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This page is part of the FHIR Specification (v5.0.0: R5 - STU). This is the current published version. For a full list of available versions, see the Directory of published versions ContentExamplesDetailed DescriptionsMappingsOperationsSearch ParamsProfilesExtensionsR4 Conversions 10.4 Resource GenomicStudy - Content Clinical Genomics Work GroupMaturity Level: 0 Trial UseSecurity Category: Patient Compartments: Patient
A GenomicStudy is a set of analyses performed to analyze and generate genomic data. Note to Implementers: The material on this page is currently undergoing work to be refactored in a future release as further analysis is done. Reviewers are encouraged to provide their comments and feedback about the example codes for terminology binding purposes. 10.4.1 Scope and UsageGenomicStudy resource aims at delineating relevant information of a genomic study. A genomic study might comprise one or more analyses, each serving a specific purpose. These analyses may vary in method (e.g., karyotyping, CNV, or SNV detection), performer, software, devices used, or regions targeted. GenomicStudy describes relevant information including the reasons, purpose, and performers of the study. It also provides technical endpoints to access these data. It could be a logical aggregator for complex genomic analyses. A GenomicStudy might be based on one or more service requests or care plans. The reasons for performing a genomic study might be driven by specific Conditions or Observations. Although the genomic study subject is the focus of the study, the analysis-level focus could be used to specify other relevant subjects or specimens. For example, trio testing may involve three subjects: the proband, and both parents. The proband would be the subject listed directly under the genomic study, while each of the analyses could represent proband, mother, and father genomic analyses. In clinical use, the study interpreters use all the results of these various analyses to provide diagnostic and therapeutic insights for the patient. Where performers are listed according to their participation in each genomic analysis. Each analysis may be based on a set of defined protocols that may differ from the performed protocols. The regionStudied and regionCalled elements can refer to DocumentReference instances carrying BED files. Other types of files used in an analysis can be provided similarly, and listed either as inputs or outputs. Detailed information about the results of the analyses may be represented by Observations and gathered in a DiagnosticReport. Both resources may refer back to the originating GenomicStudy to allow navigation. 10.4.2 Boundaries and RelationshipsA main function of GenomicStudy is to provide additional metadata for one or more clinical genomic analysis pipelines where DocumentReference instances are used to track inputs and outputs of those pipelines. Device is used to represent both hardware and software used in the sequencing and in the analyses. It is intended that this resource be referenced by Observation and DiagnosticReport in the same way that ImagingStudy is currently referenced on those resources. Of note, the results of the study would be captured in Observations and referenced on a DiagnosticReport. Important contextual references include Patient, Specimen, Encounter, ServiceRequest, Practitioner, and Organization. Observation or Condition instances may also be referenced from genomic study to designate a given reason for performing the study. GenomicStudy can support the event-definition workflow pattern by referencing PlanDefinition via the instantiatesCanonical relationship when implementers wish to describe more specifics of the pipelines and devices used in the analysis. 10.4.3 References to this Resource Implements: EventResource References: DiagnosticReport, itself and Observation 10.4.4 Resource Content Structure UML XML JSON Turtle R4 Diff AllStructure NameFlagsCard.TypeDescription & Constraints GenomicStudy TUDomainResourceGenomic StudyElements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension identifier Σ0..*IdentifierIdentifiers for this genomic study status ?!Σ1..1coderegistered | available | cancelled | entered-in-error | unknownBinding: Genomic Study Status (Required) type Σ0..*CodeableConceptThe type of the study (e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling)Binding: Genomic Study Type (Example) subject Σ1..1Reference(Patient | Group | Substance | BiologicallyDerivedProduct | NutritionProduct)The primary subject of the genomic study encounter Σ0..1Reference(Encounter)The healthcare event with which this genomics study is associated startDate 0..1dateTimeWhen the genomic study was started basedOn 0..*Reference(ServiceRequest | Task)Event resources that the genomic study is based on referrer 0..1Reference(Practitioner | PractitionerRole)Healthcare professional who requested or referred the genomic study interpreter 0..*Reference(Practitioner | PractitionerRole)Healthcare professionals who interpreted the genomic study reason 0..*CodeableReference(Condition | Observation)Why the genomic study was performed instantiatesCanonical 0..1canonical(PlanDefinition)The defined protocol that describes the study instantiatesUri 0..1uriThe URL pointing to an externally maintained protocol that describes the study note 0..*AnnotationComments related to the genomic study description 0..1markdownDescription of the genomic study analysis 0..*BackboneElementGenomic Analysis Event identifier Σ0..*IdentifierIdentifiers for the analysis event methodType Σ0..*CodeableConceptType of the methods used in the analysis (e.g., FISH, Karyotyping, MSI)Binding: Genomic Study Method Type (Example) changeType 0..*CodeableConceptType of the genomic changes studied in the analysis (e.g., DNA, RNA, or AA change)Binding: Genomic Study Change Type (Example) genomeBuild 0..1CodeableConceptGenome build that is used in this analysisBinding: HumanRefSeqNCBIBuildId (Extensible) instantiatesCanonical 0..1canonical(PlanDefinition | ActivityDefinition)The defined protocol that describes the analysis instantiatesUri 0..1uriThe URL pointing to an externally maintained protocol that describes the analysis title Σ0..1stringName of the analysis event (human friendly) focus Σ0..*Reference(Any)What the genomic analysis is about, when it is not about the subject of record specimen Σ0..*Reference(Specimen)The specimen used in the analysis event date 0..1dateTimeThe date of the analysis event note 0..*AnnotationAny notes capture with the analysis event protocolPerformed 0..1Reference(Procedure | Task)The protocol that was performed for the analysis event regionsStudied 0..*Reference(DocumentReference | Observation)The genomic regions to be studied in the analysis (BED file) regionsCalled 0..*Reference(DocumentReference | Observation)Genomic regions actually called in the analysis event (BED file) input 0..*BackboneElementInputs for the analysis event file Σ0..1Reference(DocumentReference)File containing input data type 0..1CodeableConceptType of input data (e.g., BAM, CRAM, or FASTA)Binding: Genomic Study Data Format (Example) generatedBy[x] 0..1The analysis event or other GenomicStudy that generated this input file generatedByIdentifierIdentifier generatedByReferenceReference(GenomicStudy) output 0..*BackboneElementOutputs for the analysis event file Σ0..1Reference(DocumentReference)File containing output data type Σ0..1CodeableConceptType of output data (e.g., VCF, MAF, or BAM)Binding: Genomic Study Data Format (Example) performer 0..*BackboneElementPerformer for the analysis event actor 0..1Reference(Practitioner | PractitionerRole | Organization | Device)The organization, healthcare professional, or others who participated in performing this analysis role 0..1CodeableConceptRole of the actor for this analysis device 0..*BackboneElementDevices used for the analysis (e.g., instruments, software), with settings and parameters device 0..1Reference(Device)Device used for the analysis function 0..1CodeableConceptSpecific function for the device used for the analysis Documentation for this formatSee the Extensions for this resource UML Diagram (Legend) GenomicStudy (DomainResource)Identifiers for this genomic studyidentifier : Identifier [0..*]The status of the genomic study (this element modifies the meaning of other elements)status : code [1..1] « null (Strength=Required)GenomicStudyStatus! »The type of the study, e.g., Familial variant segregation, Functional variation detection, or Gene expression profilingtype : CodeableConcept [0..*] « null (Strength=Example)GenomicStudyType?? »The primary subject of the genomic studysubject : Reference [1..1] « Patient|Group|Substance| BiologicallyDerivedProduct|NutritionProduct »The healthcare event with which this genomics study is associatedencounter : Reference [0..1] « Encounter »When the genomic study was startedstartDate : dateTime [0..1]Event resources that the genomic study is based onbasedOn : Reference [0..*] « ServiceRequest|Task »Healthcare professional who requested or referred the genomic studyreferrer : Reference [0..1] « Practitioner|PractitionerRole »Healthcare professionals who interpreted the genomic studyinterpreter : Reference [0..*] « Practitioner|PractitionerRole »Why the genomic study was performedreason : CodeableReference [0..*] « Condition|Observation »The defined protocol that describes the studyinstantiatesCanonical : canonical [0..1] « PlanDefinition »The URL pointing to an externally maintained protocol that describes the studyinstantiatesUri : uri [0..1]Comments related to the genomic studynote : Annotation [0..*]Description of the genomic studydescription : markdown [0..1]AnalysisIdentifiers for the analysis eventidentifier : Identifier [0..*]Type of the methods used in the analysis, e.g., Fluorescence in situ hybridization (FISH), Karyotyping, or Microsatellite instability testing (MSI)methodType : CodeableConcept [0..*] « null (Strength=Example)GenomicStudyMethodType?? »Type of the genomic changes studied in the analysis, e.g., DNA, RNA, or amino acid changechangeType : CodeableConcept [0..*] « null (Strength=Example)GenomicStudyChangeType?? »The reference genome build that is used in this analysisgenomeBuild : CodeableConcept [0..1] « null (Strength=Extensible)HumanRefSeqNCBIBuildId+ »The defined protocol that describes the analysisinstantiatesCanonical : canonical [0..1] « PlanDefinition| ActivityDefinition »The URL pointing to an externally maintained protocol that describes the analysisinstantiatesUri : uri [0..1]Name of the analysis event (human friendly)title : string [0..1]The focus of a genomic analysis when it is not the patient of record representing something or someone associated with the patient such as a spouse, parent, child, or sibling. For example, in trio testing, the GenomicStudy.subject would be the child (proband) and the GenomicStudy.analysis.focus of a specific analysis would be the parentfocus : Reference [0..*] « Any »The specimen used in the analysis eventspecimen : Reference [0..*] « Specimen »The date of the analysis eventdate : dateTime [0..1]Any notes capture with the analysis eventnote : Annotation [0..*]The protocol that was performed for the analysis eventprotocolPerformed : Reference [0..1] « Procedure|Task »The genomic regions to be studied in the analysis (BED file)regionsStudied : Reference [0..*] « DocumentReference|Observation »Genomic regions actually called in the analysis event (BED file)regionsCalled : Reference [0..*] « DocumentReference|Observation »InputFile containing input datafile : Reference [0..1] « DocumentReference »Type of input data, e.g., BAM, CRAM, or FASTAtype : CodeableConcept [0..1] « null (Strength=Example)GenomicStudyDataFormat?? »The analysis event or other GenomicStudy that generated this input filegeneratedBy[x] : DataType [0..1] « Identifier|Reference(GenomicStudy) »OutputFile containing output datafile : Reference [0..1] « DocumentReference »Type of output data, e.g., VCF, MAF, or BAMtype : CodeableConcept [0..1] « null (Strength=Example)GenomicStudyDataFormat?? »PerformerThe organization, healthcare professional, or others who participated in performing this analysisactor : Reference [0..1] « Practitioner|PractitionerRole| Organization|Device »Role of the actor for this analysisrole : CodeableConcept [0..1]DeviceDevice used for the analysisdevice : Reference [0..1] « Device »Specific function for the device used for the analysisfunction : CodeableConcept [0..1]Inputs for the analysis eventinput[0..*]Outputs for the analysis eventoutput[0..*]Performer for the analysis eventperformer[0..*]Devices used for the analysis (e.g., instruments, software), with settings and parametersdevice[0..*]The details about a specific analysis that was performed in this GenomicStudyanalysis[0..*]XML Template JSON Template { "resourceType" : "GenomicStudy", // from Resource: id, meta, implicitRules, and language // from DomainResource: text, contained, extension, and modifierExtension "identifier" : [{ Identifier }], // Identifiers for this genomic study "status" : "", // R! registered | available | cancelled | entered-in-error | unknown "type" : [{ CodeableConcept }], // The type of the study (e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling) "subject" : { Reference(BiologicallyDerivedProduct|Group|NutritionProduct| Patient|Substance) }, // R! The primary subject of the genomic study "encounter" : { Reference(Encounter) }, // The healthcare event with which this genomics study is associated "startDate" : "", // When the genomic study was started "basedOn" : [{ Reference(ServiceRequest|Task) }], // Event resources that the genomic study is based on "referrer" : { Reference(Practitioner|PractitionerRole) }, // Healthcare professional who requested or referred the genomic study "interpreter" : [{ Reference(Practitioner|PractitionerRole) }], // Healthcare professionals who interpreted the genomic study "reason" : [{ CodeableReference(Condition|Observation) }], // Why the genomic study was performed "instantiatesCanonical" : "", // The defined protocol that describes the study "instantiatesUri" : "", // The URL pointing to an externally maintained protocol that describes the study "note" : [{ Annotation }], // Comments related to the genomic study "description" : "", // Description of the genomic study "analysis" : [{ // Genomic Analysis Event "identifier" : [{ Identifier }], // Identifiers for the analysis event "methodType" : [{ CodeableConcept }], // Type of the methods used in the analysis (e.g., FISH, Karyotyping, MSI) "changeType" : [{ CodeableConcept }], // Type of the genomic changes studied in the analysis (e.g., DNA, RNA, or AA change) "genomeBuild" : { CodeableConcept }, // Genome build that is used in this analysis "instantiatesCanonical" : "", // The defined protocol that describes the analysis "instantiatesUri" : "", // The URL pointing to an externally maintained protocol that describes the analysis "title" : "", // Name of the analysis event (human friendly) "focus" : [{ Reference(Any) }], // What the genomic analysis is about, when it is not about the subject of record "specimen" : [{ Reference(Specimen) }], // The specimen used in the analysis event "date" : "", // The date of the analysis event "note" : [{ Annotation }], // Any notes capture with the analysis event "protocolPerformed" : { Reference(Procedure|Task) }, // The protocol that was performed for the analysis event "regionsStudied" : [{ Reference(DocumentReference|Observation) }], // The genomic regions to be studied in the analysis (BED file) "regionsCalled" : [{ Reference(DocumentReference|Observation) }], // Genomic regions actually called in the analysis event (BED file) "input" : [{ // Inputs for the analysis event "file" : { Reference(DocumentReference) }, // File containing input data "type" : { CodeableConcept }, // Type of input data (e.g., BAM, CRAM, or FASTA) // generatedBy[x]: The analysis event or other GenomicStudy that generated this input file. One of these 2: "generatedByIdentifier" : { Identifier }, "generatedByReference" : { Reference(GenomicStudy) } }], "output" : [{ // Outputs for the analysis event "file" : { Reference(DocumentReference) }, // File containing output data "type" : { CodeableConcept } // Type of output data (e.g., VCF, MAF, or BAM) }], "performer" : [{ // Performer for the analysis event "actor" : { Reference(Device|Organization|Practitioner|PractitionerRole) }, // The organization, healthcare professional, or others who participated in performing this analysis "role" : { CodeableConcept } // Role of the actor for this analysis }], "device" : [{ // Devices used for the analysis (e.g., instruments, software), with settings and parameters "device" : { Reference(Device) }, // Device used for the analysis "function" : { CodeableConcept } // Specific function for the device used for the analysis }] }] }Turtle Template @prefix fhir: . [ a fhir:GenomicStudy; fhir:nodeRole fhir:treeRoot; # if this is the parser root # from Resource: .id, .meta, .implicitRules, and .language # from DomainResource: .text, .contained, .extension, and .modifierExtension fhir:identifier ( [ Identifier ] ... ) ; # 0..* Identifiers for this genomic study fhir:status [ code ] ; # 1..1 registered | available | cancelled | entered-in-error | unknown fhir:type ( [ CodeableConcept ] ... ) ; # 0..* The type of the study (e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling) fhir:subject [ Reference(BiologicallyDerivedProduct|Group|NutritionProduct|Patient|Substance) ] ; # 1..1 The primary subject of the genomic study fhir:encounter [ Reference(Encounter) ] ; # 0..1 The healthcare event with which this genomics study is associated fhir:startDate [ dateTime ] ; # 0..1 When the genomic study was started fhir:basedOn ( [ Reference(ServiceRequest|Task) ] ... ) ; # 0..* Event resources that the genomic study is based on fhir:referrer [ Reference(Practitioner|PractitionerRole) ] ; # 0..1 Healthcare professional who requested or referred the genomic study fhir:interpreter ( [ Reference(Practitioner|PractitionerRole) ] ... ) ; # 0..* Healthcare professionals who interpreted the genomic study fhir:reason ( [ CodeableReference(Condition|Observation) ] ... ) ; # 0..* Why the genomic study was performed fhir:instantiatesCanonical [ canonical(PlanDefinition) ] ; # 0..1 The defined protocol that describes the study fhir:instantiatesUri [ uri ] ; # 0..1 The URL pointing to an externally maintained protocol that describes the study fhir:note ( [ Annotation ] ... ) ; # 0..* Comments related to the genomic study fhir:description [ markdown ] ; # 0..1 Description of the genomic study fhir:analysis ( [ # 0..* Genomic Analysis Event fhir:identifier ( [ Identifier ] ... ) ; # 0..* Identifiers for the analysis event fhir:methodType ( [ CodeableConcept ] ... ) ; # 0..* Type of the methods used in the analysis (e.g., FISH, Karyotyping, MSI) fhir:changeType ( [ CodeableConcept ] ... ) ; # 0..* Type of the genomic changes studied in the analysis (e.g., DNA, RNA, or AA change) fhir:genomeBuild [ CodeableConcept ] ; # 0..1 Genome build that is used in this analysis fhir:instantiatesCanonical [ canonical(ActivityDefinition|PlanDefinition) ] ; # 0..1 The defined protocol that describes the analysis fhir:instantiatesUri [ uri ] ; # 0..1 The URL pointing to an externally maintained protocol that describes the analysis fhir:title [ string ] ; # 0..1 Name of the analysis event (human friendly) fhir:focus ( [ Reference(Any) ] ... ) ; # 0..* What the genomic analysis is about, when it is not about the subject of record fhir:specimen ( [ Reference(Specimen) ] ... ) ; # 0..* The specimen used in the analysis event fhir:date [ dateTime ] ; # 0..1 The date of the analysis event fhir:note ( [ Annotation ] ... ) ; # 0..* Any notes capture with the analysis event fhir:protocolPerformed [ Reference(Procedure|Task) ] ; # 0..1 The protocol that was performed for the analysis event fhir:regionsStudied ( [ Reference(DocumentReference|Observation) ] ... ) ; # 0..* The genomic regions to be studied in the analysis (BED file) fhir:regionsCalled ( [ Reference(DocumentReference|Observation) ] ... ) ; # 0..* Genomic regions actually called in the analysis event (BED file) fhir:input ( [ # 0..* Inputs for the analysis event fhir:file [ Reference(DocumentReference) ] ; # 0..1 File containing input data fhir:type [ CodeableConcept ] ; # 0..1 Type of input data (e.g., BAM, CRAM, or FASTA) # generatedBy[x] : 0..1 The analysis event or other GenomicStudy that generated this input file. One of these 2 fhir:generatedBy [ a fhir:Identifier ; Identifier ] fhir:generatedBy [ a fhir:Reference ; Reference(GenomicStudy) ] ] ... ) ; fhir:output ( [ # 0..* Outputs for the analysis event fhir:file [ Reference(DocumentReference) ] ; # 0..1 File containing output data fhir:type [ CodeableConcept ] ; # 0..1 Type of output data (e.g., VCF, MAF, or BAM) ] ... ) ; fhir:performer ( [ # 0..* Performer for the analysis event fhir:actor [ Reference(Device|Organization|Practitioner|PractitionerRole) ] ; # 0..1 The organization, healthcare professional, or others who participated in performing this analysis fhir:role [ CodeableConcept ] ; # 0..1 Role of the actor for this analysis ] ... ) ; fhir:device ( [ # 0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters fhir:device [ Reference(Device) ] ; # 0..1 Device used for the analysis fhir:function [ CodeableConcept ] ; # 0..1 Specific function for the device used for the analysis ] ... ) ; ] ... ) ; ]Changes from both R4 and R4B This resource did not exist in Release R4 See the Full Difference for further information This analysis is available for R4 as XML or JSON and for R4B as XML or JSON. Structure NameFlagsCard.TypeDescription & Constraints GenomicStudy TUDomainResourceGenomic StudyElements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension identifier Σ0..*IdentifierIdentifiers for this genomic study status ?!Σ1..1coderegistered | available | cancelled | entered-in-error | unknownBinding: Genomic Study Status (Required) type Σ0..*CodeableConceptThe type of the study (e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling)Binding: Genomic Study Type (Example) subject Σ1..1Reference(Patient | Group | Substance | BiologicallyDerivedProduct | NutritionProduct)The primary subject of the genomic study encounter Σ0..1Reference(Encounter)The healthcare event with which this genomics study is associated startDate 0..1dateTimeWhen the genomic study was started basedOn 0..*Reference(ServiceRequest | Task)Event resources that the genomic study is based on referrer 0..1Reference(Practitioner | PractitionerRole)Healthcare professional who requested or referred the genomic study interpreter 0..*Reference(Practitioner | PractitionerRole)Healthcare professionals who interpreted the genomic study reason 0..*CodeableReference(Condition | Observation)Why the genomic study was performed instantiatesCanonical 0..1canonical(PlanDefinition)The defined protocol that describes the study instantiatesUri 0..1uriThe URL pointing to an externally maintained protocol that describes the study note 0..*AnnotationComments related to the genomic study description 0..1markdownDescription of the genomic study analysis 0..*BackboneElementGenomic Analysis Event identifier Σ0..*IdentifierIdentifiers for the analysis event methodType Σ0..*CodeableConceptType of the methods used in the analysis (e.g., FISH, Karyotyping, MSI)Binding: Genomic Study Method Type (Example) changeType 0..*CodeableConceptType of the genomic changes studied in the analysis (e.g., DNA, RNA, or AA change)Binding: Genomic Study Change Type (Example) genomeBuild 0..1CodeableConceptGenome build that is used in this analysisBinding: HumanRefSeqNCBIBuildId (Extensible) instantiatesCanonical 0..1canonical(PlanDefinition | ActivityDefinition)The defined protocol that describes the analysis instantiatesUri 0..1uriThe URL pointing to an externally maintained protocol that describes the analysis title Σ0..1stringName of the analysis event (human friendly) focus Σ0..*Reference(Any)What the genomic analysis is about, when it is not about the subject of record specimen Σ0..*Reference(Specimen)The specimen used in the analysis event date 0..1dateTimeThe date of the analysis event note 0..*AnnotationAny notes capture with the analysis event protocolPerformed 0..1Reference(Procedure | Task)The protocol that was performed for the analysis event regionsStudied 0..*Reference(DocumentReference | Observation)The genomic regions to be studied in the analysis (BED file) regionsCalled 0..*Reference(DocumentReference | Observation)Genomic regions actually called in the analysis event (BED file) input 0..*BackboneElementInputs for the analysis event file Σ0..1Reference(DocumentReference)File containing input data type 0..1CodeableConceptType of input data (e.g., BAM, CRAM, or FASTA)Binding: Genomic Study Data Format (Example) generatedBy[x] 0..1The analysis event or other GenomicStudy that generated this input file generatedByIdentifierIdentifier generatedByReferenceReference(GenomicStudy) output 0..*BackboneElementOutputs for the analysis event file Σ0..1Reference(DocumentReference)File containing output data type Σ0..1CodeableConceptType of output data (e.g., VCF, MAF, or BAM)Binding: Genomic Study Data Format (Example) performer 0..*BackboneElementPerformer for the analysis event actor 0..1Reference(Practitioner | PractitionerRole | Organization | Device)The organization, healthcare professional, or others who participated in performing this analysis role 0..1CodeableConceptRole of the actor for this analysis device 0..*BackboneElementDevices used for the analysis (e.g., instruments, software), with settings and parameters device 0..1Reference(Device)Device used for the analysis function 0..1CodeableConceptSpecific function for the device used for the analysis Documentation for this formatSee the Extensions for this resource UML Diagram (Legend) GenomicStudy (DomainResource)Identifiers for this genomic studyidentifier : Identifier [0..*]The status of the genomic study (this element modifies the meaning of other elements)status : code [1..1] « null (Strength=Required)GenomicStudyStatus! »The type of the study, e.g., Familial variant segregation, Functional variation detection, or Gene expression profilingtype : CodeableConcept [0..*] « null (Strength=Example)GenomicStudyType?? »The primary subject of the genomic studysubject : Reference [1..1] « Patient|Group|Substance| BiologicallyDerivedProduct|NutritionProduct »The healthcare event with which this genomics study is associatedencounter : Reference [0..1] « Encounter »When the genomic study was startedstartDate : dateTime [0..1]Event resources that the genomic study is based onbasedOn : Reference [0..*] « ServiceRequest|Task »Healthcare professional who requested or referred the genomic studyreferrer : Reference [0..1] « Practitioner|PractitionerRole »Healthcare professionals who interpreted the genomic studyinterpreter : Reference [0..*] « Practitioner|PractitionerRole »Why the genomic study was performedreason : CodeableReference [0..*] « Condition|Observation »The defined protocol that describes the studyinstantiatesCanonical : canonical [0..1] « PlanDefinition »The URL pointing to an externally maintained protocol that describes the studyinstantiatesUri : uri [0..1]Comments related to the genomic studynote : Annotation [0..*]Description of the genomic studydescription : markdown [0..1]AnalysisIdentifiers for the analysis eventidentifier : Identifier [0..*]Type of the methods used in the analysis, e.g., Fluorescence in situ hybridization (FISH), Karyotyping, or Microsatellite instability testing (MSI)methodType : CodeableConcept [0..*] « null (Strength=Example)GenomicStudyMethodType?? »Type of the genomic changes studied in the analysis, e.g., DNA, RNA, or amino acid changechangeType : CodeableConcept [0..*] « null (Strength=Example)GenomicStudyChangeType?? »The reference genome build that is used in this analysisgenomeBuild : CodeableConcept [0..1] « null (Strength=Extensible)HumanRefSeqNCBIBuildId+ »The defined protocol that describes the analysisinstantiatesCanonical : canonical [0..1] « PlanDefinition| ActivityDefinition »The URL pointing to an externally maintained protocol that describes the analysisinstantiatesUri : uri [0..1]Name of the analysis event (human friendly)title : string [0..1]The focus of a genomic analysis when it is not the patient of record representing something or someone associated with the patient such as a spouse, parent, child, or sibling. For example, in trio testing, the GenomicStudy.subject would be the child (proband) and the GenomicStudy.analysis.focus of a specific analysis would be the parentfocus : Reference [0..*] « Any »The specimen used in the analysis eventspecimen : Reference [0..*] « Specimen »The date of the analysis eventdate : dateTime [0..1]Any notes capture with the analysis eventnote : Annotation [0..*]The protocol that was performed for the analysis eventprotocolPerformed : Reference [0..1] « Procedure|Task »The genomic regions to be studied in the analysis (BED file)regionsStudied : Reference [0..*] « DocumentReference|Observation »Genomic regions actually called in the analysis event (BED file)regionsCalled : Reference [0..*] « DocumentReference|Observation »InputFile containing input datafile : Reference [0..1] « DocumentReference »Type of input data, e.g., BAM, CRAM, or FASTAtype : CodeableConcept [0..1] « null (Strength=Example)GenomicStudyDataFormat?? »The analysis event or other GenomicStudy that generated this input filegeneratedBy[x] : DataType [0..1] « Identifier|Reference(GenomicStudy) »OutputFile containing output datafile : Reference [0..1] « DocumentReference »Type of output data, e.g., VCF, MAF, or BAMtype : CodeableConcept [0..1] « null (Strength=Example)GenomicStudyDataFormat?? »PerformerThe organization, healthcare professional, or others who participated in performing this analysisactor : Reference [0..1] « Practitioner|PractitionerRole| Organization|Device »Role of the actor for this analysisrole : CodeableConcept [0..1]DeviceDevice used for the analysisdevice : Reference [0..1] « Device »Specific function for the device used for the analysisfunction : CodeableConcept [0..1]Inputs for the analysis eventinput[0..*]Outputs for the analysis eventoutput[0..*]Performer for the analysis eventperformer[0..*]Devices used for the analysis (e.g., instruments, software), with settings and parametersdevice[0..*]The details about a specific analysis that was performed in this GenomicStudyanalysis[0..*]XML Template JSON Template { "resourceType" : "GenomicStudy", // from Resource: id, meta, implicitRules, and language // from DomainResource: text, contained, extension, and modifierExtension "identifier" : [{ Identifier }], // Identifiers for this genomic study "status" : "", // R! registered | available | cancelled | entered-in-error | unknown "type" : [{ CodeableConcept }], // The type of the study (e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling) "subject" : { Reference(BiologicallyDerivedProduct|Group|NutritionProduct| Patient|Substance) }, // R! The primary subject of the genomic study "encounter" : { Reference(Encounter) }, // The healthcare event with which this genomics study is associated "startDate" : "", // When the genomic study was started "basedOn" : [{ Reference(ServiceRequest|Task) }], // Event resources that the genomic study is based on "referrer" : { Reference(Practitioner|PractitionerRole) }, // Healthcare professional who requested or referred the genomic study "interpreter" : [{ Reference(Practitioner|PractitionerRole) }], // Healthcare professionals who interpreted the genomic study "reason" : [{ CodeableReference(Condition|Observation) }], // Why the genomic study was performed "instantiatesCanonical" : "", // The defined protocol that describes the study "instantiatesUri" : "", // The URL pointing to an externally maintained protocol that describes the study "note" : [{ Annotation }], // Comments related to the genomic study "description" : "", // Description of the genomic study "analysis" : [{ // Genomic Analysis Event "identifier" : [{ Identifier }], // Identifiers for the analysis event "methodType" : [{ CodeableConcept }], // Type of the methods used in the analysis (e.g., FISH, Karyotyping, MSI) "changeType" : [{ CodeableConcept }], // Type of the genomic changes studied in the analysis (e.g., DNA, RNA, or AA change) "genomeBuild" : { CodeableConcept }, // Genome build that is used in this analysis "instantiatesCanonical" : "", // The defined protocol that describes the analysis "instantiatesUri" : "", // The URL pointing to an externally maintained protocol that describes the analysis "title" : "", // Name of the analysis event (human friendly) "focus" : [{ Reference(Any) }], // What the genomic analysis is about, when it is not about the subject of record "specimen" : [{ Reference(Specimen) }], // The specimen used in the analysis event "date" : "", // The date of the analysis event "note" : [{ Annotation }], // Any notes capture with the analysis event "protocolPerformed" : { Reference(Procedure|Task) }, // The protocol that was performed for the analysis event "regionsStudied" : [{ Reference(DocumentReference|Observation) }], // The genomic regions to be studied in the analysis (BED file) "regionsCalled" : [{ Reference(DocumentReference|Observation) }], // Genomic regions actually called in the analysis event (BED file) "input" : [{ // Inputs for the analysis event "file" : { Reference(DocumentReference) }, // File containing input data "type" : { CodeableConcept }, // Type of input data (e.g., BAM, CRAM, or FASTA) // generatedBy[x]: The analysis event or other GenomicStudy that generated this input file. One of these 2: "generatedByIdentifier" : { Identifier }, "generatedByReference" : { Reference(GenomicStudy) } }], "output" : [{ // Outputs for the analysis event "file" : { Reference(DocumentReference) }, // File containing output data "type" : { CodeableConcept } // Type of output data (e.g., VCF, MAF, or BAM) }], "performer" : [{ // Performer for the analysis event "actor" : { Reference(Device|Organization|Practitioner|PractitionerRole) }, // The organization, healthcare professional, or others who participated in performing this analysis "role" : { CodeableConcept } // Role of the actor for this analysis }], "device" : [{ // Devices used for the analysis (e.g., instruments, software), with settings and parameters "device" : { Reference(Device) }, // Device used for the analysis "function" : { CodeableConcept } // Specific function for the device used for the analysis }] }] }Turtle Template @prefix fhir: . [ a fhir:GenomicStudy; fhir:nodeRole fhir:treeRoot; # if this is the parser root # from Resource: .id, .meta, .implicitRules, and .language # from DomainResource: .text, .contained, .extension, and .modifierExtension fhir:identifier ( [ Identifier ] ... ) ; # 0..* Identifiers for this genomic study fhir:status [ code ] ; # 1..1 registered | available | cancelled | entered-in-error | unknown fhir:type ( [ CodeableConcept ] ... ) ; # 0..* The type of the study (e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling) fhir:subject [ Reference(BiologicallyDerivedProduct|Group|NutritionProduct|Patient|Substance) ] ; # 1..1 The primary subject of the genomic study fhir:encounter [ Reference(Encounter) ] ; # 0..1 The healthcare event with which this genomics study is associated fhir:startDate [ dateTime ] ; # 0..1 When the genomic study was started fhir:basedOn ( [ Reference(ServiceRequest|Task) ] ... ) ; # 0..* Event resources that the genomic study is based on fhir:referrer [ Reference(Practitioner|PractitionerRole) ] ; # 0..1 Healthcare professional who requested or referred the genomic study fhir:interpreter ( [ Reference(Practitioner|PractitionerRole) ] ... ) ; # 0..* Healthcare professionals who interpreted the genomic study fhir:reason ( [ CodeableReference(Condition|Observation) ] ... ) ; # 0..* Why the genomic study was performed fhir:instantiatesCanonical [ canonical(PlanDefinition) ] ; # 0..1 The defined protocol that describes the study fhir:instantiatesUri [ uri ] ; # 0..1 The URL pointing to an externally maintained protocol that describes the study fhir:note ( [ Annotation ] ... ) ; # 0..* Comments related to the genomic study fhir:description [ markdown ] ; # 0..1 Description of the genomic study fhir:analysis ( [ # 0..* Genomic Analysis Event fhir:identifier ( [ Identifier ] ... ) ; # 0..* Identifiers for the analysis event fhir:methodType ( [ CodeableConcept ] ... ) ; # 0..* Type of the methods used in the analysis (e.g., FISH, Karyotyping, MSI) fhir:changeType ( [ CodeableConcept ] ... ) ; # 0..* Type of the genomic changes studied in the analysis (e.g., DNA, RNA, or AA change) fhir:genomeBuild [ CodeableConcept ] ; # 0..1 Genome build that is used in this analysis fhir:instantiatesCanonical [ canonical(ActivityDefinition|PlanDefinition) ] ; # 0..1 The defined protocol that describes the analysis fhir:instantiatesUri [ uri ] ; # 0..1 The URL pointing to an externally maintained protocol that describes the analysis fhir:title [ string ] ; # 0..1 Name of the analysis event (human friendly) fhir:focus ( [ Reference(Any) ] ... ) ; # 0..* What the genomic analysis is about, when it is not about the subject of record fhir:specimen ( [ Reference(Specimen) ] ... ) ; # 0..* The specimen used in the analysis event fhir:date [ dateTime ] ; # 0..1 The date of the analysis event fhir:note ( [ Annotation ] ... ) ; # 0..* Any notes capture with the analysis event fhir:protocolPerformed [ Reference(Procedure|Task) ] ; # 0..1 The protocol that was performed for the analysis event fhir:regionsStudied ( [ Reference(DocumentReference|Observation) ] ... ) ; # 0..* The genomic regions to be studied in the analysis (BED file) fhir:regionsCalled ( [ Reference(DocumentReference|Observation) ] ... ) ; # 0..* Genomic regions actually called in the analysis event (BED file) fhir:input ( [ # 0..* Inputs for the analysis event fhir:file [ Reference(DocumentReference) ] ; # 0..1 File containing input data fhir:type [ CodeableConcept ] ; # 0..1 Type of input data (e.g., BAM, CRAM, or FASTA) # generatedBy[x] : 0..1 The analysis event or other GenomicStudy that generated this input file. One of these 2 fhir:generatedBy [ a fhir:Identifier ; Identifier ] fhir:generatedBy [ a fhir:Reference ; Reference(GenomicStudy) ] ] ... ) ; fhir:output ( [ # 0..* Outputs for the analysis event fhir:file [ Reference(DocumentReference) ] ; # 0..1 File containing output data fhir:type [ CodeableConcept ] ; # 0..1 Type of output data (e.g., VCF, MAF, or BAM) ] ... ) ; fhir:performer ( [ # 0..* Performer for the analysis event fhir:actor [ Reference(Device|Organization|Practitioner|PractitionerRole) ] ; # 0..1 The organization, healthcare professional, or others who participated in performing this analysis fhir:role [ CodeableConcept ] ; # 0..1 Role of the actor for this analysis ] ... ) ; fhir:device ( [ # 0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters fhir:device [ Reference(Device) ] ; # 0..1 Device used for the analysis fhir:function [ CodeableConcept ] ; # 0..1 Specific function for the device used for the analysis ] ... ) ; ] ... ) ; ]Changes from both R4 and R4B This resource did not exist in Release R4 See the Full Difference for further information This analysis is available for R4 as XML or JSON and for R4B as XML or JSON.
Additional definitions: Master Definition XML + JSON, XML Schema/Schematron + JSON Schema, ShEx (for Turtle) + see the extensions, the spreadsheet version & the dependency analysis 10.4.4.1 Terminology Bindings PathValueSetTypeDocumentation GenomicStudy.status GenomicStudyStatus RequiredThe status of the GenomicStudy. GenomicStudy.type GenomicStudyType ExampleThe type of the GenomicStudy. GenomicStudy.analysis.methodType GenomicStudyMethodType ExampleThe method type of the GenomicStudy analysis. GenomicStudy.analysis.changeType GenomicStudyChangeType ExampleThe change type of the GenomicStudy analysis. GenomicStudy.analysis.genomeBuild http://loinc.org/vs/LL1040-6 Extensible GenomicStudy.analysis.input.type GenomicStudyDataFormat ExampleThe data formats relevant to Genomic Study analysis. GenomicStudy.analysis.output.type GenomicStudyDataFormat ExampleThe data formats relevant to Genomic Study analysis. 10.4.4.2 Example Codes GenomicStudy uses many example codes for terminology binding. Reviewers and implementers are strongly encouraged to provide their comments and feedback about the example codes for terminology binding purposes. The attributes and example bindings are listed below. Links are included to indicate where the example codes were pulled from. 10.4.4.2.1 GenomicStudy.typeThe type example codes were based on discussions by Clinical Genomics Workgroup. 10.4.4.2.2 GenomicStudy.analysis.methodTypeThe methodType example codes were pulled from National Library of Medicine-Genetic Testing Registry (NCBI-GTR) and describe testing methods on various levels: major method category , method category , and primary methodology . 10.4.4.2.3 GenomicStudy.analysis.input.type and GenomicStudy.analysis.output.typeThe input and output type example codes were pulled from Integrative Genomics Viewer Documentation by Broad Institute. 10.4.4.2.4 GenomicStudy.analysis.changeTypeThe changeType example codes were based on discussions by Clinical Genomics Workgroup. 10.4.4.3 Implementation Notes 10.4.4.3.1 Handling markdownThe description is a markdown datatype, and implementers should carefully consider how to appropriately handle this attribute. The characters in markdown formatting can conflict with those commonly used in descriptions of genomic data. In particular, descriptions that contain mentions of "star alleles" (widely used in the pharmacogenomics and HLA domains) could be munged in a way that prevents accurate interpretation. For example, consider this text: This genomic study analyzes CYP2D6*1 and CYP2D6*2If the system producing this data treats this as a simple text string with no special processing, but a receiving system processes this via a markdown rendering engine, the two '*' characters would be processed as markdown formatting characters. This would italicize the text between '*' characters, and not display '*' characters. This could cause an inaccurate interpretation of the study description. There are several ways data producers can ensure content is appropriately rendered by receiving systems without requiring the content to be formatted as markdown prior to sending. Here are three basic approaches to consider: Escaping individual characters (with a \) that act as markdown formatting characters: This genomic study analyzes CYP2D6\*1 and CYP2D6\*2Escape words (with a `) that contain markdown formatting characters: This genomic study analyzes `CYP2D6*1` and `CYP2D6*2`Escape full text blocks (with a ```) that contain markdown formatting characters: ```This genomic study analyzes CYP2D6*1 and CYP2D6*2``` 10.4.4.4 Use CasesThe attributes subject and analysis.focus can reference many resource types besides Patient such as Group, BiologicallyDerivedProduct, or Substance. In addition, it can provide more details about involved genomic files as inputs or outputs. These various options allow the GenomicStudy resource to cover many use cases besides direct patient care, e.g., research studies that involve multiple patients or environmental samples. Through the following subsections, some of these use cases are described. 10.4.4.4.1 Trio studiesTrio studies involve a proband and two more subjects such as proband’s mother and father for a de novo mutation detection study. GenomicStudy would list the proband as subject because it is the main subject of the study. Each of the study participants, i.e., proband, mother, and father, may have their own analysis entry. When an analysis was performed on an entity other than the subject, the analysis.focus attribute would reference that entity. If a analysis entry documented the analysis of all participants of the trio, each participant would be referenced by analysis.focus. The analysis.input lists various files that may be used for each individual analysis, their types, and their generation context. analysis.input.file may link these files to DocumentReference resources to provide details about each individual file. One of the main details is the subject of a file. If a file is linked to a specific patient, the corresponding DocumentReference.subject may reference this Patient Resource. If the file contains data from multiple persons, the corresponding DocumentReference.subject may reference a Group resource that lists these persons, and their relationship to each other if available. 10.4.4.4.2 Somatic mutation detection studiesSomatic mutation studies may use multiple samples from the patient to support mutation detection, e.g., tumor-normal sample pair. analysis may describe conducted analyses per each sample, where analysis.specimen elements may provide details about each individual specimen. In addition analysis.input can list relevant input files, where the DocumentReference referenced by analysis.input.file can list the specific specimen this input file is related to using DocumentReference.subject as a Specimen resource instance. 10.4.4.4.3 EHR access to genomic studies10.4.5 Search Parameters Search parameters for this resource. See also the full list of search parameters for this resource, and check the Extensions registry for search parameters on extensions related to this resource. The common parameters also apply. See Searching for more information about searching in REST, messaging, and services. NameTypeDescriptionExpressionIn Common focusreferenceWhat the genomic study analysis is about, when it is not about the subject of recordGenomicStudy.analysis.focus(Any) identifiertokenIdentifiers for the StudyGenomicStudy.identifier patientreferenceWho the study is aboutGenomicStudy.subject.where(resolve() is Patient)(Group, BiologicallyDerivedProduct, NutritionProduct, Patient, Substance) statustokenThe status of the studyGenomicStudy.status subjectreferenceWho the study is aboutGenomicStudy.subject(Group, BiologicallyDerivedProduct, NutritionProduct, Patient, Substance) |
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