Diagnostics
This
page
is
part
of
the
FHIR
Specification
(v5.0.0:
R5
-
STU
v6.0.0-ballot1:
Release
6
Ballot
(1st
Draft)
(see
Ballot
Notes
).
This
is
the
The
current
published
version
in
it's
permanent
home
(it
will
always
be
available
at
this
URL).
is
5.0.0
.
For
a
full
list
of
available
versions,
see
the
Directory
of
published
versions
|
Clinical
Genomics
Work
Group
|
Maturity Level : 0 | Trial Use | Security 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.
GenomicStudy 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.
A 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.
Structure
| Name | Flags | Card. | Type |
Description
&
Constraints
|
|---|---|---|---|---|
GenomicStudy
|
TU | DomainResource |
Genomic
Study
Elements defined in Ancestors: id , meta , implicitRules , language , text , contained , extension , modifierExtension |
|
identifier
|
Σ | 0..* | Identifier |
Identifiers
for
this
genomic
study
|
status
|
?! Σ | 1..1 | code |
registered
|
available
|
cancelled
|
entered-in-error
|
unknown
Binding: Genomic Study Status ( Required ) |
|
type
|
Σ | 0..* | CodeableConcept |
The
type
of
the
study
(e.g.,
Familial
variant
segregation,
Functional
variation
detection,
or
Gene
expression
profiling)
Binding: Genomic Study Type ( Example ) |
subject
|
Σ | 1..1 | Reference ( Patient | Group | Substance | BiologicallyDerivedProduct | NutritionProduct ) |
The
primary
subject
of
the
genomic
study
|
|
encounter
|
Σ | 0..1 | Reference ( Encounter ) |
The
healthcare
event
with
which
this
genomics
study
is
associated
|
|
startDate
|
0..1 | dateTime |
When
the
genomic
study
was
started
|
|
|
basedOn
|
0..* | Reference ( ServiceRequest | Task ) |
Event
resources
that
the
genomic
study
is
based
on
|
|
|
referrer
|
0..1 | Reference ( 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..1 | canonical ( PlanDefinition ) |
The
defined
protocol
that
describes
the
study
|
|
|
instantiatesUri
|
0..1 | uri |
The
URL
pointing
to
an
externally
maintained
protocol
that
describes
the
study
|
|
|
note
|
0..* | Annotation |
Comments
related
to
the
genomic
study
|
|
|
description
|
0..1 | markdown |
Description
of
the
genomic
study
|
|
analysis
|
0..* | BackboneElement |
Genomic
Analysis
Event
|
|
identifier
|
Σ | 0..* | Identifier |
Identifiers
for
the
analysis
event
|
|
methodType
|
Σ | 0..* | CodeableConcept |
Type
of
the
methods
used
in
the
analysis
(e.g.,
FISH,
Karyotyping,
MSI)
Binding: Genomic Study Method Type ( Example ) |
|
changeType
|
0..* | CodeableConcept |
Type
of
the
genomic
changes
studied
in
the
analysis
(e.g.,
DNA,
RNA,
or
AA
change)
Binding: Genomic Study Change Type ( Example ) |
|
|
genomeBuild
|
0..1 | CodeableConcept |
Genome
build
that
is
used
in
this
analysis
Binding: HumanRefSeqNCBIBuildId
(
Extensible
)
|
|
|
instantiatesCanonical
|
0..1 | canonical ( PlanDefinition | ActivityDefinition ) |
The
defined
protocol
that
describes
the
analysis
|
|
|
instantiatesUri
|
0..1 | uri |
The
URL
pointing
to
an
externally
maintained
protocol
that
describes
the
analysis
|
|
|
title
|
Σ | 0..1 | string |
Name
of
the
analysis
event
(human
friendly)
|
|
focus
|
Σ | 0..* | Reference ( Any ) |
What
the
genomic
analysis
is
about,
when
it
is
not
about
the
subject
of
record
|
|
specimen
|
Σ | 0..* | Reference ( Specimen ) |
The
specimen
used
in
the
analysis
event
|
|
date
|
0..1 | dateTime |
The
date
of
the
analysis
event
|
|
|
note
|
0..* | Annotation |
Any
notes
capture
with
the
analysis
event
|
|
|
protocolPerformed
|
0..1 | Reference ( 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..* | BackboneElement |
Inputs
for
the
analysis
event
|
|
file
|
Σ | 0..1 | Reference ( DocumentReference ) |
File
containing
input
data
|
|
type
|
0..1 | CodeableConcept |
Type
of
input
data
(e.g.,
BAM,
CRAM,
or
FASTA)
Binding: Genomic Study Data Format ( Example ) |
|
generatedBy[x]
|
0..1 |
The
analysis
event
or
other
GenomicStudy
that
generated
this
input
file
|
||
|
generatedByIdentifier
|
Identifier | |||
generatedByReference
|
Reference ( GenomicStudy ) | |||
|
output
|
0..* | BackboneElement |
Outputs
for
the
analysis
event
|
|
|
file
|
Σ | 0..1 | Reference ( DocumentReference ) |
File
containing
output
data
|
|
type
|
Σ | 0..1 | CodeableConcept |
Type
of
output
data
(e.g.,
VCF,
MAF,
or
BAM)
Binding: Genomic Study Data Format ( Example ) |
|
performer
|
0..* | BackboneElement |
Performer
for
the
analysis
event
|
|
|
actor
|
0..1 | Reference ( Practitioner | PractitionerRole | Organization | Device ) |
The
organization,
healthcare
professional,
or
others
who
participated
in
performing
this
analysis
|
|
|
role
|
0..1 | CodeableConcept |
Role
of
the
actor
for
this
analysis
|
|
|
device
|
0..* | BackboneElement |
Devices
used
for
the
analysis
(e.g.,
instruments,
software),
with
settings
and
parameters
|
|
|
device
|
0..1 | Reference ( Device ) |
Device
used
for
the
analysis
|
|
|
function
|
0..1 | CodeableConcept |
Specific
function
for
the
device
used
for
the
analysis
|
|
|
Documentation
for
this
format
|
||||
See the Extensions for this resource
UML Diagram ( Legend )
XML Template
<GenomicStudy xmlns="http://hl7.org/fhir"><!-- from Resource: id, meta, implicitRules, and language --> <!-- from DomainResource: text, contained, extension, and modifierExtension --> <identifier><!-- 0..* Identifier Identifiers for this genomic study --></identifier> <status value="[code]"/><!-- 1..1 registered | available | cancelled | entered-in-error | unknown --> <type><!-- 0..* CodeableConcept The type of the study (e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling) --></type> <subject><!-- 1..1 Reference(BiologicallyDerivedProduct|Group|NutritionProduct| Patient|Substance) The primary subject of the genomic study --></subject> <encounter><!-- 0..1 Reference(Encounter) The healthcare event with which this genomics study is associated --></encounter> <startDate value="[dateTime]"/><!-- 0..1 When the genomic study was started --> <basedOn><!-- 0..* Reference(ServiceRequest|Task) Event resources that the genomic study is based on --></basedOn> <referrer><!-- 0..1 Reference(Practitioner|PractitionerRole) Healthcare professional who requested or referred the genomic study --></referrer> <interpreter><!-- 0..* Reference(Practitioner|PractitionerRole) Healthcare professionals who interpreted the genomic study --></interpreter> <reason><!-- 0..* CodeableReference(Condition|Observation) Why the genomic study was performed --></reason> <instantiatesCanonical><!-- 0..1 canonical(PlanDefinition) The defined protocol that describes the study --></instantiatesCanonical> <instantiatesUri value="[uri]"/><!-- 0..1 The URL pointing to an externally maintained protocol that describes the study --> <note><!-- 0..* Annotation Comments related to the genomic study --></note> <description value="[markdown]"/><!-- 0..1 Description of the genomic study --> <analysis> <!-- 0..* Genomic Analysis Event --> <identifier><!-- 0..* Identifier Identifiers for the analysis event --></identifier> <methodType><!-- 0..* CodeableConcept Type of the methods used in the analysis (e.g., FISH, Karyotyping, MSI) --></methodType> <changeType><!-- 0..* CodeableConcept Type of the genomic changes studied in the analysis (e.g., DNA, RNA, or AA change) --></changeType> <genomeBuild><!-- 0..1 CodeableConcept Genome build that is used in this analysis
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" : "<code>", // 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" : "<dateTime>", // 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" : "<canonical(PlanDefinition)>", // The defined protocol that describes the study
"instantiatesUri" : "<uri>", // The URL pointing to an externally maintained protocol that describes the study
"note" : [{ Annotation }], // Comments related to the genomic study
"description" : "<markdown>", // 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" : "<canonical(PlanDefinition|ActivityDefinition)>", // The defined protocol that describes the analysis
"instantiatesUri" : "<uri>", // The URL pointing to an externally maintained protocol that describes the analysis
"title" : "<string>", // 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" : "<dateTime>", // 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: <http://hl7.org/fhir/> .
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
| Name | Flags | Card. | Type |
Description
&
Constraints
|
|---|---|---|---|---|
|
GenomicStudy
|
TU | DomainResource |
Genomic
Study
Elements defined in Ancestors: id , meta , implicitRules , language , text , contained , extension , modifierExtension |
|
|
identifier
|
Σ | 0..* | Identifier |
Identifiers
for
this
genomic
study
|
|
status
|
?! Σ | 1..1 | code |
registered
|
available
|
cancelled
|
entered-in-error
|
unknown
Binding: Genomic Study Status ( Required ) |
|
type
|
Σ | 0..* | CodeableConcept |
The
type
of
the
study
(e.g.,
Familial
variant
segregation,
Functional
variation
detection,
or
Gene
expression
profiling)
Binding: Genomic Study Type ( Example ) |
|
subject
|
Σ | 1..1 | Reference ( Patient | Group | Substance | BiologicallyDerivedProduct | NutritionProduct ) |
The
primary
subject
of
the
genomic
study
|
|
encounter
|
Σ | 0..1 | Reference ( Encounter ) |
The
healthcare
event
with
which
this
genomics
study
is
associated
|
|
startDate
|
0..1 | dateTime |
When
the
genomic
study
was
started
|
|
|
basedOn
|
0..* | Reference ( ServiceRequest | Task ) |
Event
resources
that
the
genomic
study
is
based
on
|
|
|
referrer
|
0..1 | Reference ( 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..1 | canonical ( PlanDefinition ) |
The
defined
protocol
that
describes
the
study
|
|
|
instantiatesUri
|
0..1 | uri |
The
URL
pointing
to
an
externally
maintained
protocol
that
describes
the
study
|
|
|
note
|
0..* | Annotation |
Comments
related
to
the
genomic
study
|
|
|
description
|
0..1 | markdown |
Description
of
the
genomic
study
|
|
|
analysis
|
0..* | BackboneElement |
Genomic
Analysis
Event
|
|
|
identifier
|
Σ | 0..* | Identifier |
Identifiers
for
the
analysis
event
|
|
methodType
|
Σ | 0..* | CodeableConcept |
Type
of
the
methods
used
in
the
analysis
(e.g.,
FISH,
Karyotyping,
MSI)
Binding: Genomic Study Method Type ( Example ) |
|
changeType
|
0..* | CodeableConcept |
Type
of
the
genomic
changes
studied
in
the
analysis
(e.g.,
DNA,
RNA,
or
AA
change)
Binding: Genomic Study Change Type ( Example ) |
|
|
genomeBuild
|
0..1 | CodeableConcept |
Genome
build
that
is
used
in
this
analysis
Binding: HumanRefSeqNCBIBuildId
(
Extensible
)
|
|
|
instantiatesCanonical
|
0..1 | canonical ( PlanDefinition | ActivityDefinition ) |
The
defined
protocol
that
describes
the
analysis
|
|
|
instantiatesUri
|
0..1 | uri |
The
URL
pointing
to
an
externally
maintained
protocol
that
describes
the
analysis
|
|
|
title
|
Σ | 0..1 | string |
Name
of
the
analysis
event
(human
friendly)
|
|
focus
|
Σ | 0..* | Reference ( Any ) |
What
the
genomic
analysis
is
about,
when
it
is
not
about
the
subject
of
record
|
|
specimen
|
Σ | 0..* | Reference ( Specimen ) |
The
specimen
used
in
the
analysis
event
|
|
date
|
0..1 | dateTime |
The
date
of
the
analysis
event
|
|
|
note
|
0..* | Annotation |
Any
notes
capture
with
the
analysis
event
|
|
|
protocolPerformed
|
0..1 | Reference ( 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..* | BackboneElement |
Inputs
for
the
analysis
event
|
|
|
file
|
Σ | 0..1 | Reference ( DocumentReference ) |
File
containing
input
data
|
|
type
|
0..1 | CodeableConcept |
Type
of
input
data
(e.g.,
BAM,
CRAM,
or
FASTA)
Binding: Genomic Study Data Format ( Example ) |
|
|
generatedBy[x]
|
0..1 |
The
analysis
event
or
other
GenomicStudy
that
generated
this
input
file
|
||
|
generatedByIdentifier
|
Identifier | |||
|
generatedByReference
|
Reference ( GenomicStudy ) | |||
|
output
|
0..* | BackboneElement |
Outputs
for
the
analysis
event
|
|
|
file
|
Σ | 0..1 | Reference ( DocumentReference ) |
File
containing
output
data
|
|
type
|
Σ | 0..1 | CodeableConcept |
Type
of
output
data
(e.g.,
VCF,
MAF,
or
BAM)
Binding: Genomic Study Data Format ( Example ) |
|
performer
|
0..* | BackboneElement |
Performer
for
the
analysis
event
|
|
|
actor
|
0..1 | Reference ( Practitioner | PractitionerRole | Organization | Device ) |
The
organization,
healthcare
professional,
or
others
who
participated
in
performing
this
analysis
|
|
|
role
|
0..1 | CodeableConcept |
Role
of
the
actor
for
this
analysis
|
|
|
device
|
0..* | BackboneElement |
Devices
used
for
the
analysis
(e.g.,
instruments,
software),
with
settings
and
parameters
|
|
|
device
|
0..1 | Reference ( Device ) |
Device
used
for
the
analysis
|
|
|
function
|
0..1 | CodeableConcept |
Specific
function
for
the
device
used
for
the
analysis
|
|
|
Documentation
for
this
format
|
||||
See the Extensions for this resource
XML Template
<GenomicStudy xmlns="http://hl7.org/fhir">
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" : "<code>", // 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" : "<dateTime>", // 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" : "<canonical(PlanDefinition)>", // The defined protocol that describes the study
"instantiatesUri" : "<uri>", // The URL pointing to an externally maintained protocol that describes the study
"note" : [{ Annotation }], // Comments related to the genomic study
"description" : "<markdown>", // 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" : "<canonical(PlanDefinition|ActivityDefinition)>", // The defined protocol that describes the analysis
"instantiatesUri" : "<uri>", // The URL pointing to an externally maintained protocol that describes the analysis
"title" : "<string>", // 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" : "<dateTime>", // 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: <http://hl7.org/fhir/> .
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
| Path | ValueSet | Type | Documentation |
|---|---|---|---|
| GenomicStudy.status | GenomicStudyStatus | Required |
The status of the GenomicStudy. |
| GenomicStudy.type | GenomicStudyType | Example |
The type of the GenomicStudy. |
| GenomicStudy.analysis.methodType | GenomicStudyMethodType | Example |
The method type of the GenomicStudy analysis. |
| GenomicStudy.analysis.changeType | GenomicStudyChangeType | Example |
The change type of the GenomicStudy analysis. |
| GenomicStudy.analysis.genomeBuild |
http://loinc.org/vs/LL1040-6
|
Extensible | |
| GenomicStudy.analysis.input.type | GenomicStudyDataFormat | Example |
The data formats relevant to Genomic Study analysis. |
| GenomicStudy.analysis.output.type | GenomicStudyDataFormat | Example |
The data formats relevant to Genomic Study analysis. |
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.
The
type
example
codes
were
based
on
discussions
by
Clinical
Genomics
Workgroup.
The
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
.
The
input
and
output
type
example
codes
were
pulled
from
Integrative
Genomics
Viewer
Documentation
by
Broad
Institute.
The
changeType
example
codes
were
based
on
discussions
by
Clinical
Genomics
Workgroup.
The
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*2
If 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\*2
Escape 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```
The
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.
Trio
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.
Somatic
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.
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.
| Name | Type | Description | Expression | In Common |
| focus | reference | What the genomic study analysis is about, when it is not about the subject of record |
GenomicStudy.analysis.focus
(Any) |
|
| identifier | token | Identifiers for the Study | GenomicStudy.identifier | |
| patient | reference | Who the study is about |
GenomicStudy.subject.where(resolve()
is
Patient)
( Group , BiologicallyDerivedProduct , NutritionProduct , Patient , Substance ) |
|
| status | token | The status of the study | GenomicStudy.status | |
| subject | reference | Who the study is about |
GenomicStudy.subject
( Group , BiologicallyDerivedProduct , NutritionProduct , Patient , Substance ) |
FHIR
®©
HL7.org
2011+.
FHIR
R5
hl7.fhir.core#5.0.0
R6
hl7.fhir.core#6.0.0-ballot1
generated
on
Sun,
Mar
26,
Mon,
Dec
18,
2023
15:24+1100.
15:17+1100.
Links:
Search
|
Version
History
|
Contents
|
Glossary
|
QA
|
Compare
to
R4
|
Compare
to
R4B
R5
|
|
Propose
a
change