Example of representing complex variants in MolecularSequence resource
{
"resourceType" : "MolecularSequence",
"id" : "sequence-complex-variant",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: MolecularSequence</b><a name=\"sequence-complex-variant\"> </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 "sequence-complex-variant" </p></div><p><b>identifier</b>: id:\u00a0?ngen-9?\u00a0(use:\u00a0OFFICIAL)</p><p><b>type</b>: dna</p><p><b>specimen</b>: <a href=\"broken-link.html\">Specimen/genetics-example1-somatic: Molecular Specimen ID: MLD45-Z4-1234</a></p><p><b>device</b>: <span>: 12 lead EKG Device Metric</span></p><p><b>performer</b>: <a href=\"organization-example.html\">Organization/hl7: HL7</a> "Health Level Seven International"</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>Strand</b></td></tr><tr><td>*</td><td>NC_000002.12 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (nuccore#NC_000002.12)</span></td><td>128273724</td><td>128273754</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>128273724</td><td>128273736</td><td>CTCATTGT</td><td>CTCCATTGCATGCGTT</td></tr></table></blockquote></div>"
},
"identifier" : [{
"use" : "official"
}],
"type" : "dna",
"specimen" : {
"reference" : "Specimen/genetics-example1-somatic",
"display" : "Molecular Specimen ID: MLD45-Z4-1234"
},
"device" : {
"display" : "12 lead EKG Device Metric"
},
"performer" : {
"reference" : "Organization/hl7",
"display" : "HL7"
},
"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" : "NC_000002.12"
}]
},
"windowStart" : 128273724,
"windowEnd" : 128273754,
"strand" : "watson"
},
"edit" : [{
"start" : 128273724,
"end" : 128273736,
"replacementSequence" : "CTCATTGT",
"replacedSequence" : "CTCCATTGCATGCGTT"
}]
}]
}
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.