Copy Number Change

A copy number change is used to represent the change in copy number of a sequence in a genome.

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

An assessment of the copy number of a Location within a system (e.g. genome, cell, etc.) relative to a baseline ploidy.

GA4GH Digest

Prefix	Inherent
CX	[‘copyChange’, ‘location’, ‘type’]

Information Model

Some CopyNumberChange attributes are inherited from Variation.

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.
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.
digest		string	0..1	A sha512t24u digest created using the VRS Computed Identifier algorithm.
expressions	⋮	Expression	0..m
type		string	1..1	MUST be “CopyNumberChange”
location		iriReference | Location	1..1	The location of the subject of the copy change.
copyChange		string	1..1	MUST use one of the defined enumerations that are based on the corresponding EFO ontological terms for copy number variation. See Implementation Guidance for more details.

Copy Change term definitions

The CopyChange attribute uses a valueset derived from the Experimental Factor Ontology (EFO):

• gain (EFO:0030070 - copy number gain): Assessment of genomic copy number gain.

  • high-level gain (EFO:0030072 - high-level copy number gain): Assessment of high-level genomic copy number gain.

  • low-level gain (EFO:0030071 - low-level copy number gain): Assessment of low-level genomic copy number gain.

• regional base ploidy (EFO:0030064 - regional base ploidy): Copy number assessment of regional base ploidy.

• loss (EFO:0030067 - copy number loss): Assessment of genomic copy number loss.

  • low-level loss (EFO:0030068 - low-level copy number loss): Assessment of low-level genomic copy number loss.

  • high-level loss (EFO:0020073 - high-level copy number loss): Assessment of high-level genomic copy number loss.

    • complete genomic loss (EFO:0030069 - complete genomic deletion: Assessment of complete genomic deletion.

Example

{
  "id": "ga4gh:CX.2_fT_6-IpUm5aS0wp8ZAkJ01MCE569L2",
  "type": "CopyNumberChange",
  "copyChange": "low-level gain",
  "location": {
    "sequenceReference": {
      "refgetAccession": "SQ.jdEWLvLvT8827O59m1Agh5H3n6kTzBsJ",
      "type": "SequenceReference"
    },
    "end": 44909393,
    "start": 44905795,
    "type": "SequenceLocation"
  }
}