Copy Change Constraint

Definition and Information Model

Warning

This data class is at a draft maturity level and may change significantly in future releases. Maturity levels are described in the GKS Maturity Model.

Computational Definition

The relative assessment of the change in copies that members of this categorical variant satisfy.

Information Model

Some CopyChangeConstraint attributes are inherited from Constraint.

Field	Flags	Type	Limits	Description
type		string	1..1	MUST be “CopyChangeConstraint”
copyChange		string	1..1	The relative assessment of the change in copies that members of this categorical variant satisfies.

Examples

The following example Categorical Variants utilize this Constraint:

• GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3

• TP53 Loss

A representative example of this Constraint, from GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3:

    {
      "type": "CopyChangeConstraint",
      "copyChange": "gain"
    },

Implementation Guidance

This Constraint is used when constructing a Categorical Copy Number Variant when a copy number variation is classified into a category. If looking to express the copy number variation as an integer or Range, consider instead applying the Copy Count Constraint.

copyChange

The copyChange attribute is required and uses a value set derived from the Experimental Factor Ontology (EFO), with definitions reproduced from EFO. The EFO describes these categories hierarchically; subtypes are indicated by indentation in the table below. Broadly, a copy number amplification or gain should be represented using gain or one of its subtypes, and a copy number deletion or loss should be represented using loss or one of its subtypes. When the source data does not distinguish between subtypes, the parent term (for example, loss) should be preferred over a more specific subtype. Any of the following Name values can be used to populate this attribute:

Name	EFO ID	EFO Definition	EFO Name
gain	EFO:0030070	Assessment of genomic copy number gain.	copy number gain
|indent| high-level gain	EFO:0030072	Assessment of high-level genomic copy number gain.	high-level copy number gain
|indent| low-level gain	EFO:0030071	Assessment of low-level genomic copy number gain.	low-level copy number gain
loss	EFO:0030067	Assessment of genomic copy number loss.	copy number loss
|indent| low-level loss	EFO:0030068	Assessment of low-level genomic copy number loss.	low-level copy number loss
|indent| high-level loss	EFO:0020073	Assessment of high-level genomic copy number loss.	high-level copy number loss
|indent| |indent| complete genomic loss	EFO:0030069	Assessment of complete genomic deletion.	complete genomic deletion
regional base ploidy	EFO:0030064	Copy number assessment of regional base ploidy.	regional base ploidy