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

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

ARCHETYPE ID	openEHR-EHR-CLUSTER.genomic_insertion_variant.v1
Concept	Genomic insertion variant
Description	A human genetic sequence change where, compared to the genomic reference sequence, one or more nucleotides are inserted and where the insertion is not a copy of a sequence immediately 5'.
Use	Use to record the details about an 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 to record a change when the extra copy of a sequence detected is in tandem (directly 3’-flanking the original copy). Use the CLUSTER.genomic_duplication_variant archetype for this purpose.
Purpose	To record the details about an 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 - Insertion Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/insertion/
Copyright	© openEHR Foundation
Authors	Author name: Cecilia Mascia Organisation: CRS4, Italy Email: cecilia.mascia@crs4.it Date originally authored: 2017-02-23
Other Details Language	Author name: Cecilia Mascia Organisation: CRS4, Italy Email: cecilia.mascia@crs4.it Date originally authored: 2017-02-23
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 - Insertion Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/insertion/, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=98872A5FB3B08507F48CB34F51A3A8AA, build_uid=88521f3b-5e70-4f10-b137-6f7b0c49e6a2, revision=1.0.3}
Keywords	insertion, variation, genetic, genomic, variant, DNA, chromosome, mutation, nucleotide
Lifecycle	published
UID	d9f75b85-a5d0-4f62-80da-038c547a86c6
Language used	en
Citeable Identifier	1051.32.887
Revision Number	1.0.3
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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, Oslo University hospital, Norway, liv.laugen@ous-hf.no , subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={state=[], content=[], capabilities=[], relationships=[], activities=[], events=[], contacts=[], description=[], target=[], context=[], identities=[], protocol=[], other_participations=[], items=[ResourceSimplifiedHierarchyItem [path=/items[at0001], code=at0001, itemType=ELEMENT, level=1, text=Start position, description=The position of the first of the two flanking nucleotides., comment=For example: for a variant where the reference sequence 'AGTAGAGG' is changed to 'AGTAGatAGG', 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=The position of the last of the two flanking nucleotides., comment=For example: for a variant where the reference sequence 'AGTAGAGG' is changed to 'AGTAGatAGG', the end position is 6., uncommonOntologyItems=null, occurencesFormal=1..1, occurencesText=Mandatory, cardinalityFormal=null, cardinalityText=null, subCardinalityFormal=null, subCardinalityText=null, 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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=The position of the last of the two flanking nucleotides., comment=For example: for a variant where the reference sequence 'AGTAGAGG' is changed to 'AGTAGatAGG', the end position is 6., 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[at0006], code=at0006, itemType=ELEMENT, level=1, text=Inserted sequence, description=The inserted nucleotide or sequence., comment=For 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