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Retrieve Variant Cancers for a Variant Identifier

get

/ohfapi/cg/v3.3/variants/{id}/cancer

This endpoint supports the retrieval of Variant Cancers for a Variant Identifier. It retuns Variant Cancer information like HUGO Name, Transcript Identifier, Assembly/Alignment Name, Ensembl Version, Amino Acid Change and other Variant Cancer associated information.

Request

Supported Media Types

• application/json
• application/xml

Path Parameters

• id: integer(int64)
  Variant Row ID

Security

• basicAuth: basic
  Type: basic

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Response

Supported Media Types

• application/json
• application/xml

200 Response

successful operation

Body ()

Root Schema : VariantCancers

Type: object

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• cancerVariant(optional): array cancerVariant
  List of Variant Cancers
• identifier(optional): object Identifier
  Identifier assigned by a given system
• resourceType(optional): string
• variantReferences(optional): object LinkedReference

{
    "type":"object",
    "properties":{
        "resourceType":{
            "type":"string"
        },
        "identifier":{
            "description":"Variant Row ID",
            "$ref":"#/definitions/Identifier"
        },
        "cancerVariant":{
            "type":"array",
            "description":"List of Variant Cancers",
            "items":{
                "$ref":"#/definitions/VariantCancer"
            }
        },
        "variantReferences":{
            "example":"{href: '/variants/{variantRecordId}'}",
            "description":"A link containing href to retrieve Variant Annotation details",
            "$ref":"#/definitions/LinkedReference"
        }
    }
}

Nested Schema : cancerVariant

Type: array

List of Variant Cancers

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• Array of: object VariantCancer

{
    "type":"array",
    "description":"List of Variant Cancers",
    "items":{
        "$ref":"#/definitions/VariantCancer"
    }
}

Nested Schema : Identifier

Type: object

Identifier assigned by a given system

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• system(optional): string
  System which assigned this identifier
• value(optional): string
  Identifier value

{
    "type":"object",
    "properties":{
        "system":{
            "type":"string",
            "description":"System which assigned this identifier"
        },
        "value":{
            "type":"string",
            "description":"Identifier value"
        }
    },
    "description":"Identifier assigned by a given system"
}

Nested Schema : LinkedReference

Type: object

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• display(optional): string
• reference(optional): string

{
    "type":"object",
    "properties":{
        "reference":{
            "type":"string"
        },
        "display":{
            "type":"string"
        }
    }
}

Nested Schema : VariantCancer

Type: object

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• accession(optional): string
  Accession Name
• anatomicalSubtype(optional): string
  Anatomical Subtype
• assembly(optional): string
  Assembly/Alignment Name. For ex.,GRCh38
• coding(optional): string
  Mutation in Coding Sequence Flag
• curationSource(optional): string
  Curation Source Name
• gwScreen(optional): string
  Sample Genome Wide Screen Flag
• hgncId(optional): string
  HUGO Gene Nomenclature Reference ID
• histologySubtype(optional): string
  Histology Subtype Name
• hugoName(optional): string
  Approved HUGO symbol for species loci, including protein coding genes, RNA genes and pseudogenes, e.g. 'SRY', 'DMRT1', 'FOXL2', etc.
• mutationSomaticStatus(optional): string
  Somatic Mutation Status
• primaryHistology(optional): string
  Anatomical Primary Site Name
• referenceID(optional): string
  Cosmic Mutation ID
• siteSubType(optional): string
  Site Subtype
• version(optional): string
  Version Label. For ex.,SIFT_VER2_75
• zygosity(optional): string
  Zygosity of Mutation

{
    "type":"object",
    "properties":{
        "primaryHistology":{
            "type":"string",
            "description":"Anatomical Primary Site Name"
        },
        "histologySubtype":{
            "type":"string",
            "description":"Histology Subtype Name"
        },
        "siteSubType":{
            "type":"string",
            "description":"Site Subtype"
        },
        "anatomicalSubtype":{
            "type":"string",
            "description":"Anatomical Subtype"
        },
        "hugoName":{
            "type":"string",
            "description":"Approved HUGO symbol for species loci, including protein coding genes, RNA genes and pseudogenes, e.g. 'SRY', 'DMRT1', 'FOXL2', etc. "
        },
        "accession":{
            "type":"string",
            "description":"Accession Name"
        },
        "hgncId":{
            "type":"string",
            "description":"HUGO Gene Nomenclature Reference ID"
        },
        "mutationSomaticStatus":{
            "type":"string",
            "description":"Somatic Mutation Status"
        },
        "referenceID":{
            "type":"string",
            "description":"Cosmic Mutation ID"
        },
        "zygosity":{
            "type":"string",
            "description":"Zygosity of Mutation"
        },
        "gwScreen":{
            "type":"string",
            "description":"Sample Genome Wide Screen Flag"
        },
        "coding":{
            "type":"string",
            "description":"Mutation in Coding Sequence Flag"
        },
        "curationSource":{
            "type":"string",
            "description":"Curation Source Name"
        },
        "version":{
            "type":"string",
            "description":"Version Label. For ex.,SIFT_VER2_75"
        },
        "assembly":{
            "type":"string",
            "description":"Assembly/Alignment Name. For ex.,GRCh38"
        }
    }
}

400 Response

Variant Id is not supplied

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Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/variants/7678/cancer

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType" : "CancerVariants",
  "identifier" : {
    "system" : "ODB",
    "value" : "7678"
  },
  "cancerVariant" : [ {
    "primaryHistology" : "carcinoma",
    "histologySubtype" : "adenocarcinoma",
    "siteSubType" : "large_intestine",
    "anatomicalSubtype" : "colon",
    "hugoName" : "SAMD11",
    "accession" : "ENST00000342066",
    "hgncId" : "28706",
    "mutationSomaticStatus" : "Variant of unknown origin",
    "referenceID" : "COSM1344644",
    "zygosity" : "het",
    "gwScreen" : "y",
    "coding" : "Y",
    "curationSource" : "COSMIC",
    "version" : "COSMIC.V67",
    "assembly" : "GRCh37"
  }, {
    "primaryHistology" : "carcinoma",
    "histologySubtype" : "NS",
    "siteSubType" : "liver",
    "anatomicalSubtype" : "NS",
    "hugoName" : "SAMD11",
    "accession" : "ENST00000342066",
    "hgncId" : "28706",
    "mutationSomaticStatus" : "Variant of unknown origin",
    "referenceID" : "COSM1344644",
    "zygosity" : "het",
    "gwScreen" : "y",
    "coding" : "Y",
    "curationSource" : "COSMIC",
    "version" : "COSMIC.V67",
    "assembly" : "GRCh37"
  } ],
  "variantReferences" : {
    "reference" : "/ohfapi/cg/v3.3/variants/7678"
  }
}

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