Annotate Important Mutations with Gene and Function Information

This use case shows you how to annotate important mutations with gene and function information.

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Use Case

I have a set of mutations meeting a set of criteria. I need to annotate them with gene and function information.

Description

This use case shows you how to extract different types of annotations for a set of mutations of interest like effect of mutation, associated gene, associated gene component and other details.

Step 1: Retrieve Variant Identifiers for Reference Identifiers

This API fetches the Variant Identifiers for the Reference Identifier (Mutation ??? COSM297314) and Assembly or Alignment Identifier (1). For details, see the Retrieve Variants for Reference Identifiers and Database with GET Request endpoint.

Request URL

http://localhost:7010/ohfapi/cg/v3.3/variants/byReferenceId?alignmentId=1&referenceId=COSM297314

Request Type

GET

JSON Response

{
  "resourceType" : "Variants",
  "items" : [ {
    "identifier" : {
      "system" : "ODB",
      "value" : "3966561"
    }
  } ],
  "count" : 1,
  "hasMore" : false,
  "links" : [ {
    "rel" : "self",
    "href" : "http://localhost:7010/ohfapi/cg/v3.3/variants/byReferenceId?alignmentId=1&referenceId=COSM297314"
  } ]
}

Step 2: Retrieve Variant Annotations for Variant Identifier

This API fetches the Variant Annotations for the desired Variant Identifier (3966561) retrieved in Step 1. For details, see the Retrieve Variant Annotations for a Variant Identifier endpoint.

Request URL

http://localhost:7010/ohfapi/cg/v3.3/ variants/3966561

Request Type

GET

JSON Response

{
  "resourceType" : "VariantDetails",
  "identifier" : {
    "system" : "ODB",
    "value" : "3966561"
  },
  "chromosome" : "1",
  "startPosition" : "248551598",
  "endPosition" : "248551598",
  "strand" : "+",
  "referenceAllele" : "C",
  "alternateAllele" : "T",
  "variantType" : "substitution",
  "variantLength" : "1",
  "status" : "KNOWN",
  "assembly" : "GRCh37",
  "geneInfo" : [ {
    "geneWid" : "17695",
    "hugoName" : "OR2T6",
    "geneComponents" : [ {
      "ensemblVersion" : "GRCH37.P7",
      "transcripts" : [ {
        "componentTypes" : [ "exon" ]
      }, {
        "transcriptId" : "ENST00000355728",
        "componentTypes" : [ "CDS", "mRNA" ]
      } ]
    }, {
      "ensemblVersion" : "GRCH37.P8",
      "transcripts" : [ {
        "componentTypes" : [ "exon" ]
      }, {
        "transcriptId" : "ENST00000355728",
        "componentTypes" : [ "CDS", "mRNA" ]
      } ]
    } ],
    "gene" : {
      "reference" : "/ohfapi/cg/v3.3/genes/17695"
    }
  } ],
  "variantXref" : {
    "reference" : "/ohfapi/cg/v3.3/variants/3966561/variantXRef"
  },
  "variantPrediction" : {
    "reference" : "/ohfapi/cg/v3.3/variants/3966561/variantPredictions"
  },
  "variantEffect" : {
    "reference" : "/ohfapi/cg/v3.3/variants/3966561/variantEffects"
  },
  "diseaseVariants" : {
    "reference" : "/ohfapi/cg/v3.3/variants/3966561/diseases"
  },
  "cancerVariants" : {
    "reference" : "/ohfapi/cg/v3.3/variants/3966561/cancer"
  }
}

Annotation details on the variant can be obtained by clicking the reference links in the JSON Response. Fox example, Cancer Annotated Information can be retrieved through following URL.

"cancerVariants" : {
    "reference" : "/ohfapi/cg/v3.3/variants/3966561/cancer"
  }