archetype (adl_version=1.4; uid=690722f9-b919-4c4d-9fe3-429a3b1373a9)
	openEHR-EHR-CLUSTER.genomic_deletion_insertion_variant.v1

concept
	[at0000]	-- Genomic deletion-insertion variant
language
	original_language = <[ISO_639-1::en]>
	translations = <
		["de"] = <
			language = <[ISO_639-1::de]>
			author = <
				["name"] = <"Aurelie Tomczak, Natalia Strauch">
				["organisation"] = <"Institute of Pathology, University Hospital Heidelberg, Germany, Medizinische Hochschule Hannover">
				["email"] = <"au.tomczak@yahoo.com, Strauch.Natalia@mh-hannover.de">
			>
		>
		["nb"] = <
			language = <[ISO_639-1::nb]>
			author = <
				["name"] = <"Liv Laugen">
				["organisation"] = <"OUS, ​Oslo University Hospital, Norway">
				["email"] = <"liv.laugen@ous-hf.no">
			>
		>
	>
description
	original_author = <
		["name"] = <"Cecilia Mascia">
		["organisation"] = <"CRS4, Italy">
		["email"] = <"cecilia.mascia@crs4.it">
		["date"] = <"2017-02-24">
	>
	details = <
		["de"] = <
			language = <[ISO_639-1::de]>
			purpose = <"Zur Beschreibung der in einer Sequenz beobachteten \"Deletion-insertion variant\" menschlicher DNA.">
			use = <"Verwenden Sie diesen Archetyp, um die Details einer Deletions-Insertions-Variante menschlicher DNA darzustellen, die in einer genomischen Sequenz beobachtet wurde.

Dieser Archetyp wurde speziell für die Verwendung im SLOT \"Structured variant\" innerhalb des Archetyps CLUSTER.genomic_variant_result entwickelt, kann jedoch auch in anderen ENTRY- oder CLUSTER-Archetypen verwendet werden, sofern dies klinisch angemessen ist.

In den Beispielen in diesem Archetyp sollen Nukleotide in Kleinbuchstaben nur die veränderten Positionen der DNA-Sequenz hervorheben.

Alle Definitionen und Beispiele in diesem Archetyp folgen den HGVS-Standard.">
			keywords = <"Indel", "Variation", "genetisch", "genomisch", "Variante", "Delins", "DNA", "Chromosom", "Mutation", "Nukleotid">
			misuse = <"Nicht zur Darstellung von Informationen über Varianten nicht-menschlicher DNA oder jeglicher Art von RNA oder Protein verwenden.

Nicht zur Darstellung von Informationen über eine Variante verwenden, bei der ein Nukleotid durch ein anderes Nukleotid ersetzt wird. Dies ist eine Substitution und für diesen Zweck sollte der Archetyp CLUSTER.genomic_substitution_variant verwendet werden.

Nicht zur Darstellung von Informationen über zwei durch ein oder mehrere Nukleotide getrennte Varianten zu verwenden, es sei denn, die beiden Varianten sind durch ein Nukleotid getrennt und betreffen nur eine Aminosäure.">
		>
		["nb"] = <
			language = <[ISO_639-1::nb]>
			purpose = <"For å registrere detaljene om en delesjon-insersjon (delin) variant i humant DNA, funnet i en genomisk sekvens.">
			use = <"Brukes for å registrere detaljene om en delesjon-insersjon (delin) variant i humant DNA, funnet i en genomisk sekvens.

Denne arketypen har blitt laget for å brukes i SLOT'et \"Strukturert variantbeskrivelse\" i arketypen CLUSTER.genomic_variant_result (Genetisk variant resultat). Den kan også brukes i andre ENTRY- eller CLUSTER-arketyper der det er klinisk hensiktsmessig.

I eksemplene i denne arketypen er det brukt små bokstaver på nukleotidene for å markere endringen/-e i DNA-sekvensen.
Alle definisjoner og eksempler i denne arketypen følger HGVS-nomenklaturen.">
			keywords = <"indel", "delin", "variasjon", "genetisk", "genom", "deletion", "insertion", "base", "sekvens", "mutasjon", "gen", "kromosom", "nukleinsyrer", "nukleotid", "DNA">
			misuse = <"Skal ikke brukes til å registrere informasjon om varianter av ikke-humant DNA, eller noen form for RNA eller protein.

Skal ikke brukes til å registrere informasjon om en variant der ett nukleotid erstattes av et annet nukleotid da dette er en substitusjon og arketypen CLUSTER.substitution_variant skal brukes til dette formålet.

Skal ikke brukes til å registrere informasjon der to varianter blir atskilt med en eller flere nukleotider, bortsett fra når de to variantene er atskilt med ett nukleotid og de bare påvirker en aminosyre.">
		>
		["en"] = <
			language = <[ISO_639-1::en]>
			purpose = <"To record the details about a deletion-insertion variant of human DNA, observed in a genomic sequence.">
			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.">
			keywords = <"indel", "variation", "genetic", "genomic", "variant", "delins", "DNA", "chromosome", "mutation", "nucleotide">
			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.">
			copyright = <"© openEHR Foundation">
		>
	>
	lifecycle_state = <"published">
	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">
	other_details = <
		["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">
	>

definition
	CLUSTER[at0000] matches {    -- Genomic deletion-insertion variant
		items cardinality matches {2..*; ordered} matches {
			ELEMENT[at0001] matches {    -- Start position
				value matches {
					DV_COUNT matches {*}
				}
			}
			ELEMENT[at0003] occurrences matches {0..1} matches {    -- End position
				value matches {
					DV_COUNT matches {*}
				}
			}
			ELEMENT[at0005] occurrences matches {0..1} matches {    -- Deleted sequence
				value matches {
					DV_TEXT matches {*}
				}
			}
			ELEMENT[at0007] matches {    -- Inserted sequence
				value matches {
					DV_TEXT matches {*}
				}
			}
			allow_archetype CLUSTER[at0008] occurrences matches {0..*} matches {    -- Reference sequence
				include
					archetype_id/value matches {/openEHR-EHR-CLUSTER\.reference_sequence(-[a-zA-Z0-9_]+)*\.v1/}
			}
		}
	}


ontology
	term_definitions = <
		["en"] = <
			items = <
				["at0000"] = <
					text = <"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.">
					comment = <"For example: changing 'AGGCtcaTT' to 'AGGCcTT'.">
				>
				["at0001"] = <
					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.">
				>
				["at0003"] = <
					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.">
				>
				["at0005"] = <
					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'.">
				>
				["at0007"] = <
					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'.">
				>
				["at0008"] = <
					text = <"Reference sequence">
					description = <"The sequence file used as a reference to describe this variant.">
				>
			>
		>
		["nb"] = <
			items = <
				["at0000"] = <
					text = <"Genetisk variant - delesjon-insersjon">
					description = <"En endring i DNA-sekvensen hvor en eller flere nukleotider erstattes av en eller flere nukleotider, og som verken er en substitusjon, inversjon eller genkonversjon Også kalt DELIN variant. Engelsk: deletion-insertion.">
					comment = <"For eksempel: erndring av 'AGGCtcaTT' til 'AGGCcTT'.">
				>
				["at0001"] = <
					text = <"Startposisjon">
					description = <"Posisjonen til det slettede nukleotidet eller det første nukleotidet i det slettede området.">
					comment = <"For eksempel: for en variant hvor referansesekvensen 'AGGCtcaTT' har blitt endret til 'AGGCcTT' er startposisjonen 5.">
				>
				["at0003"] = <
					text = <"Sluttposisjon">
					description = <"Posisjonen til det siste nukleotidet i det slettede området.">
					comment = <"For eksempel: for en variant hvor referansesekvensen 'AGGCtcaTT' har blitt endret til 'AGGCcTT' er sluttposisjonen 7.">
				>
				["at0005"] = <
					text = <"Slettet sekvens">
					description = <"Nukleotidet eller nukleotidesekvensen som er fjernet.">
					comment = <"For eksempel: for en variant hvor referansesekvensen 'AGGCtcaTT' har blitt endret til 'AGGCcTT' er den slettede nukleotidesekvensen 'TCA'.">
				>
				["at0007"] = <
					text = <"Innsatte sekvens">
					description = <"Nukleotidet eller nukleotidesekvensen som er satt inn/lagt til.">
					comment = <"For eksempel: for en variant hvor referansesekvensen 'AGGCtcaTT' har blitt endret til 'AGGCcTT' er det insatte nukleotidet 'C'.">
				>
				["at0008"] = <
					text = <"Referansesekvens">
					description = <"Sekvensfilen som har blitt brukt som en referanse for å beskrive varianten.">
				>
			>
		>
		["de"] = <
			items = <
				["at0000"] = <
					text = <"Genomic deletion-insertion variant">
					description = <"Eine menschliche genetische Sequenzänderung, bei der im Vergleich zu einer genomischen Referenzsequenz ein oder mehrere Nukleotide durch ein oder mehrere andere Nukleotide ersetzt werden und die keine Substitution, Inversion oder Umwandlung darstellt.">
					comment = <"For example: changing \"AGGCtcaTT\" to \"AGGCcTT\".">
				>
				["at0001"] = <
					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.">
				>
				["at0003"] = <
					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.">
				>
				["at0005"] = <
					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 nucleotides are \"TCA\".">
				>
				["at0007"] = <
					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\".">
				>
				["at0008"] = <
					text = <"Reference sequence">
					description = <"The sequence file used as a reference to describe this variant.">
				>
			>
		>
	>