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</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 "example-TPMT-one" </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> "Peter CHALMERS"</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>"
"resourceType" : "MolecularSequence",
"id" : "example-TPMT-one",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: MolecularSequence</b><a name=\"example-TPMT-one\"> </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 "example-TPMT-one" </p></div><p><b>type</b>: dna</p><p><b>subject</b>: <a href=\"patient-example.html\">Patient/example</a> "Peter CHALMERS"</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><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>Strand</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>18130918</td><td>18143955</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>18139214</td><td>18139214</td><td>A</td><td>G</td></tr></table></blockquote></div>"
},
"type": "dna",
"coordinateSystem": 1,
"patient": {
"reference": "Patient/example"
"type" : "dna",
"subject" : {
"reference" : "Patient/example"
},
"referenceSeq": {
"referenceSeqId": {
"coding": [
{
"system": "http://www.ncbi.nlm.nih.gov/nuccore",
"code": "NT_007592.15"
}
]
"relative" : [{
"coordinateSystem" : {
"coding" : [{
"system" : "http://loinc.org",
"code" : "LA30102-0",
"display" : "1-based character counting"
}]
},
"strand": "watson",
"windowStart": 18130918,
"windowEnd": 18143955
},
"variant": [
{
"start": 18139214,
"end": 18139214,
"observedAllele": "A",
"referenceAllele": "G"
}
],
"observedSeq": "T-C-C-C-A-C-C-C"
"startingSequence" : {
"sequenceCodeableConcept" : {
"coding" : [{
"system" : "http://www.ncbi.nlm.nih.gov/nuccore",
"code" : "NT_007592.15"
}]
},
"windowStart" : 18130918,
"windowEnd" : 18143955,
"strand" : "watson"
},
"edit" : [{
"start" : 18139214,
"end" : 18139214,
"replacementSequence" : "A",
"replacedSequence" : "G"
}]
}]
}
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.