ARCHETYPE Genomic deletion variant (openEHR-EHR-CLUSTER.genomic_deletion_variant.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.genomic_deletion_variant.v0
ConceptGenomic deletion variant
DescriptionA human sequence change where, compared to a genomic reference sequence, one or more nucleotides are not present (deleted).
UseUse to record the details about a deletion 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.genetic_variant 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.
MisuseNot to be used to record information about variants of non-human DNA, or any kind of RNA or protein.
PurposeTo record the details about a deletion variant of human DNA, observed in a genomic sequence.
Referencesden 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 Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/deletion/
Copyright© openEHR Foundation
AuthorsAuthor name: Cecilia Mascia
Organisation: CRS4, Italy
Email: cecilia.mascia@crs4.it
Date originally authored: 2017-02-23
Other Details LanguageAuthor 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 - Deletion Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/deletion/, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=00BA71A606D8A549E1426432880E862A, build_uid=cca91018-2d4c-49c6-8b70-fe718bb091e0, revision=0.0.1-alpha}
Keywordsdeletion, variation, genetic, genomic, variant
Lifecyclein_development
UIDe1dc8400-cabb-4eb3-ba40-fa95fa7a4a33
Language useden
Citeable Identifier1246.145.739
Revision Number0.0.1-alpha
AllArchetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=A human sequence change where, compared to a genomic reference sequence, one or more nucleotides are not present (deleted)., archetypeConceptComment=For example: changing 'AGAAtCACA' to 'AGAA_CACA'., otherContributors=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, originalLanguage=en, translators=German: Aurelie Tomczak, Institute of Pathology, University Hospital Heidelberg, Germany, au.tomczak@yahoo.com
Norwegian Bokmål: Liv Laugen, ​Oslo University Hospital, Norway, liv.laugen@ous-hf.no
, subjectOfData=unconstrained, archetypeTranslationTree=null, topLevelToAshis={events=[], source=[], contacts=[], content=[], details=[], description=[], ism_transition=[], provider=[], activities=[], target=[], identities=[], data=[], state=[], other_participations=[], capabilities=[], context=[], credentials=[], 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 'AGAatcACA' is changed to 'AGA___ACA' the start position is 4., 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[at0005], code=at0005, 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 'AGAatcACA' is changed to 'AGA___ACA' the end position is 6., 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[at0008], code=at0008, itemType=ELEMENT, level=1, text=Deleted sequence, description=The deleted nucleotide or sequence., comment=For example: for a variant where the reference sequence 'AGAatcACA' is changed to 'AGA___ACA' the deleted sequence is 'ATC'., 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[at0009], code=at0009, 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:
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