Study Result Profiles

Study Results represent collections of data items about a single variant from a particular study or analysis (e.g. 1-55051215-G-GA (GRCh38) from the gnomAD allele frequency dataset) - along with provenance and other supporting metadata.

Study Result Profiles are defined as concrete subclasses of the Core Study Result class - each tailored to represent data from a particular type of study or analysis.

Below are the Study Result Profiles currently defined as part of the VA-Spec, and available for adoption or extension by implementations.

Cohort Allele Frequency Study Result

Trial Use

May change in future releases. See Maturity Model.

Computational Definition

A StudyResult that reports measures related to the frequency of an Allele in a cohort

Information Model

Some CohortAlleleFrequencyStudyResult attributes are inherited from Study Result.

Field	Flags	Type	Limits	Description
id		string	0..1	The ‘logical’ identifier of the Entity in the system of record, e.g. a UUID. This ‘id’ is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
type		string	1..1	MUST be “CohortAlleleFrequencyStudyResult”.
name		string	0..1	A primary name for the entity.
description		string	0..1	A free-text description of the Entity.
aliases	⋮	string	0..m	Alternative name(s) for the Entity.
extensions	⋮	Extension	0..m	A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
specifiedBy		Method | iriReference	0..1	A specification that describes all or part of the process that led to creation of the Information Entity
contributions	↓	Contribution	0..m	Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.
reportedIn	⋮	Document | iriReference	0..m	A document in which the the Information Entity is reported.
focus		Allele | iriReference	1..1	The Allele for which frequency results are reported.
sourceDataSet		Data Set | iriReference	0..1	The dataset from which the CohortAlleleFrequencyStudyResult was reported.
ancillaryResults	D	object	0..1	An object in which implementers can define custom fields to capture additional results derived from analysis of primary data items captured in standard attributes in the main body of the Study Result. e.g. in a Cohort Allele Frequency Study Result, this maybe a grpMaxFAF95 calculation, or homozygote/heterozygote calls derived from analyzing raw allele count data.
qualityMeasures	D	object	0..1	An object in which implementers can define custom fields to capture metadata about the quality/provenance of the primary data items captured in standard attributes in the main body of the Study Result. e.g. a sequencing coverage metric in a Cohort Allele Frequency Study Result.
focusCount		integer	1..1	The number of occurrences of the focus Allele in the cohort.
locusCount		integer	1..1	The number of occurrences of all alleles at the locus in the cohort.
alleleFrequency		number	1..1	The frequency of the focus Allele in the cohort.
cohort		Study Group | iriReference	1..1	The cohort from which the frequency was derived.
subCohortFrequency	⋮	Cohort Allele Frequency Study Result	0..m	A list of CohortAlleleFrequency objects describing subcohorts of the cohort currently being described. Subcohorts can be further subdivided into more subcohorts. This enables, for example, the description of different ancestry groups and sexes among those ancestry groups.

Inherits: Study Result

Artifacts

• Cohort Allele Frequency Study Result Source Yaml

• Cohort Allele Frequency Study Result Json Schema

Use Cases and Implementations

This Study Result profile was defined to support gnomAD data in an early implementation for the GREGoR consortium. It provides a format to represent and share the diverse types of allele frequency data, quality measures, and derived ancillary results this resource provides. The model may be generalized in the future to support broader use cases, as new requirements and implementers emerge.

Experimental Variant Functional Impact Study Result

Trial Use

May change in future releases. See Maturity Model.

Computational Definition

A StudyResult that reports a functional impact score from a variant functional assay or study.

Information Model

Some ExperimentalVariantFunctionalImpactStudyResult attributes are inherited from Study Result.

Field	Flags	Type	Limits	Description
id		string	0..1	The ‘logical’ identifier of the Entity in the system of record, e.g. a UUID. This ‘id’ is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
type		string	1..1	MUST be “ExperimentalVariantFunctionalImpactStudyResult”.
name		string	0..1	A primary name for the entity.
description		string	0..1	A free-text description of the Entity.
aliases	⋮	string	0..m	Alternative name(s) for the Entity.
extensions	⋮	Extension	0..m	A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
specifiedBy		Method | iriReference	0..1	The assay that was performed to generate the reported functional impact score.
contributions	↓	Contribution	0..m	Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.
reportedIn	⋮	Document | iriReference	0..m	A document in which the the Information Entity is reported.
focus		MolecularVariation | iriReference	1..1	The genetic variant for which a functional impact score is generated.
sourceDataSet		Data Set | iriReference	0..1	The full data set that provided the reported the functional impact score.
ancillaryResults	D	object	0..1	An object in which implementers can define custom fields to capture additional results derived from analysis of primary data items captured in standard attributes in the main body of the Study Result. e.g. in a Cohort Allele Frequency Study Result, this maybe a grpMaxFAF95 calculation, or homozygote/heterozygote calls derived from analyzing raw allele count data.
qualityMeasures	D	object	0..1	An object in which implementers can define custom fields to capture metadata about the quality/provenance of the primary data items captured in standard attributes in the main body of the Study Result. e.g. a sequencing coverage metric in a Cohort Allele Frequency Study Result.
functionalImpactScore		number	0..1	The score of the variant impact measured in the assay or study.

Inherits: Study Result

Artifacts

• Experimental Variant Functional Impact Study Result Source Yaml

• Experimental Variant Functional Impact Study Result Json Schema

Use Cases and Implementations

This Study Result profile was defined to support an early MAVE-DB implementation of the VA-Spec, as a format to represent high-throughput, quantitative multiplex-assay based functional impact data. This is a very unique type of assay and functional impact data, and the model may be generalized in the future to support broader use cases, as new requirements and implementers emerge.

Tumor Variant Frequency Study Result

Draft

May change significantly in future releases. See Maturity Model.

Computational Definition

A Study Result that reports measures related to the frequency of a variant in a particular tumor type.

Information Model

Some TumorVariantFrequencyStudyResult attributes are inherited from Study Result.

Field	Flags	Type	Limits	Description
id		string	0..1	The ‘logical’ identifier of the Entity in the system of record, e.g. a UUID. This ‘id’ is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
type		string	1..1	MUST be “TumorVariantFrequencyStudyResult”.
name		string	0..1	A primary name for the entity.
description		string	0..1	A free-text description of the Entity.
aliases	⋮	string	0..m	Alternative name(s) for the Entity.
extensions	⋮	Extension	0..m	A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
specifiedBy		Method | iriReference	0..1	A specification that describes all or part of the process that led to creation of the Information Entity
contributions	↓	Contribution	0..m	Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.
reportedIn	⋮	Document | iriReference	0..m	A document in which the the Information Entity is reported.
focus		Allele | iriReference | CategoricalVariant	1..1	The variant for which frequency data is reported in the Study Result.
sourceDataSet		Data Set | iriReference	0..1	The dataset from which data in the Tumor Variant Frequency Study Result was taken.
ancillaryResults	D	object	0..1	An object in which implementers can define custom fields to capture additional results derived from analysis of primary data items captured in standard attributes in the main body of the Study Result. e.g. in a Cohort Allele Frequency Study Result, this maybe a grpMaxFAF95 calculation, or homozygote/heterozygote calls derived from analyzing raw allele count data.
qualityMeasures	D	object	0..1	An object in which implementers can define custom fields to capture metadata about the quality/provenance of the primary data items captured in standard attributes in the main body of the Study Result. e.g. a sequencing coverage metric in a Cohort Allele Frequency Study Result.
affectedSampleCount		integer	1..1	The number of tumor samples in the sample group that contain the focus variant.
totalSampleCount		integer	1..1	The total number of tumor samples in the sample group.
affectedFrequency		number	1..1	The frequency of tumor samples that include the focus variant in the sample group.
sampleGroup		Study Group | iriReference	0..1	The set of samples about which the frequency data was generated.
subGroupFrequency	⋮	Tumor Variant Frequency Study Result	0..m	A list of Tumor Variant Frequency Study Result objects describing variant frequency in different subsets of larger sample group described in the root Study Result. Subgroups can be further subdivided into more subgroups. This enables, for example, further breakdown of frequency measures in sample groups with a narrower categorical variant than the root focus variant, or sample groups with a more specific tumor type.

Inherits: Study Result

Artifacts

• Tumor Variant Frequency Study Result Source Yaml

• Tumor Variant Frequency Study Result Json Schema

Use Cases and Implementations

This Study Result profile is intended to represent the frequency of a variant in a tumor sample cohort or subgroup, together with the study context and supporting provenance needed to interpret those measurements. This is designed for use cases such as aggregating somatic variant prevalence across tumor datasets, summarizing biomarker frequencies in disease-specific cohorts, or exchanging tumor variant frequency evidence derived from curated knowledgebases. The model may be generalized in the future to support broader use cases, as new requirements and implementers emerge.

Computational Variant Functional Impact Analysis Result

Draft

May change significantly in future releases. See Maturity Model.

Computational Definition

An AnalysisResult that reports the output of a single in silico tool’s analysis of a variant’s functional impact, including any numeric score(s) and optional categorical interpretation.

Information Model

Some ComputationalVariantFunctionalImpactAnalysisResult attributes are inherited from Study Result.

Field	Flags	Type	Limits	Description
id		string	0..1	The ‘logical’ identifier of the Entity in the system of record, e.g. a UUID. This ‘id’ is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
type		string	1..1	MUST be “ComputationalVariantFunctionalImpactAnalysisResult”.
name		string	0..1	A primary name for the entity.
description		string	0..1	A free-text description of the Entity.
aliases	⋮	string	0..m	Alternative name(s) for the Entity.
extensions	⋮	Extension	0..m	A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
specifiedBy		iriReference | Method	0..1	The in silico method or algorithm that was applied to generate the reported score(s).
contributions	↓	Contribution	0..m	Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of this Information Entity.
reportedIn	⋮	Document | iriReference	0..m	A document in which the the Information Entity is reported.
focus		iriReference | Allele | CategoricalVariant	1..1	The genetic variant for which the in silico analysis was performed.
sourceDataSet		Data Set | iriReference	0..1	The dataset from which the in silico scores were retrieved or derived (e.g., an Ensembl VEP annotation dataset).
ancillaryResults	D	object	0..1	An object in which implementers can define custom fields to capture additional scores or outputs produced by the in silico tool beyond the primary score. For example, CADD reports both a raw score and a Phred-scaled score; the primary score field would hold one, and ancillaryResults would hold the other.
qualityMeasures	D	object	0..1	An object in which implementers can define custom fields to capture metadata about the quality/provenance of the primary data items captured in standard attributes in the main body of the Study Result. e.g. a sequencing coverage metric in a Cohort Allele Frequency Study Result.
transcriptVariationContext		iriReference | Allele	1..1	The transcript in the context of which the in silico analysis was performed.
impactScore		number	1..1	The primary numeric score produced by the in silico tool for this variant.
impactScoreType		iriReference | Mappable Concept	0..1	A descriptor indicating what the score represents (e.g., ‘SIFT impact score’, ‘CADD Phred-scaled impact score’).
categoricalImpact		iriReference | Mappable Concept	0..1	The categorical interpretation derived from the score by the in silico tool (e.g., ‘tolerated’, ‘benign’, ‘pathogenic’).
impactedFeatureType		iriReference | Mappable Concept	0..1	A descriptor indicating the type of feature for which the focus variant has a predicted impact
impactedFeature		iriReference | Mappable Concept	0..1	The specific feature for which the focus variant has a predicted impact

Inherits: Study Result