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Example MolecularSequence/example-pgx-2 (JSON)

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

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

Example of another single varaint on a reference MolecularSequence related to a haplotype observation in PGx example, which will form with the other haplotype data to be a diplotype observation.

{
  "resourceType": "MolecularSequence",
  "id": "example-pgx-2",
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: MolecularSequence</b><a name=\"example-pgx-2\"> </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;example-pgx-2&quot; </p></div><p><b>type</b>: dna</p><p><b>subject</b>: <a href=\"patient-example.html\">Patient/example</a> &quot;Peter CHALMERS&quot;</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><td><b>Orientation</b></td><td><b>Strand</b></td></tr><tr><td>*</td><td>NG_007726.3 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (nuccore#NG_007726.3)</span></td><td>55227970</td><td>55227980</td><td>sense</td><td>watson</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>55227978</td><td>55227979</td><td>G</td><td>T</td></tr></table></blockquote></div>"
  },
  "type": "dna",
  "subject": {
    "reference": "Patient/example"
  },
  "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": "NG_007726.3"
            }
          ]
        },
        "windowStart": 55227970,
        "windowEnd": 55227980,
        "orientation": "sense",
        "strand": "watson"
      },
      "edit": [
        {
          "start": 55227978,
          "end": 55227979,
          "replacementSequence": "G",
          "replacedSequence": "T"
        }
      ]
    }
  ]
}

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.