Release 4 4B

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Sequence-example-TPMT-one.json

Clinical Genomics Work Group Maturity Level : N/A Standards Status : Informative Compartments : Patient

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

Example of a TPMT SNP data that support a haplotype observation 

{
  "resourceType": "MolecularSequence",
  "id": "example-TPMT-one",
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: example-TPMT-one</p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 1</p><p><b>patient</b>: <a>Patient/example</a></p><h3>ReferenceSeqs</h3><table><tr><td>-</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>NT_007592.15 <span>(Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NT_007592.15' = 'NT_007592.15)</span></td><td>watson</td><td>18130918</td><td>18143955</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></tr><tr><td>*</td><td>18139214</td><td>18139214</td><td>A</td><td>G</td></tr></table><p><b>observedSeq</b>: T-C-C-C-A-C-C-C</p></div>"

    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></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 &quot;example-TPMT-one&quot; </p></div><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 1</p><p><b>patient</b>: <a href=\"patient-example.html\">Patient/example</a> &quot;Peter CHALMERS&quot;</p><h3>ReferenceSeqs</h3><table class=\"grid\"><tr><td>-</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>NT_007592.15 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (nuccore#NT_007592.15)</span></td><td>watson</td><td>18130918</td><td>18143955</td></tr></table><h3>Variants</h3><table class=\"grid\"><tr><td>-</td><td><b>Start</b></td><td><b>End</b></td><td><b>ObservedAllele</b></td><td><b>ReferenceAllele</b></td></tr><tr><td>*</td><td>18139214</td><td>18139214</td><td>A</td><td>G</td></tr></table><p><b>observedSeq</b>: T-C-C-C-A-C-C-C</p></div>"

  },
  "type": "dna",
  "coordinateSystem": 1,
  "patient": {
    "reference": "Patient/example"
  },
  "referenceSeq": {
    "referenceSeqId": {
      "coding": [
        {
          "system": "http://www.ncbi.nlm.nih.gov/nuccore",
          "code": "NT_007592.15"
        }
      ]
    },
    "strand": "watson",
    "windowStart": 18130918,
    "windowEnd": 18143955
  },
  "variant": [
    {
      "start": 18139214,
      "end": 18139214,
      "observedAllele": "A",
      "referenceAllele": "G"
    }
  ],
  "observedSeq": "T-C-C-C-A-C-C-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.