Release 4

This page is part of the FHIR Specification (v4.0.1: R4 - Mixed Normative and STU) in it's permanent home (it will always be available at this URL). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions . Page versions: R5 R4B R4

Sequence-genetics-example-breastcancer.json

Clinical Genomics Work Group

Maturity Level: N/A

Standards Status: Informative

Compartments: Patient

Raw JSON (canonical form + also see JSON Format Specification)

MolecularSequence example for patient with breast cancer gene variant

{
  "resourceType": "MolecularSequence",
  "id": "breastcancer",
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: breastcancer</p><p><b>type</b>: rna</p><p><b>coordinateSystem</b>: 0</p><p><b>patient</b>: <a>Patient/brcapat</a></p><h3>ReferenceSeqs</h3><table><tr><td>-</td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>Homo sapiens BRCA2, DNA repair associated (BRCA2), mRNA <span>(Details : {http://www.ncbi.nlm.nih.gov/nuccore/ code 'NM_000059.3' = 'NM_000059.3', given as 'Homo sapiens BRCA2, DNA repair associated (BRCA2), mRNA'})</span></td><td>101488058</td><td>101499444</td></tr></table><h3>Variants</h3><table><tr><td>-</td><td><b>Start</b></td><td><b>End</b></td><td><b>ObservedAllele</b></td><td><b>ReferenceAllele</b></td></tr><tr><td>*</td><td>32316186</td><td>32316187</td><td>A</td><td>C</td></tr></table></div>"
  },
  "type": "rna",
  "coordinateSystem": 0,
  "patient": {
    "reference": "Patient/brcapat"
  },
  "referenceSeq": {
    "referenceSeqId": {
      "coding": [
        {
          "system": "http://www.ncbi.nlm.nih.gov/nuccore/",
          "code": "NM_000059.3",
          "display": "Homo sapiens BRCA2, DNA repair associated (BRCA2), mRNA"
        }
      ]
    },
    "windowStart": 101488058,
    "windowEnd": 101499444
  },
  "variant": [
    {
      "start": 32316186,
      "end": 32316187,
      "observedAllele": "A",
      "referenceAllele": "C"
    }
  ]
}

Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.