Snapshot 3: Connectathon 32 Base

This is Snapshot #3 for FHIR R5, released to support Connectathon 32. For a full list of available versions, see the Directory of published versions.

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.