ARCHETYPE Genomic deletion-insertion variant (openEHR-EHR-CLUSTER.genomic_deletion_insertion_variant.v1)

Name: Genomic deletion-insertion variant
License: http://creativecommons.org/licenses/by-sa/4.0/

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
OtherDetails Language Independent	{licence=This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/., custodian_organisation=openEHR Foundation, 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/, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=C976F7E7EE199950211D76C45FC16EF0, build_uid=b9615084-bbfc-41d2-9f3e-83686fbf5901, revision=1.0.3}
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
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(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, originalLanguage=en, translators= German: Aurelie Tomczak, Natalia Strauch, Institute of Pathology, University Hospital Heidelberg, Germany, Medizinische Hochschule Hannover, au.tomczak@yahoo.com, Strauch.Natalia@mh-hannover.de Norwegian Bokmål: Liv Laugen, OUS, Oslo University Hospital, Norway, liv.laugen@ous-hf.no , subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={relationships=[], source=[], capabilities=[], activities=[], details=[], context=[], ism_transition=[], other_participations=[], data=[], credentials=[], target=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0001], code=at0001, itemType=ELEMENT, level=1, text=Start position, description=Position of the deleted nucleotide or the first nucleotide of the deleted range., comment=For example: for a variant where the reference sequence 'AGGCtcaTT' is changed to 'AGGCcTT', the start position is 5., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0003], code=at0003, itemType=ELEMENT, level=1, text=End position, description=Position of the last nucleotide of the deleted range., comment=For example: for a variant where the reference sequence 'AGGCtcaTT' is changed to 'AGGCcTT', the end position is 7., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0005], code=at0005, itemType=ELEMENT, level=1, text=Deleted sequence, description=The deleted nucleotide or sequence., comment=For example: for a variant where the reference sequence 'AGGCtcaTT' is changed to 'AGGCcTT', the deleted sequence is 'TCA'., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0007], code=at0007, itemType=ELEMENT, level=1, text=Inserted sequence, description=The inserted nucleotide or sequence., comment=For example: for a variant where the reference sequence 'AGGCtcaTT' is changed to 'AGGCcTT', the inserted nucleotide is 'C'., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, 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occurencesText=Mandatory, cardinalityFormal=2.., cardinalityText=Minimum of 2 items (Cardinality: 2.., ordered), subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=null, extendedValues=null]}, addHierarchyItemsTo=items, currentHierarchyItemsForAdding=[ResourceSimplifiedHierarchyItem [path=/items[at0001], code=at0001, itemType=ELEMENT, level=1, text=Start position, description=Position of the deleted nucleotide or the first nucleotide of the deleted range., comment=For example: for a variant where the reference sequence 'AGGCtcaTT' is changed to 'AGGCcTT', the start position is 5., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0003], code=at0003, itemType=ELEMENT, level=1, text=End position, description=Position of the last nucleotide of the deleted range., comment=For example: for a variant where the reference sequence 'AGGCtcaTT' is changed to 'AGGCcTT', the end position is 7., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_COUNT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0005], code=at0005, itemType=ELEMENT, level=1, text=Deleted sequence, description=The deleted nucleotide or sequence., comment=For example: for a variant where the reference sequence 'AGGCtcaTT' is changed to 'AGGCcTT', the deleted sequence is 'TCA'., uncommonOntologyItems=null, occurencesFormal=0..1, occurencesText=Optional, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0007], code=at0007, itemType=ELEMENT, level=1, text=Inserted sequence, description=The inserted nucleotide or sequence., comment=For example: for a variant where the reference sequence 'AGGCtcaTT' is changed to 'AGGCcTT', the inserted nucleotide is 'C'., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=DV_TEXT, bindings=null, values=, extendedValues=null], ResourceSimplifiedHierarchyItem [path=/items[at0008], code=at0008, itemType=SLOT, level=1, text=Reference sequence, description=The sequence file used as a reference to describe this variant., comment=null, uncommonOntologyItems=null, occurencesFormal=0.., occurencesText=Optional, repeating, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, dataType=CLUSTER, bindings=null, values=Include:* openEHR-EHR-CLUSTER.reference_sequence.v1 and 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