomic Study Analysis

bundle-CG-IG-HLA-FullBundle-01

Example of a HLA bundle

bundle-CYP2C19

Example bundle containing CYP2C19 report and variants

bundle-cgexample

Example bundle showing a variety of profiles.

bundle-cgexample-withGrouping

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

bundle-complexVariant-nonHGVS

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

bundle-compound-heterozygote

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

bundle-oncology-diagnostic

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

bundle-oncology-report-example

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

bundle-oncologyexamples-r4

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

bundle-oncologyexamples-r4-withGrouping

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

bundle-pgxexample

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

bundle-sequence-phase-relation-CYP2C19

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

denovoChild

Child of a trio

denovoFather

Father of a trio

denovoMother

Mother of a trio

diagnosticImplication-interact-smn1-smn2

Diagnostic Implication for SMN1/SMN2 CNV example

diagnosticreport-hla-glstring-r4

Example GenomicReport including an HLA glstring

eMERGEServiceRequest

Example PGx Service Request

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

genomicPatient

Example patient

genomicServiceRequest

Example of Molecular genetic test

genomicSpecimen

Example of lung specimen obtained by biopsy

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.

genomicstudy-trio2

GenomicStudy example of a trio analysis

genomicstudyanalysis-trio2

GenomicStudy Analysis example of a trio analysis

genotype-hla-a-glstring-r4

Genotype example: Sequence-based typing of HLA-A

haplotype-hla-a-1-r4

Example Haplotype Sequence-based typing of HLA-A

lungMass

Example of solid tumor whole exome sequencing panel

lungMass-analysis1

Example of Sequence analysis of the entire coding region

lungMass-analysis2

Example of Deletion/duplication analysis

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

normalSpecimen

Example for normal specimen

obs-idh-ex

Example DiagnosticImplication - Pathogenic for CF

obs1-interact-smn1-smn2

SMN1 CNV companion for SMN1/SMN2 CNV example

obs2-interact-smn1-smn2

SMN2 CNV companion for SMN1/SMN2 CNV example

orderingPractitioner

Example of an ordering provider

pathologistPractitioner

Example of a pathologist

performingOrganization

Example of a Pathology lab

practitioner02

Example practitioner

servicerequest-hla-a-r4

Example ServiceRequest for genomics

somaticPatient

Somatic example Patient

somaticReport

Example somatic GenomicReport

somaticServiceRequest

Example for Somatic Testing Request

somaticStudy

Example for somatic genetic study

somaticVCFfile

Example for Genomic Data File somaticVCFfile

specimen-hla-r4

Example HLA specimen

supervisorPractitioner

Example of a supervisor

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

triodenovo-software

Triodenovo Software

tumorSpecimen

Example for tumor specimen

variant-with-molec-consequences

Variant with molecular consequences