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Genomics API v1

The Cerner variant model represents genomic variants acquired by sequencing the DNA, RNA, or amino acid chains of a sample and defines the framework necessary to support future genomic information in a health care environment. The Variant API is based on the Genetic Observation Fast Healthcare Interoperability Resources (FHIR) resource, and variant data is gathered from multiple sources using FHIR.

Note: You must have a HealtheIntent population ID and data partition ID for your tenant before you can use this API. To get started, log a service record (SR) in eService to the solution of Lab Sequence or contact your Cerner representative.

URL: https://cernerdemo.api.us-1.healtheintent.com/genomics/v1

Variants

Variants are alterations in the most common DNA nucleotide sequence. The term variant can be used to describe an alteration that can be benign, pathogenic, or of unknown significance. The term variant is frequently used in place of the term mutation.

Create a Variant or Variants

Example Request:




require 'httparty' # Using HTTParty 0.16.2
require 'json'

headers = {
  'Authorization' => '<auth_header>',
  'Content-Type' => 'application/json',
  'Accept' => 'application/json'
} 

result = HTTParty.post('https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants', headers: headers, body: {"sourcePersonId":"3040865","partitionId":"ab9176be-4303-4e6c-aa8d-219d31e29d76","populationId":"99f31909-5b3b-4560-8c83-627828b2c97d","orderId":"57","variants":[{"text":{"status":"generated","div":"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"},"secondaryFinding":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"identifiers":[{"use":"official","type":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"system":"http://www.example.com/patients","value":"44552","period":{"start":"2019-08-29T06:25:13Z","end":"2019-10-29T06:12:21Z"},"assigner":"registry"}],"status":"final","bodySite":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"categories":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"issued":"2018-06-29T06:25:13Z","effectiveDateTime":"2019-03-19T06:15:23Z","value":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genes":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"cytogeneticLocations":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"refSequenceAssemblies":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"dnaChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"dnaChgType":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"functionalAnnotations":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"variationCode":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicDnaChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicSourceClass":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"aminoAcidChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"aminoAcidChgType":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"transcriptRefSeq":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicRefSeq":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"sampleAllelicFrequency":{"value":"25","comparator":"&gt;","unit":"mcg/L","system":"http://unitsofmeasure.org","code":"ug"},"allelicReadDepths":[{"value":"25","comparator":"&gt;","unit":"mcg/L","system":"http://unitsofmeasure.org","code":"ug"}],"allelicState":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"copyNumber":"1","refAllele":"normal","altAllele":"test","coordinateSystem":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"exactStartEnd":{"low":"1.6","high":"1.9"},"outerStartEnd":{"low":"1.6","high":"1.9"},"innerStartEnd":{"low":"1.6","high":"1.9"},"cytogenomicNomenclature":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"variantInheritance":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"tags":[{"key":"result","value":"+ve"}],"comments":[{"authorType":"RelatedPerson","author":"Labseq Admin","time":"2020-11-05T08:15:30+05:30","text":"Modified"}]}]}.to_json )

print JSON.pretty_generate(result)




# You can also use wget
curl -X POST https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants \
-H 'Authorization: {auth_header}' \
-H 'Content-Type: application/json' \ \
-H 'Accept: application/json' \
-d {"sourcePersonId":"3040865","partitionId":"ab9176be-4303-4e6c-aa8d-219d31e29d76","populationId":"99f31909-5b3b-4560-8c83-627828b2c97d","orderId":"57","variants":[{"text":{"status":"generated","div":"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"},"secondaryFinding":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"identifiers":[{"use":"official","type":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"system":"http://www.example.com/patients","value":"44552","period":{"start":"2019-08-29T06:25:13Z","end":"2019-10-29T06:12:21Z"},"assigner":"registry"}],"status":"final","bodySite":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"categories":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"issued":"2018-06-29T06:25:13Z","effectiveDateTime":"2019-03-19T06:15:23Z","value":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genes":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"cytogeneticLocations":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"refSequenceAssemblies":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"dnaChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"dnaChgType":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"functionalAnnotations":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"variationCode":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicDnaChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicSourceClass":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"aminoAcidChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"aminoAcidChgType":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"transcriptRefSeq":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicRefSeq":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"sampleAllelicFrequency":{"value":"25","comparator":"&gt;","unit":"mcg/L","system":"http://unitsofmeasure.org","code":"ug"},"allelicReadDepths":[{"value":"25","comparator":"&gt;","unit":"mcg/L","system":"http://unitsofmeasure.org","code":"ug"}],"allelicState":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"copyNumber":"1","refAllele":"normal","altAllele":"test","coordinateSystem":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"exactStartEnd":{"low":"1.6","high":"1.9"},"outerStartEnd":{"low":"1.6","high":"1.9"},"innerStartEnd":{"low":"1.6","high":"1.9"},"cytogenomicNomenclature":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"variantInheritance":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"tags":[{"key":"result","value":"+ve"}],"comments":[{"authorType":"RelatedPerson","author":"Labseq Admin","time":"2020-11-05T08:15:30+05:30","text":"Modified"}]}]}

POST /variants

Creates or adds a variant or variants and saves them to the repository retrieved from FHIR. The variants are saved in the Variants service. The API treats the created or added variant information as the new, complete set of data for the variant.

Parameters

Parameter In Type Required Default Description Accepted Values
body body postVariants true N/A No description -

Response Statuses

Status Meaning Description Schema
201 Created Created None
400 Bad Request Bad Request Error
401 Unauthorized Unauthorized Error
403 Forbidden Forbidden Error

Retrieve a List of Variants

Example Request:


require 'httparty' # Using HTTParty 0.16.2
require 'json'

headers = {
  'Authorization' => '<auth_header>',
  'Accept' => 'application/json'
} 

result = HTTParty.get('https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants', headers: headers)

print JSON.pretty_generate(result)


# You can also use wget
curl -X GET https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants \
-H 'Authorization: {auth_header}' \
-H 'Accept: application/json'

Example response

{
  "items": [
    {
      "sourcePersonId": "d4sad40b-fa0e-4f13-bc5d-645cea7ed1ds",
      "orderId": "a2dad45b-fa0e-4f13-bc5d-645cea7ed3fd",
      "id": "f1dad40b-fa0e-4f13-bc5d-645cea7ed1eb",
      "text": {
        "status": "generated",
        "div": "<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"
      },
      "secondaryFinding": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "identifiers": [
        {
          "use": "official",
          "type": {
            "text": "Cellulitis of the foot",
            "codings": [
              {
                "system": "http://snomed.info/sct",
                "version": "V1",
                "code": "laboratory",
                "display": "AR2"
              }
            ]
          },
          "system": "http://www.example.com/patients",
          "value": "44552",
          "period": {
            "start": "2019-08-29T06:25:13Z",
            "end": "2019-10-29T06:12:21Z"
          },
          "assigner": "registry"
        }
      ],
      "status": "final",
      "bodySite": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "categories": [
        {
          "text": "Cellulitis of the foot",
          "codings": [
            {
              "system": "http://snomed.info/sct",
              "version": "V1",
              "code": "laboratory",
              "display": "AR2"
            }
          ]
        }
      ],
      "issued": "2018-06-29T06:25:13Z",
      "effectiveDateTime": "2019-03-19T06:15:23Z",
      "value": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "genes": [
        {
          "text": "Cellulitis of the foot",
          "codings": [
            {
              "system": "http://snomed.info/sct",
              "version": "V1",
              "code": "laboratory",
              "display": "AR2"
            }
          ]
        }
      ],
      "cytogeneticLocations": [
        {
          "text": "Cellulitis of the foot",
          "codings": [
            {
              "system": "http://snomed.info/sct",
              "version": "V1",
              "code": "laboratory",
              "display": "AR2"
            }
          ]
        }
      ],
      "refSequenceAssemblies": [
        {
          "text": "Cellulitis of the foot",
          "codings": [
            {
              "system": "http://snomed.info/sct",
              "version": "V1",
              "code": "laboratory",
              "display": "AR2"
            }
          ]
        }
      ],
      "dnaChg": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "dnaChgType": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "functionalAnnotations": [
        {
          "text": "Cellulitis of the foot",
          "codings": [
            {
              "system": "http://snomed.info/sct",
              "version": "V1",
              "code": "laboratory",
              "display": "AR2"
            }
          ]
        }
      ],
      "variationCode": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "genomicDnaChg": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "genomicSourceClass": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "aminoAcidChg": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "aminoAcidChgType": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "transcriptRefSeq": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "genomicRefSeq": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "sampleAllelicFrequency": {
        "value": "25",
        "comparator": "&gt;",
        "unit": "mcg/L",
        "system": "http://unitsofmeasure.org",
        "code": "ug"
      },
      "allelicReadDepths": [
        {
          "value": "25",
          "comparator": "&gt;",
          "unit": "mcg/L",
          "system": "http://unitsofmeasure.org",
          "code": "ug"
        }
      ],
      "allelicState": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "copyNumber": "1",
      "refAllele": "normal",
      "altAllele": "test",
      "coordinateSystem": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "exactStartEnd": {
        "low": "1.6",
        "high": "1.9"
      },
      "outerStartEnd": {
        "low": "1.6",
        "high": "1.9"
      },
      "innerStartEnd": {
        "low": "1.6",
        "high": "1.9"
      },
      "cytogenomicNomenclature": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "variantInheritance": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "tags": [
        {
          "key": "result",
          "value": "+ve"
        }
      ],
      "comments": [
        {
          "authorType": "RelatedPerson",
          "author": "Labseq Admin",
          "time": "2020-11-05T08:15:30+05:30",
          "text": "Modified"
        }
      ]
    }
  ],
  "totalResults": 1,
  "firstLink": "https://cernerdemo.api.us-1.healtheintent.com/example/v1/examples?offset=0&limit=20",
  "lastLink": "https://cernerdemo.api.us-1.healtheintent.com/example/v1/examples?offset=0&limit=20"
}

GET /variants

Retrieves a list of all active variants that meet the specified parameters.

Parameters

Parameter In Type Required Default Description Accepted Values
sourcePersonId query string false N/A The unique ID of the person. -
orderId query string false N/A The unique ID of the order. -
geneName query string false N/A The gene name of the variant. -
offset query integer(int32) false 0 The number of results to skip from the beginning of the list of results (typically for the purpose of paging). The minimum offset is 0. There is no maximum offset. -
limit query integer(int32) false 20 The maximum number of results to display per page. The minimum limit is 1. The maximum limit is 100. -

Response Statuses

Status Meaning Description Schema
200 OK OK VariantsData
400 Bad Request Bad Request Error
401 Unauthorized Unauthorized Error
403 Forbidden Forbidden Error
404 Not Found Not Found Error

Update a Variant

Example Request:




require 'httparty' # Using HTTParty 0.16.2
require 'json'

headers = {
  'Authorization' => '<auth_header>',
  'Content-Type' => 'application/json',
  'Accept' => 'application/json'
} 

result = HTTParty.put('https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants/65752b39-78ed-496d-983e-64b361ad7890', headers: headers, body: {"sourcePersonId":"3040865","partitionId":"ab9176be-4303-4e6c-aa8d-219d31e29d76","populationId":"99f31909-5b3b-4560-8c83-627828b2c97d","orderId":"57","variant":{"text":{"status":"generated","div":"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"},"secondaryFinding":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"identifiers":[{"use":"official","type":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"system":"http://www.example.com/patients","value":"44552","period":{"start":"2019-08-29T06:25:13Z","end":"2019-10-29T06:12:21Z"},"assigner":"registry"}],"status":"final","bodySite":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"categories":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"issued":"2018-06-29T06:25:13Z","effectiveDateTime":"2019-03-19T06:15:23Z","value":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genes":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"cytogeneticLocations":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"refSequenceAssemblies":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"dnaChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"dnaChgType":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"functionalAnnotations":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"variationCode":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicDnaChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicSourceClass":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"aminoAcidChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"aminoAcidChgType":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"transcriptRefSeq":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicRefSeq":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"sampleAllelicFrequency":{"value":"25","comparator":"&gt;","unit":"mcg/L","system":"http://unitsofmeasure.org","code":"ug"},"allelicReadDepths":[{"value":"25","comparator":"&gt;","unit":"mcg/L","system":"http://unitsofmeasure.org","code":"ug"}],"allelicState":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"copyNumber":"1","refAllele":"normal","altAllele":"test","coordinateSystem":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"exactStartEnd":{"low":"1.6","high":"1.9"},"outerStartEnd":{"low":"1.6","high":"1.9"},"innerStartEnd":{"low":"1.6","high":"1.9"},"cytogenomicNomenclature":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"variantInheritance":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"tags":[{"key":"result","value":"+ve"}],"comments":[{"authorType":"RelatedPerson","author":"Labseq Admin","time":"2020-11-05T08:15:30+05:30","text":"Modified"}]}}.to_json )

print JSON.pretty_generate(result)




# You can also use wget
curl -X PUT https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants/65752b39-78ed-496d-983e-64b361ad7890 \
-H 'Authorization: {auth_header}' \
-H 'Content-Type: application/json' \ \
-H 'Accept: application/json' \
-d {"sourcePersonId":"3040865","partitionId":"ab9176be-4303-4e6c-aa8d-219d31e29d76","populationId":"99f31909-5b3b-4560-8c83-627828b2c97d","orderId":"57","variant":{"text":{"status":"generated","div":"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"},"secondaryFinding":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"identifiers":[{"use":"official","type":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"system":"http://www.example.com/patients","value":"44552","period":{"start":"2019-08-29T06:25:13Z","end":"2019-10-29T06:12:21Z"},"assigner":"registry"}],"status":"final","bodySite":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"categories":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"issued":"2018-06-29T06:25:13Z","effectiveDateTime":"2019-03-19T06:15:23Z","value":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genes":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"cytogeneticLocations":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"refSequenceAssemblies":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"dnaChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"dnaChgType":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"functionalAnnotations":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"variationCode":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicDnaChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicSourceClass":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"aminoAcidChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"aminoAcidChgType":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"transcriptRefSeq":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicRefSeq":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"sampleAllelicFrequency":{"value":"25","comparator":"&gt;","unit":"mcg/L","system":"http://unitsofmeasure.org","code":"ug"},"allelicReadDepths":[{"value":"25","comparator":"&gt;","unit":"mcg/L","system":"http://unitsofmeasure.org","code":"ug"}],"allelicState":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"copyNumber":"1","refAllele":"normal","altAllele":"test","coordinateSystem":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"exactStartEnd":{"low":"1.6","high":"1.9"},"outerStartEnd":{"low":"1.6","high":"1.9"},"innerStartEnd":{"low":"1.6","high":"1.9"},"cytogenomicNomenclature":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"variantInheritance":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"tags":[{"key":"result","value":"+ve"}],"comments":[{"authorType":"RelatedPerson","author":"Labseq Admin","time":"2020-11-05T08:15:30+05:30","text":"Modified"}]}}

PUT /variants/{variantId}

Updates the variant with the specified ID. The API does not support PATCH requests to update only certain pieces of the variant data. This means that all known variant data must be specified in each request to update existing variants using all the information.

Parameters

Parameter In Type Required Default Description Accepted Values
variantId path string true N/A The unique ID of the variant. -
body body putVariants true N/A No description -

Response Statuses

Status Meaning Description Schema
204 No Content No content None
400 Bad Request Bad Request Error
401 Unauthorized Unauthorized Error
403 Forbidden Forbidden Error
404 Not Found Not Found Error

Retrieve a Single Variant

Example Request:


require 'httparty' # Using HTTParty 0.16.2
require 'json'

headers = {
  'Authorization' => '<auth_header>',
  'Accept' => 'application/json'
} 

result = HTTParty.get('https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants/e92ca89f-8524-451a-9346-666d6ff39329', headers: headers)

print JSON.pretty_generate(result)


# You can also use wget
curl -X GET https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants/e92ca89f-8524-451a-9346-666d6ff39329 \
-H 'Authorization: {auth_header}' \
-H 'Accept: application/json'

Example response

{
  "sourcePersonId": "d4sad40b-fa0e-4f13-bc5d-645cea7ed1ds",
  "orderId": "a2dad45b-fa0e-4f13-bc5d-645cea7ed3fd",
  "id": "f1dad40b-fa0e-4f13-bc5d-645cea7ed1eb",
  "text": {
    "status": "generated",
    "div": "<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"
  },
  "secondaryFinding": {
    "text": "Cellulitis of the foot",
    "codings": [
      {
        "system": "http://snomed.info/sct",
        "version": "V1",
        "code": "laboratory",
        "display": "AR2"
      }
    ]
  },
  "identifiers": [
    {
      "use": "official",
      "type": {
        "text": "Cellulitis of the foot",
        "codings": [
          {
            "system": "http://snomed.info/sct",
            "version": "V1",
            "code": "laboratory",
            "display": "AR2"
          }
        ]
      },
      "system": "http://www.example.com/patients",
      "value": "44552",
      "period": {
        "start": "2019-08-29T06:25:13Z",
        "end": "2019-10-29T06:12:21Z"
      },
      "assigner": "registry"
    }
  ],
  "status": "final",
  "bodySite": {
    "text": "Cellulitis of the foot",
    "codings": [
      {
        "system": "http://snomed.info/sct",
        "version": "V1",
        "code": "laboratory",
        "display": "AR2"
      }
    ]
  },
  "categories": [
    {
      "text": "Cellulitis of the foot",
      "codings": [
        {
          "system": "http://snomed.info/sct",
          "version": "V1",
          "code": "laboratory",
          "display": "AR2"
        }
      ]
    }
  ],
  "issued": "2018-06-29T06:25:13Z",
  "effectiveDateTime": "2019-03-19T06:15:23Z",
  "value": {
    "text": "Cellulitis of the foot",
    "codings": [
      {
        "system": "http://snomed.info/sct",
        "version": "V1",
        "code": "laboratory",
        "display": "AR2"
      }
    ]
  },
  "genes": [
    {
      "text": "Cellulitis of the foot",
      "codings": [
        {
          "system": "http://snomed.info/sct",
          "version": "V1",
          "code": "laboratory",
          "display": "AR2"
        }
      ]
    }
  ],
  "cytogeneticLocations": [
    {
      "text": "Cellulitis of the foot",
      "codings": [
        {
          "system": "http://snomed.info/sct",
          "version": "V1",
          "code": "laboratory",
          "display": "AR2"
        }
      ]
    }
  ],
  "refSequenceAssemblies": [
    {
      "text": "Cellulitis of the foot",
      "codings": [
        {
          "system": "http://snomed.info/sct",
          "version": "V1",
          "code": "laboratory",
          "display": "AR2"
        }
      ]
    }
  ],
  "dnaChg": {
    "text": "Cellulitis of the foot",
    "codings": [
      {
        "system": "http://snomed.info/sct",
        "version": "V1",
        "code": "laboratory",
        "display": "AR2"
      }
    ]
  },
  "dnaChgType": {
    "text": "Cellulitis of the foot",
    "codings": [
      {
        "system": "http://snomed.info/sct",
        "version": "V1",
        "code": "laboratory",
        "display": "AR2"
      }
    ]
  },
  "functionalAnnotations": [
    {
      "text": "Cellulitis of the foot",
      "codings": [
        {
          "system": "http://snomed.info/sct",
          "version": "V1",
          "code": "laboratory",
          "display": "AR2"
        }
      ]
    }
  ],
  "variationCode": {
    "text": "Cellulitis of the foot",
    "codings": [
      {
        "system": "http://snomed.info/sct",
        "version": "V1",
        "code": "laboratory",
        "display": "AR2"
      }
    ]
  },
  "genomicDnaChg": {
    "text": "Cellulitis of the foot",
    "codings": [
      {
        "system": "http://snomed.info/sct",
        "version": "V1",
        "code": "laboratory",
        "display": "AR2"
      }
    ]
  },
  "genomicSourceClass": {
    "text": "Cellulitis of the foot",
    "codings": [
      {
        "system": "http://snomed.info/sct",
        "version": "V1",
        "code": "laboratory",
        "display": "AR2"
      }
    ]
  },
  "aminoAcidChg": {
    "text": "Cellulitis of the foot",
    "codings": [
      {
        "system": "http://snomed.info/sct",
        "version": "V1",
        "code": "laboratory",
        "display": "AR2"
      }
    ]
  },
  "aminoAcidChgType": {
    "text": "Cellulitis of the foot",
    "codings": [
      {
        "system": "http://snomed.info/sct",
        "version": "V1",
        "code": "laboratory",
        "display": "AR2"
      }
    ]
  },
  "transcriptRefSeq": {
    "text": "Cellulitis of the foot",
    "codings": [
      {
        "system": "http://snomed.info/sct",
        "version": "V1",
        "code": "laboratory",
        "display": "AR2"
      }
    ]
  },
  "genomicRefSeq": {
    "text": "Cellulitis of the foot",
    "codings": [
      {
        "system": "http://snomed.info/sct",
        "version": "V1",
        "code": "laboratory",
        "display": "AR2"
      }
    ]
  },
  "sampleAllelicFrequency": {
    "value": "25",
    "comparator": "&gt;",
    "unit": "mcg/L",
    "system": "http://unitsofmeasure.org",
    "code": "ug"
  },
  "allelicReadDepths": [
    {
      "value": "25",
      "comparator": "&gt;",
      "unit": "mcg/L",
      "system": "http://unitsofmeasure.org",
      "code": "ug"
    }
  ],
  "allelicState": {
    "text": "Cellulitis of the foot",
    "codings": [
      {
        "system": "http://snomed.info/sct",
        "version": "V1",
        "code": "laboratory",
        "display": "AR2"
      }
    ]
  },
  "copyNumber": "1",
  "refAllele": "normal",
  "altAllele": "test",
  "coordinateSystem": {
    "text": "Cellulitis of the foot",
    "codings": [
      {
        "system": "http://snomed.info/sct",
        "version": "V1",
        "code": "laboratory",
        "display": "AR2"
      }
    ]
  },
  "exactStartEnd": {
    "low": "1.6",
    "high": "1.9"
  },
  "outerStartEnd": {
    "low": "1.6",
    "high": "1.9"
  },
  "innerStartEnd": {
    "low": "1.6",
    "high": "1.9"
  },
  "cytogenomicNomenclature": {
    "text": "Cellulitis of the foot",
    "codings": [
      {
        "system": "http://snomed.info/sct",
        "version": "V1",
        "code": "laboratory",
        "display": "AR2"
      }
    ]
  },
  "variantInheritance": {
    "text": "Cellulitis of the foot",
    "codings": [
      {
        "system": "http://snomed.info/sct",
        "version": "V1",
        "code": "laboratory",
        "display": "AR2"
      }
    ]
  },
  "tags": [
    {
      "key": "result",
      "value": "+ve"
    }
  ],
  "comments": [
    {
      "authorType": "RelatedPerson",
      "author": "Labseq Admin",
      "time": "2020-11-05T08:15:30+05:30",
      "text": "Modified"
    }
  ]
}

GET /variants/{variantId}

Retrieves all data for a specified variant ID.

Parameters

Parameter In Type Required Default Description Accepted Values
variantId path string true N/A The unique ID of the variant. -

Response Statuses

Status Meaning Description Schema
200 OK OK VariantValue
400 Bad Request Bad Request Error
401 Unauthorized Unauthorized Error
403 Forbidden Forbidden Error
404 Not Found Not Found Error

Schema Definitions

postVariants

Name Type Required Description Accepted Values
sourcePersonId string true The unique ID of the person. -
partitionId string true The unique ID of the partition associated with the HealtheIntent population for a specified client. -
populationId string true The unique ID of the HealtheIntent population for a specified client. -
orderId string true The unique ID of the order. -
variants [object] true The collection of variant data. -
» status string true The status of the variant observation or result. -
» categories object true A code that classifies the general type of the observation. -
» value string true Indicates whether the specified variation was found. -
» text string false A human-readable narrative that contains a summary of the content in a resource. The narrative must contain enough detail to make it clinically safe for a human to read only the narrative, but it is not required to encode all the structured data. Resource definitions can define what content should be represented in the narrative to ensure clinical safety. -
» secondaryFinding string false Enables flagging variants that should be considered secondary findings. -
» identifiers object false A unique ID assigned to the observation. -
» bodySite string false Indicates the site on the patient’s body where the observation was made (the target site). -
» issued string(date-time) false The date and time on which this version of the observation was made available to providers. This is typically after the results have been reviewed and verified. -
» effectiveDateTime string(date-time) false The time or time period during which the value was observed. For biological subjects (human patients), this is usually called the physiologically relevant time and is usually the time of either the procedure or specimen collection. The source of the date and time is not usually known, only the date and time itself. -
» genes object false The HUGO Gene Nomenclature Committee (HGNC) ID for a gene. List the gene or genes that were examined in full or in part by the study. If the study addresses multiple genes, they can be recorded in multiple gene-studied components. The required coding uses the HGNC gene symbol as the display text and the HGNC gene ID as the code. -
» cytogeneticLocations object false The cytogenetic (chromosome) location. Some observations contain multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes; for example, systolic and diastolic component observations for blood pressure measurements and multiple component observations for genetics observations. -
» refSequenceAssemblies object false The human reference sequence assembly version. Some observations contain multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes; for example, systolic and diastolic component observations for blood pressure measurements and multiple component observations for genetics observations. -
» dnaChg string false The DNA change transcript (cHGVS), which is the Human Genome Variation Society (HGVS) nomenclature for a single DNA marker. -
» dnaChgType string false The codified type for the associated DNA marker. DNA markers use the HGVS notation to imply the DNA marker type, but this code allows you to use a standard and explicit type for technical and display convenience. -
» functionalAnnotations object false Annotated changes that this variant made to sequence features. -
» variationCode string false The unique ID of the simple variant found in this study. -
» genomicDnaChg string false The DNA change genomic (gHGVS), which is the HGVS nomenclature for the name of a structural variant. -
» genomicSourceClass string false The genomic class of the specimen being analyzed. You can use germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome. -
» aminoAcidChg string false The HGVS nomenclature for an amino acid sequence. You can derive this value from the DNA marker value if it is available. This value is provided for convenience. The use of the nomenclature must be extended to describe nonvariations (wild types). -
» aminoAcidChgType string false The codified type for the associated amino acid marker. Amino acid markers use the HGVS notation to imply the amino acid marker type, but the concurrent use of this code enables you to use a standard and explicit type for technical and display convenience. -
» transcriptRefSeq string false The ID for the transcribed reference sequence. This value is the portion of the genomic reference sequence that is converted to messenger RNA after the introns are removed. -
» genomicRefSeq string false The ID for the genomic reference sequence. The genomic reference sequence is a contiguous stretch of chromosome DNA that spans all of the exons of the gene and includes transcribed and nontranscribed stretches. You can use either the National Center for Biotechnology Information (NCBI) genomic nucleotide RefSeq IDs with their version number (see the RefSeq page on the NCBI Reference Sequence Database website for more information) or the Locus Reference Genomic (LRG) IDs without transcript (t or p) extensions when they become available (see the Locus Reference Genomic website for more information. The NCBI RefSeq genomic IDs are distinguished by a prefix of NG for genes from the nuclear chromosomes and a prefix of NC for genes from mitochondria. The LRG IDs use a prefix of LRG_. Mitochondrial genes are not in the scope of LRG. -
» sampleAllelicFrequency string false The sample allelic frequency. Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes; for example, the systolic and diastolic component observations for blood pressure measurements and multiple component observations for genetics observations. -
» allelicReadDepths object false The allelic read depth specifies the number of reads that identified the allele, whether it consists of one nucleotide or a small sequence of contiguous nucleotides. Different methods and purposes require different numbers of reads, usually more than 400 but possibly as few as 2 to 4. -
» allelicState string false The allelic state is the level of occurrence of a single DNA marker in a set of chromosomes. Heterozygous indicates that the DNA marker is present in only one of the two genes contained in homologous chromosomes. Homozygous indicates that the DNA marker is present in both genes contained in homologous chromosomes. Hemizygous indicates that the DNA marker exists in the only single copy of a gene in a nonhomologous chromosome; for example, the male X and Y chromosomes are nonhomologous. Hemiplasmic indicates that the DNA marker is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA marker is present in all of the copies of mitochondrial DNA. -
» copyNumber string false The genomic structural variant copy number is the copy number of the large variant. In HGVS, this is the numeric value following the X. It is a unitless value. A copy number of 1 implies a deletion. The copy number can usually be inferred from the HGVS or International System for Human Cytogenetic Nomenclature (ISCN) fields. -
» refAllele string false The genomic reference allele contains reference values (for example, normal) examined in the reference sequence. -
» altAllele string false The genomic alternative allele is the contiguous segment of DNA in the test sample that differs from the reference allele at the same location and thus defines a variant. -
» coordinateSystem string false The base number of the coordinate system. This can be 0-based, with an inclusive start and exclusive end (interval), or 1-based, with an inclusive start and end. Two versions of 1-based are in common use: HGVS 1-based (variant method) and VCF 1-based (alignment method). In general, HGVS recommends right justification and Variant Call Format (VCF) recommends left justification. These systems address questions such as insertion placement relative to the nucleotide and after the end of the sequence. Additionally, the systems handle the boundary effects of numbers between features. For more information, see the HGVS and VCF guides. -
» exactStartEnd string false The location of the first genomic position in the reference allele that contains a change from the reference allele. For example, for the simple variant NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys), the location is Chr3: 128906220 on Assembly GRCh38. -
» outerStartEnd string false The genomic coordinates of the widest genomic range in which the variant may reside. -
» innerStartEnd string false The genomic coordinates of the narrowest genomic range in which the structural variant may reside. -
» cytogenomicNomenclature string false The cytogenomic nomenclature fully describes a variant with a single code. This is typically a large variant, such as a mosaic, or abnormal chromosome numbers. -
» variantInheritance string false The variant inheritance. Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes; for example, systolic and diastolic component observations for blood pressure measurements and multiple component observations for genetics observations. -
» tags object false No description -
» comments object false No description -

Error

Name Type Required Description Accepted Values
code integer(int32) true The HTTP response status code that represents the error. -
message string true A human-readable description of the error. -
errorDetails [ErrorDetail] false A list of additional error details. -

ErrorDetail

Name Type Required Description Accepted Values
domain string false A subsystem or context where an error occurred. -
reason string false A codified value that represents the specific error that caused the current error status. -
message string false A human-readable description of an error. -
locationType string false The location or type of the field that caused an error. query, header, path, formData, body
location string false The name of the field that caused an error. -

VariantsData

Name Type Required Description Accepted Values
items [VariantsData] true An array containing the current page of results. -
totalResults integer(int32) false The total number of results for the specified parameters. -
firstLink string true The first page of results. -
lastLink string false The last page of results. -
prevLink string false The previous page of results. -
nextLink string false The next page of results. -

putVariants

Name Type Required Description Accepted Values
sourcePersonId string true The unique ID of the person. -
partitionId string true The unique ID of the partition associated with the HealtheIntent population for a specified client. -
populationId string true The unique ID of the HealtheIntent population for a specified client. -
orderId string true The unique ID of the order. -
variant object true The collection of variant data. -
» status string true The status of the variant observation or result. -
» categories [object] true A code that classifies the general type of the observation. -
» value string true Indicates whether the specified variation was found. -
» text string false A human-readable narrative that contains a summary of the content in a resource. The narrative must contain enough detail to make it clinically safe for a human to read only the narrative, but it is not required to encode all the structured data. Resource definitions can define what content should be represented in the narrative to ensure clinical safety. -
» secondaryFinding string false Enables flagging variants that should be considered secondary findings. -
» identifiers [object] false A unique ID assigned to the observation. -
» bodySite string false Indicates the site on the patient’s body where the observation was made (the target site). -
» issued string(date-time) false The date and time on which this version of the observation was made available to providers. This is typically after the results have been reviewed and verified. -
» effectiveDateTime string(date-time) false The time or time period during which the value was observed. For biological subjects (human patients), this is usually called the physiologically relevant time and is usually the time of either the procedure or specimen collection. The source of the date and time is not usually known, only the date and time itself. -
» genes [object] false The HUGO Gene Nomenclature Committee (HGNC) ID for a gene. List the gene or genes that were examined in full or in part by the study. If the study addresses multiple genes, they can be recorded in multiple gene-studied components. The required coding uses the HGNC gene symbol as the display text and the HGNC gene ID as the code. -
» cytogeneticLocations [object] false The cytogenetic (chromosome) location. Some observations contain multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes; for example, systolic and diastolic component observations for blood pressure measurements and multiple component observations for genetics observations. -
» refSequenceAssemblies [object] false The human reference sequence assembly version. Some observations contain multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes; for example, systolic and diastolic component observations for blood pressure measurements and multiple component observations for genetics observations. -
» dnaChg string false The DNA change transcript (cHGVS), which is the Human Genome Variation Society (HGVS) nomenclature for a single DNA marker. -
» dnaChgType string false The codified type for the associated DNA marker. DNA markers use the HGVS notation to imply the DNA marker type, but this code allows you to use a standard and explicit type for technical and display convenience. -
» functionalAnnotations [object] false Annotated changes that this variant made to sequence features. -
» variationCode string false The unique ID of the simple variant found in this study. -
» genomicDnaChg string false The DNA change genomic (gHGVS), which is the HGVS nomenclature for the name of a structural variant. -
» genomicSourceClass string false The genomic class of the specimen being analyzed. You can use germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome. -
» aminoAcidChg string false The HGVS nomenclature for an amino acid sequence. You can derive this value from the DNA marker value if it is available. This value is provided for convenience. The use of the nomenclature must be extended to describe nonvariations (wild types). -
» aminoAcidChgType string false The codified type for the associated amino acid marker. Amino acid markers use the HGVS notation to imply the amino acid marker type, but the concurrent use of this code enables you to use a standard and explicit type for technical and display convenience. -
» transcriptRefSeq string false The ID for the transcribed reference sequence. This value is the portion of the genomic reference sequence that is converted to messenger RNA after the introns are removed. -
» genomicRefSeq string false The ID for the genomic reference sequence. The genomic reference sequence is a contiguous stretch of chromosome DNA that spans all of the exons of the gene and includes transcribed and nontranscribed stretches. You can use either the National Center for Biotechnology Information (NCBI) genomic nucleotide RefSeq IDs with their version number (see the RefSeq page on the NCBI Reference Sequence Database website for more information) or the Locus Reference Genomic (LRG) IDs without transcript (t or p) extensions when they become available (see the Locus Reference Genomic website for more information. The NCBI RefSeq genomic IDs are distinguished by a prefix of NG for genes from the nuclear chromosomes and a prefix of NC for genes from mitochondria. The LRG IDs use a prefix of LRG_. Mitochondrial genes are not in the scope of LRG. -
» sampleAllelicFrequency string false The sample allelic frequency. Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes; for example, the systolic and diastolic component observations for blood pressure measurements and multiple component observations for genetics observations. -
» allelicReadDepths [object] false The allelic read depth specifies the number of reads that identified the allele, whether it consists of one nucleotide or a small sequence of contiguous nucleotides. Different methods and purposes require different numbers of reads, usually more than 400 but possibly as few as 2 to 4. -
» allelicState string false The allelic state is the level of occurrence of a single DNA marker in a set of chromosomes. Heterozygous indicates that the DNA marker is present in only one of the two genes contained in homologous chromosomes. Homozygous indicates that the DNA marker is present in both genes contained in homologous chromosomes. Hemizygous indicates that the DNA marker exists in the only single copy of a gene in a nonhomologous chromosome; for example, the male X and Y chromosomes are nonhomologous. Hemiplasmic indicates that the DNA marker is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA marker is present in all of the copies of mitochondrial DNA. -
» copyNumber string false The genomic structural variant copy number is the copy number of the large variant. In HGVS, this is the numeric value following the X. It is a unitless value. A copy number of 1 implies a deletion. The copy number can usually be inferred from the HGVS or International System for Human Cytogenetic Nomenclature (ISCN) fields. -
» refAllele string false The genomic reference allele contains reference values (for example, normal) examined in the reference sequence. -
» altAllele string false The genomic alternative allele is the contiguous segment of DNA in the test sample that differs from the reference allele at the same location and thus defines a variant. -
» coordinateSystem string false The base number of the coordinate system. This can be 0-based, with an inclusive start and exclusive end (interval), or 1-based, with an inclusive start and end. Two versions of 1-based are in common use: HGVS 1-based (variant method) and VCF 1-based (alignment method). In general, HGVS recommends right justification and Variant Call Format (VCF) recommends left justification. These systems address questions such as insertion placement relative to the nucleotide and after the end of the sequence. Additionally, the systems handle the boundary effects of numbers between features. For more information, see the HGVS and VCF guides. -
» exactStartEnd string false The location of the first genomic position in the reference allele that contains a change from the reference allele. For example, for the simple variant NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys), the location is Chr3: 128906220 on Assembly GRCh38. -
» outerStartEnd string false The genomic coordinates of the widest genomic range in which the variant may reside. -
» innerStartEnd string false The genomic coordinates of the narrowest genomic range in which the structural variant may reside. -
» cytogenomicNomenclature string false The cytogenomic nomenclature fully describes a variant with a single code. This is typically a large variant, such as a mosaic, or abnormal chromosome numbers. -
» variantInheritance string false The variant inheritance. Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes; for example, systolic and diastolic component observations for blood pressure measurements and multiple component observations for genetics observations. -
» tags [object] false No description -
» comments [object] false No description -

VariantValue

Name Type Required Description Accepted Values
sourcePersonId string false The unique ID of the person. -
orderId string false The unique ID of the order. -
id string false The unique ID of the variant. -
text Narrative false A human-readable narrative that contains a summary of the content in a resource. The narrative must contain enough detail to make it clinically safe for a human to read only the narrative, but it is not required to encode all the structured data. Resource definitions can define what content should be represented in the narrative to ensure clinical safety. -
secondaryFinding CodeableConcept false Enables flagging variants that should be considered secondary findings. -
identifiers [Identifier] false A unique ID assigned to the observation. -
status string false The status of the variant observation or result. -
bodySite CodeableConcept false Indicates the site on the patient’s body where the observation was made (the target site). -
categories [CodeableConcept] false A code that classifies the general type of the observation. -
issued string(date-time) false The date and time on which this version of the observation was made available to providers. This is typically after the results have been reviewed and verified. -
effectiveDateTime string(date-time) false The time or time period during which the value was observed. For biological subjects (human patients), this is usually called the physiologically relevant time and is usually the time of either the procedure or specimen collection. The source of the date and time is not usually known, only the date and time itself. -
value CodeableConcept false Indicates whether the specified variation was found. -
genes [CodeableConcept] false The HUGO Gene Nomenclature Committee (HGNC) ID for a gene. List the gene or genes that were examined in full or in part by the study. If the study addresses multiple genes, they can be recorded in multiple gene-studied components. The required coding uses the HGNC gene symbol as the display text and the HGNC gene ID as the code. -
cytogeneticLocations [CodeableConcept] false The cytogenetic (chromosome) location. Some observations contain multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes; for example, systolic and diastolic component observations for blood pressure measurements and multiple component observations for genetics observations. -
refSequenceAssemblies [CodeableConcept] false The human reference sequence assembly version. Some observations contain multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes; for example, systolic and diastolic component observations for blood pressure measurements and multiple component observations for genetics observations. -
dnaChg CodeableConcept false The DNA change transcript (cHGVS), which is the Human Genome Variation Society (HGVS) nomenclature for a single DNA marker. -
dnaChgType CodeableConcept false The codified type for the associated DNA marker. DNA markers use the HGVS notation to imply the DNA marker type, but this code allows you to use a standard and explicit type for technical and display convenience. -
functionalAnnotations [CodeableConcept] false Annotated changes that this variant made to sequence features. -
variationCode CodeableConcept false The unique ID of the simple variant found in this study. -
genomicDnaChg CodeableConcept false The DNA change genomic (gHGVS), which is the HGVS nomenclature for the name of a structural variant. -
genomicSourceClass CodeableConcept false The genomic class of the specimen being analyzed. You can use germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome. -
aminoAcidChg CodeableConcept false The HGVS nomenclature for an amino acid sequence. You can derive this value from the DNA marker value if it is available. This value is provided for convenience. The use of the nomenclature must be extended to describe nonvariations (wild types). -
aminoAcidChgType CodeableConcept false The codified type for the associated amino acid marker. Amino acid markers use the HGVS notation to imply the amino acid marker type, but the concurrent use of this code enables you to use a standard and explicit type for technical and display convenience. -
transcriptRefSeq CodeableConcept false The ID for the transcribed reference sequence. This value is the portion of the genomic reference sequence that is converted to messenger RNA after the introns are removed. -
genomicRefSeq CodeableConcept false The ID for the genomic reference sequence. The genomic reference sequence is a contiguous stretch of chromosome DNA that spans all of the exons of the gene and includes transcribed and nontranscribed stretches. You can use either the National Center for Biotechnology Information (NCBI) genomic nucleotide RefSeq IDs with their version number (see the RefSeq page on the NCBI Reference Sequence Database website for more information) or the Locus Reference Genomic (LRG) IDs without transcript (t or p) extensions when they become available (see the Locus Reference Genomic website for more information. The NCBI RefSeq genomic IDs are distinguished by a prefix of NG for genes from the nuclear chromosomes and a prefix of NC for genes from mitochondria. The LRG IDs use a prefix of LRG_. Mitochondrial genes are not in the scope of LRG. -
sampleAllelicFrequency Quantity false The sample allelic frequency. Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes; for example, the systolic and diastolic component observations for blood pressure measurements and multiple component observations for genetics observations. -
allelicReadDepths [Quantity] false The allelic read depth specifies the number of reads that identified the allele, whether it consists of one nucleotide or a small sequence of contiguous nucleotides. Different methods and purposes require different numbers of reads, usually more than 400 but possibly as few as 2 to 4. -
allelicState CodeableConcept false The allelic state is the level of occurrence of a single DNA marker in a set of chromosomes. Heterozygous indicates that the DNA marker is present in only one of the two genes contained in homologous chromosomes. Homozygous indicates that the DNA marker is present in both genes contained in homologous chromosomes. Hemizygous indicates that the DNA marker exists in the only single copy of a gene in a nonhomologous chromosome; for example, the male X and Y chromosomes are nonhomologous. Hemiplasmic indicates that the DNA marker is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA marker is present in all of the copies of mitochondrial DNA. -
copyNumber string false The genomic structural variant copy number is the copy number of the large variant. In HGVS, this is the numeric value following the X. It is a unitless value. A copy number of 1 implies a deletion. The copy number can usually be inferred from the HGVS or International System for Human Cytogenetic Nomenclature (ISCN) fields. -
refAllele string false The genomic reference allele contains reference values (for example, normal) examined in the reference sequence. -
altAllele string false The genomic alternative allele is the contiguous segment of DNA in the test sample that differs from the reference allele at the same location and thus defines a variant. -
coordinateSystem CodeableConcept false The base number of the coordinate system. This can be 0-based, with an inclusive start and exclusive end (interval), or 1-based, with an inclusive start and end. Two versions of 1-based are in common use: HGVS 1-based (variant method) and VCF 1-based (alignment method). In general, HGVS recommends right justification and Variant Call Format (VCF) recommends left justification. These systems address questions such as insertion placement relative to the nucleotide and after the end of the sequence. Additionally, the systems handle the boundary effects of numbers between features. For more information, see the HGVS and VCF guides. -
exactStartEnd Range false The location of the first genomic position in the reference allele that contains a change from the reference allele. For example, for the simple variant NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys), the location is Chr3: 128906220 on Assembly GRCh38. -
outerStartEnd Range false The genomic coordinates of the widest genomic range in which the variant may reside. -
innerStartEnd Range false The genomic coordinates of the narrowest genomic range in which the structural variant may reside. -
cytogenomicNomenclature CodeableConcept false The cytogenomic nomenclature fully describes a variant with a single code. This is typically a large variant, such as a mosaic, or abnormal chromosome numbers. -
variantInheritance CodeableConcept false The variant inheritance. Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes; for example, systolic and diastolic component observations for blood pressure measurements and multiple component observations for genetics observations. -
tags [Tags] false No description -
comments [Comments] false No description -

Narrative

Name Type Required Description Accepted Values
status string true The status of the narrative. See the Valueset-narrative-status page in the FHIR standard on the Health Level Seven (HL7) website for more information about the accepted values. generated, extensions, additional, empty
div string true The XHTML content of the narrative, which is limited to basic HTML formatting elements and attributes. -

CodeableConcept

Name Type Required Description Accepted Values
text string false A codeable concept is a value that is usually supplied by providing a reference to one or more terminologies or ontologies, but it can also be defined by the provision of text. -
codings [Coding] false A coding is a concept defined using a symbol from a specific code system. -

Coding

Name Type Required Description Accepted Values
system string false A URI that identifies the system. -
version string false The version of the system. -
code string false A concept defined in the code system. -
display string false A description of the concept as defined in the code system. -

Identifier

Name Type Required Description Accepted Values
use string false No description -
type CodeableConcept false The type of the ID. -
system string false The namespace of the ID. -
value string false The unique value of the ID. -
period Period false The time period during which the ID is or was valid for use. -
assigner string false The organization that issued the ID. This can be only text. -

Period

Name Type Required Description Accepted Values
start string(date-time) false The start date and time with an inclusive boundary. -
end string(date-time) false The end date and time with an inclusive boundary if the period is not ongoing. -

Quantity

Name Type Required Description Accepted Values
value number(double) false A numeric value with implicit precision. -
comparator string false How the quantity should be understood and represented. -
unit string false The unit of the quantity. -
system string false The system that defines the coded form of the unit. -
code string false The coded form of the unit. -

Range

Name Type Required Description Accepted Values
low string false The lowest boundary of the reference range. -
high string false The highest boundary of the reference range. -

Tags

Name Type Required Description Accepted Values
key string false The variant tag key. -
value string false Indicates whether the variation value of the variant tag is found. -

Comments

Name Type Required Description Accepted Values
authorType string false The type of user who made the annotation. -
author string false The user who made the annotation. -
time string(date-time) false The date and time at which a specific annotation was created. -
text string true The text of the annotation in markdown format. -