This page is part of the FHIR Specification (v5.0.0-ballot: FHIR R5 Ballot Preview). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions . Page versions: R5 R4B R4 R3
Clinical Genomics Work Group | Maturity Level: N/A | Standards Status: Informative | Compartments: Patient |
Raw XML (canonical form + also see XML Format Specification)
Example of representing complex variants in MolecularSequence resource (id = "sequence-complex-variant")
<?xml version="1.0" encoding="UTF-8"?> <MolecularSequence xmlns="http://hl7.org/fhir"> <id value="sequence-complex-variant"/> <text> <status value="generated"/> <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> </text> <identifier> <use value="official"/> </identifier> <type value="dna"/> <specimen> <reference value="Specimen/genetics-example1-somatic"/> <display value="Molecular Specimen ID: MLD45-Z4-1234"/> </specimen> <device> <display value="12 lead EKG Device Metric"/> </device> <performer> <reference value="Organization/hl7"/> <display value="HL7"/> </performer> <relative> <coordinateSystem> <coding> <system value="http://loinc.org"/> <code value="LA30100-4"/> <display value="0-based interval counting"/> </coding> </coordinateSystem> <startingSequence> <sequenceCodeableConcept> <coding> <system value="http://www.ncbi.nlm.nih.gov/nuccore"/> <code value="NC_000002.12"/> </coding> </sequenceCodeableConcept> <windowStart value="128273724"/> <windowEnd value="128273754"/> <strand value="watson"/> </startingSequence> <edit> <start value="128273724"/> <end value="128273736"/> <replacementSequence value="CTCATTGT"/> <replacedSequence value="CTCCATTGCATGCGTT"/> </edit> </relative> </MolecularSequence>
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.