Retrieve Annotations for a Chromosome Region of Interest

This use case shows you how to fetch variants based on chromosome region.

Use Case

This use case retrieves annotations of a chromosome region of interest. You can extract both variant details and gene related annotations from the chromosome region. Various other types of reference information can also be extracted from variant and gene.

Step 1: Retrieve Chromosome Details for Assembly Identifier

This API fetches the Chromosome details for an Assembly Identifier (1) to view the different chromosomes loaded in the database. For details, see the Retrieve Genomic Assembly Details for an Assembly Identifier endpoint.

Request URL

http://localhost:7010/ohfapi/cg/v3.3/genomeAssemblyDetails/1

Request Type

GET

JSON Response

{
  "resourceType" : "GenomeDetails",
  "items" : [ {
    "identifier" : {
      "system" : "ODB",
      "value" : "1"
    },
    "assembly" : "GRCh37",
    "assemblyAlias" : "GRCh37",
    "species" : "homo sapiens",
    "PAR" : [ {
      "chromosome" : "X",
      "startPosition" : 60001,
      "endPosition" : 2699520
    }
],
    "ensemblVersion" : [ {
      "versionWID" : 2,
      "ensemblVersion" : "GRCH37.75",
      "chromosome" : [ {
        "chromosome" : "1",
        "startPosition" : 1,
        "endPosition" : 249250621,
        "dateOfLoading" : "01/25/2016",
        "ensemblReleaseDate" : "02/08/2014"
      }
 ],
      "isPreferred" : "Y"
    } ]
  } ],
  "count" : 1,
  "hasMore" : false,
  "links" : [ {
    "rel" : "self",
    "href" : "http://localhost:7010/ohfapi/cg/v3.3/genomeAssemblyDetails/1"
  } ]
}

Step 2a: Retrieve Variant Identifiers for Chromosome Details

This API fetches the Variant Identifiers for the following details (retrieved in Step 1) within the chromosome 1 and between the 1 and 249250621 positions. For details, see the Retrieve Variants for Chromosome endpoint.

Chromosome	1
Start Position	1
End Position	249250621
Assembly Identifier	1

Note:

After obtaining a list of variant identifiers, you can extract different variant annotation like variant effect, variant xref, COSMIC details and other reference details. For details on this annotation API, see the Retrieve Variant Annotations for a Variant Identifier endpoint.

Request URL

http://localhost:7010/ohfapi/cg/v3.3/variants/byChromosome?chromosome=1&startPosition=1&endPosition=249250621&alignmentId=1&limit=5&offset=0

Request Type

GET

JSON Response

{
  "resourceType" : "Variants",
  "items" : [ {
    "identifier" : {
      "system" : "ODB",
      "value" : "6"
    }
  }, {
    "identifier" : {
      "system" : "ODB",
      "value" : "7"
    }
  }
  } ],
  "count" : 2,
  "hasMore" : true,
  "links" : [ {
    "rel" : "self",
    "href" : "http:// localhost:7010/ohfapi/cg/v3.3/variants/byChromosome?chromosome=1&startPosition=1&endPosition=249250621&alignmentId=1&limit=5&offset=0"
  }
 ]
}

Step 2b: Retrieve Genes for Chromosome Details

This API fetches the Gene Information for the following details (retrieved in Step 1) within the chromosome 1 and between the 1 and 249250621 position.. For details, see the Retrieve Genes for Chromosome endpoint.

Chromosome	1
Start Position	1
End Position	249250621
Assembly Identifier	1

Request URL

http://localhost:7010/ohfapi/cg/v3.3/genes/byChromosome/1/1?start_pos=1&end_pos=249250621&limit=5&offset=0

Request Type

GET

JSON Response

{
  "resourceType" : "Genes",
  "items" : [ {
    "identifier" : {
      "system" : "ODB",
      "value" : "2"
    },
    "geneName" : "ENSG00000223972",
    "hugoName" : "DDX11L1",
    "assembly" : "GRCh37",
    "chromosome" : "1",
    "geneReference" : {
      "reference" : "/ohfapi/cg/v3.3/genes/2"
    }
  }
  } ],
  "count" : 1,
  "hasMore" : true,
  "links" : [ {
    "rel" : "self",
    "href" : "http://localhost:7010/ohfapi/cg/v3.3/genes/byChromosome/1/1?start_pos=1&end_pos=249250621&limit=5&offset=0"
  }
]
}

Step 3: Retrieve Gene EXON Component Details for Gene Identifier

This API fetches the Gene EXON Component Information for the Gene Identifier (2) retrieved in Step 2b. For details, see the Retrieve Exon Components for a Gene Identifier endpoint.

Note:

• Similar to the Gene EXON Component API, other gene components can be retrieved using the APIs described under Gene REST Endpoints.

• You can retrieve gene annotation details for any gene identifier using the API Retrieve Gene for a Gene Identifier.

Request URL

http://localhost:7010/ohfapi/cg/v3.3/genes/2/components/exon

Request Type

GET

JSON Response

{
  "resourceType" : "GeneComponents",
  "items" : [ {
    "identifier" : {
      "system" : "ODB",
      "value" : "2"
    },
    "geneName" : "ENSG00000223972",
    "ensemblVersion" : "GRCH37.75",
    "componentSource" : {
      "componentType" : [ {
        "componentName" : "exon",
        "componentId" : 5812,
        "genomicPosition" : [ {
          "chromosome" : "1",
          "startPosition" : 13661,
          "endPosition" : 14409,
          "strand" : "+",
          "numberInSequence" : 1
        } ]
      }, {
        "componentName" : "exon",
        "componentId" : 5813,
        "genomicPosition" : [ {
          "chromosome" : "1",
          "startPosition" : 13221,
          "endPosition" : 14409,
          "strand" : "+",
          "numberInSequence" : 1
        } ]
      }
 ]
    },
    "geneReference" : {
      "reference" : "/ohfapi/cg/v3.3/genes/2"
    }
  } ],
  "count" : 1,
  "hasMore" : false,
  "links" : [ {
    "rel" : "self",
    "href" : "http://localhost:7010/ohfapi/cg/v3.3/genes/2/components/exon"
  } ]
}