Release 5 Ballot

This page is part of the FHIR Specification (v5.0.0-ballot: R5 Ballot - see ballot notes). 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

Example MolecularSequence/breastcancer (JSON)

Clinical Genomics Work GroupMaturity Level: N/AStandards Status: InformativeCompartments: 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: MolecularSequence</b><a name=\"breastcancer\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource MolecularSequence &quot;breastcancer&quot; </p></div><p><b>type</b>: rna</p><p><b>subject</b>: <a href=\"broken-link.html\">Patient/brcapat</a></p><blockquote><p><b>relative</b></p><p><b>coordinateSystem</b>: 0-based interval counting <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA30100-4)</span></p><h3>StartingSequences</h3><table class=\"grid\"><tr><td>-</td><td><b>Sequence[x]</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 style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (#NM_000059.3)</span></td><td>101488058</td><td>101499444</td></tr></table><h3>Edits</h3><table class=\"grid\"><tr><td>-</td><td><b>Start</b></td><td><b>End</b></td><td><b>ReplacementSequence</b></td><td><b>ReplacedSequence</b></td></tr><tr><td>*</td><td>32316186</td><td>32316187</td><td>A</td><td>C</td></tr></table></blockquote></div>"
  },
  "type": "rna",
  "subject": {
    "reference": "Patient/brcapat"
  },
  "relative": [
    {
      "coordinateSystem": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA30100-4",
            "display": "0-based interval counting"
          }
        ]
      },
      "startingSequence": {
        "sequenceCodeableConcept": {
          "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
      },
      "edit": [
        {
          "start": 32316186,
          "end": 32316187,
          "replacementSequence": "A",
          "replacedSequence": "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.