Sequence-example-pgx-1.json

Example of a single varaint on a reference MolecularSequence related to a haplotype observation in PGx example

{
  "resourceType": "MolecularSequence",
  "id": "example-pgx-1",
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 0</p><p><b>patient</b>: <a>Generated Summary: Medical record number: 12345 (USUAL); active; Peter James Chalmers (OFFICIAL), Jim , Peter James Windsor (MAIDEN); , Phone: (03) 5555 6473, Phone: (03) 3410 5613, Phone: (03) 5555 8834; gender: male; birthDate: 1974-12-25; </a></p><h3>ReferenceSeqs</h3><table><tr><td>-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>Strand</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>sense</td><td><span>NG_007726.3</span></td><td>watson</td><td>55227970</td><td>55227980</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><td><b>VariantPointer</b></td></tr><tr><td>*</td><td>55227976</td><td>55227977</td><td>G</td><td>T</td><td><a>Target Haplotype Observation. Generated Summary: status: unknown; <span>Genetic analysis master panel-- This is the parent OBR for the panel holding all of the associated observations that can be reported with a molecular genetics analysis result.</span>; issued: 4 Apr. 2013, 1:30:10 am; <span>*35B</span></a></td></tr></table></div>"
  },
  "type": "dna",
  "coordinateSystem": 0,
  "patient": {
    "reference": "Patient/example"
  },
  "referenceSeq": {
    "orientation": "sense",
    "referenceSeqId": {
      "coding": [
        {
          "system": "http://www.ncbi.nlm.nih.gov/nuccore",
          "code": "NG_007726.3"
        }
      ]
    },
    "strand": "watson",
    "windowStart": 55227970,
    "windowEnd": 55227980
  },
  "variant": [
    {
      "start": 55227976,
      "end": 55227977,
      "observedAllele": "G",
      "referenceAllele": "T",
      "variantPointer": {
        "reference": "Observation/example-haplotype1",
        "display": "Target Haplotype Observation"
      }
    }
  ]
}