| ARCHETYPE ID | openEHR-EHR-CLUSTER.genomic_deletion_insertion_variant.v1 |
|---|---|
| Concept | Genomic deletion-insertion variant |
| Description | A human genetic sequence change where, compared to a genomic reference sequence, one or more nucleotides are replaced by one or more other nucleotides and which is not a substitution, inversion or conversion. |
| Use | Use to record the details about a deletion-insertion variant of human DNA, observed in a genomic sequence. This archetype has been specifically designed to be used in the 'Structured variant' SLOT within the CLUSTER.genomic_variant_result archetype, but can also be used within other ENTRY or CLUSTER archetypes, where clinically appropriate. In the examples in this archetype, lower case nucleotides are only intended to highlight the changed positions of the DNA sequence. All definitions and examples in this archetype follow the HGVS nomenclature. |
| Misuse | Not to be used to record information about variants of non-human DNA, or any kind of RNA or protein. Not to be used for recording information about a variant where one nucleotide is replaced by one other nucleotide. This is a substitution, and the archetype CLUSTER.genomic_substitution_variant should be used for this purpose. Not to be used for recording information about two variants separated by one or more nucleotides, except when the two variants are separated by one nucleotide and they affect only one amino acid. |
| Purpose | To record the details about a deletion-insertion variant of human DNA, observed in a genomic sequence. |
| References | den Dunnen JT, Dalgleish R, Maglott DR, Hart RK, Greenblatt MS, McGowan-Jordan J, Roux AF, Smith T, Antonarakis SE, Taschner PE. HGVS Recommendations for the Description of Sequence Variants: 2016 Update. Hum Mutat. 2016 Jun;37(6):564-9. doi: 10.1002/humu.22981. Epub 2016 Mar 25. PubMed PMID: 26931183. Sequence Variant Nomenclature - DNA Recommendations - Deletion-insertion Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/delins/ |
| Copyright | © openEHR Foundation |
| Authors | Author name: Cecilia Mascia Organisation: CRS4, Italy Email: cecilia.mascia@crs4.it Date originally authored: 2017-02-24 |
| Other Details Language | Author name: Cecilia Mascia Organisation: CRS4, Italy Email: cecilia.mascia@crs4.it Date originally authored: 2017-02-24 |
| Other Details (Language Independent) |
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| Keywords | indel, variation, genetic, genomic, variant, delins, DNA, chromosome, mutation, nucleotide |
| Lifecycle | published |
| UID | 690722f9-b919-4c4d-9fe3-429a3b1373a9 |
| Language used | en |
| Citeable Identifier | 1246.145.734 |
| Revision Number | 1.0.3 |
| Archetype Concept Comment | For example: changing 'AGGCtcaTT' to 'AGGCcTT'. |
| items | |
| Start position | Start position: Position of the deleted nucleotide or the first nucleotide of the deleted range. For example: for a variant where the reference sequence 'AGGCtcaTT' is changed to 'AGGCcTT', the start position is 5. |
| End position | End position: Position of the last nucleotide of the deleted range. For example: for a variant where the reference sequence 'AGGCtcaTT' is changed to 'AGGCcTT', the end position is 7. |
| Deleted sequence | Deleted sequence: The deleted nucleotide or sequence. For example: for a variant where the reference sequence 'AGGCtcaTT' is changed to 'AGGCcTT', the deleted sequence is 'TCA'. |
| Inserted sequence | Inserted sequence: The inserted nucleotide or sequence. For example: for a variant where the reference sequence 'AGGCtcaTT' is changed to 'AGGCcTT', the inserted nucleotide is 'C'. |
| Reference sequence | Reference sequence: The sequence file used as a reference to describe this variant. Include: openEHR-EHR-CLUSTER.reference_ |
| Other contributors | Vebjørn Arntzen, Oslo University Hospital, Norway (openEHR Editor) Silje Ljosland Bakke, Helse Vest IKT AS, Norway (openEHR Editor) SB Bhattacharyya, Sudisa Consultancy Services, India Francesca Frexia, CRS4 - Center for advanced studies, research and development in Sardinia, Italy Gideon Giacomelli, Charité Berlin, Germany Heather Grain, Llewelyn Grain Informatics, Australia Evelyn Hovenga, EJSH Consulting, Australia Christina Jaeger-Schmidt, Heidelberg University Hospital, Germany Florian Kaercher, Charité Berlin, Germany Heather Leslie, Atomica Informatics, Australia (openEHR Editor) Cecilia Mascia, CRS4, Italy (openEHR Editor) Ian McNicoll, freshEHR Clinical Informatics, United Kingdom (openEHR Editor) Andrej Orel, Marand d.o.o., Slovenia Simon Schumacher, HiGHmed, Germany Natalia Strauch, Medizinische Hochschule Hannover, Germany Aurelie Tomczak, Uniklinikum Heidelberg, Germany Paolo Uva, CRS4, Italy Gianluigi Zanetti, CRS4, Italy |
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