Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT 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
Contents:
This page provides a list of the FHIR artifacts defined as part of this implementation guide.
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). |
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. |
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. |
These define constraints on FHIR data types for systems conforming to this implementation guide.
Coded Annotation |
Annotation DataType with added CodeableConcept extension element |
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). |
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. |
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. |
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 |
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 |