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Clinical Genomics Work Group | Maturity Level: N/A | Standards Status: Informative | Compartments: Patient |
Raw JSON (canonical form + also see JSON Format Specification)
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: ?ngen-9? (OFFICIAL)</p><p><b>type</b>: dna</p><p><b>specimen</b>: <a href=\"todo.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.