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Example MolecularSequence/sequence-example-fusion (JSON)

Clinical Genomics Work GroupMaturity Level: N/AStandards Status: InformativeCompartments: Patient

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

BCR-ABL1 fusion (COSMIC https://cancer.sanger.ac.uk/cosmic/fusion/summary?id=1755). 5-prime end comprised of BCR exons 1-14. 3-prime end comprised of ABL1 exons 2-11.

{
  "resourceType": "MolecularSequence",
  "id": "sequence-example-fusion",
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: MolecularSequence</b><a name=\"sequence-example-fusion\"> </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;sequence-example-fusion&quot; </p></div><p><b>type</b>: rna</p><blockquote><p><b>relative</b></p><p><b>coordinateSystem</b>: 1-based character counting <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA30102-0)</span></p><p><b>ordinalPosition</b>: 1</p><p><b>sequenceRange</b>: 1-3234</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>NM_004327.4 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (nuccore#NM_004327.4)</span></td><td>1</td><td>3234</td></tr></table></blockquote><blockquote><p><b>relative</b></p><p><b>coordinateSystem</b>: 1-based character counting <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA30102-0)</span></p><p><b>ordinalPosition</b>: 2</p><p><b>sequenceRange</b>: 3235-8367</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>NM_005157.6 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (nuccore#NM_005157.6)</span></td><td>174</td><td>5306</td></tr></table></blockquote></div>"
  },
  "type": "rna",
  "relative": [
    {
      "coordinateSystem": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA30102-0",
            "display": "1-based character counting"
          }
        ]
      },
      "ordinalPosition": 1,
      "sequenceRange": {
        "low": {
          "value": 1
        },
        "high": {
          "value": 3234
        }
      },
      "startingSequence": {
        "sequenceCodeableConcept": {
          "coding": [
            {
              "system": "http://www.ncbi.nlm.nih.gov/nuccore",
              "code": "NM_004327.4"
            }
          ]
        },
        "windowStart": 1,
        "windowEnd": 3234
      }
    },
    {
      "coordinateSystem": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA30102-0",
            "display": "1-based character counting"
          }
        ]
      },
      "ordinalPosition": 2,
      "sequenceRange": {
        "low": {
          "value": 3235
        },
        "high": {
          "value": 8367
        }
      },
      "startingSequence": {
        "sequenceCodeableConcept": {
          "coding": [
            {
              "system": "http://www.ncbi.nlm.nih.gov/nuccore",
              "code": "NM_005157.6"
            }
          ]
        },
        "windowStart": 174,
        "windowEnd": 5306
      }
    }
  ]
}

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.