TP53 Loss

This is the annotated version of TP53 Loss. It is structurally equivalent to that example and includes inline YAML comments throughout the source file explaining the role and rationale of each field. This version is intended for readers learning to work with the Cat-VRS specification.

Source

CIViC variant id 4452: TP53 Loss (annotated)

Recipes that this example satisfies

None

Properties

id: civic.id:4452: Derived from the Variant ID provided by CIViC.
type: CategoricalVariant: This value is required by the specification for all Categorical Variant objects.
name: TP53 Loss: The name of the variant as provided by CIViC.
description: A plain text description of the variant.: This notes that TP53 Copy Number Loss is a categorical copy-number variant resulting from the deletion of one copy of the TP53 gene.
aliases: TP53 Copy Number Loss, P53 Copy Number Loss: Included to clearly specify that this is a copy number event.
extensions: cytogenetic location: The cytogenetic location (17p13) was obtained from HGNC for TP53.
mappings: CIViC (exactMatch and relatedMatch): Mappings to CIViC’s page for TP53 Loss (exactMatch) and the related CIViC molecular profile for TP53 Deletion (relatedMatch) are included.

Constraints

Defining Location Constraint: The defining location is a VRS Sequence Location on chromosome 17 (refseq:NC_000017.11, GRCh38) spanning the genomic region of the TP53 gene (positions 7,668,420 to 7,687,490). The matchCharacteristic is set to is_within, and a liftover relation is included.
Feature Context Constraint: The featureContext is a MappableConcept for TP53, with a primaryCoding linking to HGNC:11998 and a cytogenetic location extension of 17p13.1.
Copy Change Constraint: The copyChange field is set to loss to specify the category of copy change.

Members

This example does not include members, as VRS does not support large-scale copy-number events of this type.

Full example: JSON

{
  "id": "civic.id:4452",
  "type": "CategoricalVariant",
  "name": "TP53 Loss (annotated)",
  "description": "TP53 Copy Number Loss is a categorical copy-number variant resulting from the deletion of one copy of the TP53 gene.",
  "aliases": [
    "TP53 Copy Number Loss",
    "P53 Copy Number Loss"
  ],
  "extensions": [
    {
      "name": "cytogenetic location",
      "value": "17p13"
    }
  ],
  "constraints": [
    {
      "type": "DefiningLocationConstraint",
      "location": {
        "id": "ga4gh:SL.u9R1nbh-BFBoRI8Ravn3yBBSvp-u10LW",
        "description": "Genomic region between positions 7,668,420 to 7,687,490 on chromosome 17 (refseq:NC_000017.11, GRCh38).",
        "extensions": [
          {
            "name": "GRCh38 1-based, inclusive interval",
            "value": "chr17:(7668421\u20137687490)",
            "description": "Genomic region between positions 7,668,421 to 7,687,490 on chromosome 17 (refseq:NC_000017.11, GRCh38); 1-based, inclusive interval notation."
          },
          {
            "name": "GRCh38 0-based, half-open interval",
            "value": "chr17:(7668420\u20137687490)",
            "description": "Genomic region between positions 7,668,420 to 7,687,490 on chromosome 17 (refseq:NC_000017.11, GRCh38); 0-based, half-open interval notation."
          }
        ],
        "type": "SequenceLocation",
        "digest": "u9R1nbh-BFBoRI8Ravn3yBBSvp-u10LW",
        "sequenceReference": {
          "id": "refseq:NC_000017.11",
          "name": "NC_000017.11",
          "description": "Reference sequence for GRCh38 chromosome 17.",
          "aliases": [
            "GRCh38:17",
            "GRCh38:chr17",
            "ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7"
          ],
          "type": "SequenceReference",
          "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
        },
        "start": [
          null,
          7668420
        ],
        "end": [
          7687490,
          null
        ]
      },
      "relations": [
        {
          "primaryCoding": {
            "code": "liftover_to",
            "system": "ga4gh-gks-term:allele-relation"
          }
        }
      ],
      "matchCharacteristic": {
        "primaryCoding": {
          "code": "is_within",
          "system": "ga4gh-gks-term:location-match"
        }
      }
    },
    {
      "type": "FeatureContextConstraint",
      "featureContext": {
        "id": "TP53",
        "name": "TP53",
        "conceptType": "gene",
        "primaryCoding": {
          "id": "hgnc:11998",
          "name": "TP53",
          "system": "https://genenames.org",
          "code": "HGNC:11998",
          "iris": [
            "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:11998"
          ]
        },
        "extensions": [
          {
            "name": "cytogenetic location",
            "value": "17p13.1"
          }
        ]
      }
    },
    {
      "type": "CopyChangeConstraint",
      "copyChange": "loss"
    }
  ],
  "members": [],
  "mappings": [
    {
      "coding": {
        "name": "TP53 Loss",
        "system": "https://civicdb.org",
        "code": "civic.vid:4452",
        "iris": [
          "https://civicdb.org/variants/4452/summary"
        ]
      },
      "relation": "exactMatch"
    },
    {
      "coding": {
        "name": "TP53 Deletion",
        "system": "https://civicdb.org/",
        "code": "civic.mpid:4456",
        "iris": [
          "https://civicdb.org/molecular-profiles/4456/summary"
        ]
      },
      "relation": "relatedMatch"
    }
  ]
}

Full example: YAML

# Read more about the Cat-VRS data model, here:
# https://cat-vrs.readthedocs.io/en/latest/concepts/catvrs_model.html

# id: 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.
id: civic.id:4452

# All categorical variants must have the type "CategoricalVariant"
type: CategoricalVariant

# name: A primary name for the entity.
name: TP53 Loss (annotated)

# description: A free-text description of the entity
description: TP53 Copy Number Loss is a categorical copy-number variant resulting from the deletion of one copy of the TP53 gene.

# Alternative name(s) for the Entity.
aliases:
  - TP53 Copy Number Loss
  - P53 Copy Number Loss

# extensions: A list of extensions to the Entity, that allow for capture of information not directly
# supported by elements defined in the model.
# The decision of how to structure extensions are left to implementers, though we recommend
# documenting an implementation's use of extensions in the Standard Operating Procedure to
# promote ease of use
extensions:
  - name: cytogenetic location
    value: 17p13

# constraints: A rule or set of rules that must bve satisfied for a Categorical Variant to be considered valid.
# constraints are defined within schema/cat-vrs/cat-vrs-source.yaml
# and they are also described online: https://cat-vrs.readthedocs.io/en/latest/concepts/catvrs_model.html#constraint
# For each categorical variant, there may be 0 to n constraints.

# When trying to decide what constraints to use to model a categorical variant, it may be useful to refer to "recipes"
# of constraints to model common types of variation, found in schema/cat-vrs/recipes-source.yaml.

constraints:
  # The DefiningLocationConstraint describes variation relative to a VRS location
  # The VRS location can be transcribed in full, or abbreviated with the notation vrs.json#/ga4gh:VA...
  - type: DefiningLocationConstraint
    location:
      id: ga4gh:SL.u9R1nbh-BFBoRI8Ravn3yBBSvp-u10LW
      description: Genomic region between positions 7,668,420 to 7,687,490 on chromosome 17 (refseq:NC_000017.11, GRCh38).
      extensions:
        - name: GRCh38 1-based, inclusive interval
          value: chr17:(7668421–7687490)
          description: Genomic region between positions 7,668,421 to 7,687,490 on chromosome 17 (refseq:NC_000017.11, GRCh38); 1-based, inclusive interval notation.
        - name: GRCh38 0-based, half-open interval
          value: chr17:(7668420–7687490)
          description: Genomic region between positions 7,668,420 to 7,687,490 on chromosome 17 (refseq:NC_000017.11, GRCh38); 0-based, half-open interval notation.
      type: SequenceLocation
      digest: u9R1nbh-BFBoRI8Ravn3yBBSvp-u10LW
      sequenceReference:
        id: refseq:NC_000017.11
        name: NC_000017.11
        description: Reference sequence for GRCh38 chromosome 17.
        aliases:
          - GRCh38:17
          - GRCh38:chr17
          - ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7
        type: SequenceReference
        refgetAccession: SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul
      start:
        - null
        - 7668420
      end:
        - 7687490
        - null
    relations:
      - primaryCoding:
          code: liftover_to
          system: ga4gh-gks-term:allele-relation
    matchCharacteristic:
      primaryCoding:
        code: is_within
        system: ga4gh-gks-term:location-match

  # The FeatureContextConstraint denotes the feature (e.g. gene, pseudogene, or sequence) that members of this
  # categorical variant are associated with.
  # the type should be "FeatureContextConstraint" and featureContext is a mappable concept.
  - type: FeatureContextConstraint
    featureContext:
      # 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.
      # id is not intended or required ot be human-readable.  In this case it just happens to be so
      id: TP53

      # A primary name for the concept (usually a human-readable one)
      name: TP53

      # The type of feature being denoted: gene, pseudogene, sequence, region, etc
      conceptType: gene

      # A primary coding for the concept.
      # A coding is structured representation of a code for a defined concept in a terminology or code system.
      primaryCoding:
        id: hgnc:11998
        name: TP53
        system: https://genenames.org
        code: HGNC:11998
        iris:
          - https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:11998

      # A list of extensions to the Entity, which allow for capture of information not directly supported by
      # elements defined in the model.
      extensions:
        - name: cytogenetic location
          value: 17p13.1

  # The CopyChangeConstraint captures the relative change in copy count of the assayed feature relative to base ploidy
  - type: CopyChangeConstraint
    copyChange: loss

# members: A non-exhaustive list of VRS variation Constraints that satisfy the constraints of this categorical variant.
# Here, however, VRS doesn't support large-scale copy-number events, so there are no valid VRS members of this
# categorical variant.  However, if this categorical variant had been about loss-of-function or expression variants,
# then there exist vrs member variants, e.g. protein missense, or premature stop variants that would cause TP53 loss
# and therefore be members of this categorical variant.
members: []

# mappings: A list of mappings to concepts in terminologies or code systems.
# Each mapping should include a coding and a relation.
# Usually, this is intended to describe relations to concepts in _other_ websites or systems
# For example, linking out to clinvar or dbSNP
# Here, we reference a related match (an expression/function variant as opposed to a purely copy-number loss) in CIViC
mappings:
  - coding:
      name: TP53 Loss
      system: https://civicdb.org
      code: civic.vid:4452
      iris:
        - https://civicdb.org/variants/4452/summary
    relation: exactMatch
  - coding:
      name: TP53 Deletion
      system: https://civicdb.org/
      code: civic.mpid:4456
      iris:
        - https://civicdb.org/molecular-profiles/4456/summary
    relation: relatedMatch