Norwegian openEHR Repository
Name
Genomic duplication variant
Description
A human genetic sequence change where, compared to a genomic reference sequence, a copy of one or more nucleotides are inserted directly 3' of the original copy of that sequence.
Comment
For example: changing 'AGtagaGG' to 'AGtagatagaGG'.
Keywords
duplication
variation
genetic
genomic
variant
DNA
chromosome
mutation
nucleotide
Purpose
To record the details about a duplication variant of human DNA, observed in a genomic sequence.
Use
Use to record the details about a duplication 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.
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 there is no evidence that the extra copy of a sequence detected is in tandem (directly 3’-flanking the original copy). Use the CLUSTER.genomic_insertion_variant archetype for this purpose.
Not to be used to record a change when there is no evidence that the extra copy of a sequence detected is in tandem (directly 3’-flanking the original copy). Use the CLUSTER.genomic_insertion_variant archetype for this purpose.
References
Avgrenet fra: https://ckm.openehr.org/ckm/archetypes/1013.1.3752
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 - Duplication Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/duplication/
Archetype Id
openEHR-EHR-CLUSTER.genomic_duplication_variant.v1
Copyright
© openEHR Foundation
Licencing
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/.
Original Author
Cecilia Mascia
CRS4, Italy
CRS4, Italy
Date Originally Authored
2017-02-23
| Language | Details |
|---|---|
| German |
Aurelie Tomczak, Natalia Strauch
Institute of Pathology, University Hospital Heidelberg, Germany, Medizinische Hochschule Hannover
|
| Norwegian Bokmal |
Liv Laugen
Oslo University Hospital, Norway, Oslo University Hospital, Norway
|
| Name | Card | Type | Description |
|---|---|---|---|
|
Start position
|
1..1 | DV_COUNT |
Position of the duplicated nucleotide or the first nucleotide of the duplicated range.
Comment
For example: for a variant where the reference sequence 'AGtagaGG' is changed to 'AGtagatagaGG', the start position is 3.
|
|
End position
|
0..1 | DV_COUNT |
Position of the last nucleotide of the duplicated range.
Comment
For example: for a variant where the reference sequence 'AGtagaGG' is changed to 'AGtagatagaGG', the end position is 6.
|
|
Duplicated sequence
|
0..1 | DV_TEXT |
The duplicated nucleotide or sequence.
Comment
For example: for a variant where the reference sequence 'AGtagaGG' is changed to 'AGtagatagaGG', the duplicated sequence is 'TAGA'.
|
|
Reference sequence
|
0..* | Slot (Cluster) |
The sequence file used as a reference to describe this variant.
Slot
Slot
|
archetype (adl_version=1.4; uid=b419cf41-f7fa-422a-9817-6852e00ab9da) openEHR-EHR-CLUSTER.genomic_duplication_variant.v1 concept [at0000] -- Genomic duplication 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"] = <"Oslo University Hospital, Norway, 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"] = <"2017-02-23"> > details = < ["de"] = < language = <[ISO_639-1::de]> purpose = <"Zur Beschreibung der in einer Sequenz beobachteten \"Duplication variant\" menschlicher DNA."> use = <"Verwenden Sie diesen Archetyp, um die Details einer Duplication 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 = <"Duplikation", "Variation", "genetisch", "genomisch", "Variante", "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 einer Änderung verwenden, wenn keine Beweise dafür vorliegen, dass die zusätzliche Kopie einer erkannten Sequenz im Tandem liegt (direkt 3'-flankierend zur Originalkopie). Verwenden Sie zu diesem Zweck den Archetyp CLUSTER.genomic_insertion_variant. "> > ["nb"] = < language = <[ISO_639-1::nb]> purpose = <"For å registrere detaljene om en duplikasjonsvariant i humant DNA, funnet i en genomisk sekvens."> use = <"Brukes for å registrere detaljene om en duplikasjonsvariant 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 = <"duplisering", "duplication", "duplikasjon", "dup", "variasjon", "gen", "variant", "base", "DNA", "sekvens", "mutasjon", "nukleotid", "nukleinsyrer"> 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 en endring når det ikke er bevis for at den ekstra kopien av sekvensen er en tandem (har blitt satt direkte inn i 3' (-enden) av den originale sekvenskopien). Bruk heller arketypen CLUSTER.insertion_variant (Genetisk variant - insersjon) til dette."> > ["en"] = < language = <[ISO_639-1::en]> purpose = <"To record the details about a duplication variant of human DNA, observed in a genomic sequence."> use = <"Use to record the details about a duplication 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 = <"duplication", "variation", "genetic", "genomic", "variant", "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 to record a change when there is no evidence that the extra copy of a sequence detected is in tandem (directly 3’-flanking the original copy). Use the CLUSTER.genomic_insertion_variant archetype for this purpose."> 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)", "Francesca Frexia, CRS4, Italy", "Gideon Giacomelli, Charité Berlin, Germany", "Sjur Gjerald, Oslo University Hospital, Norway", "Christina Jaeger-Schmidt, Heidelberg University Hospital, Germany", "Florian Kaercher, Charité Berlin, Germany", "Liv Laugen, Oslo University Hospital, Norway, Norway", "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", "Aurelie Tomczak, Uniklinikum Heidelberg, Germany (openEHR Editor)", "Paolo Uva, CRS4, Italy", "Gianluigi Zanetti, CRS4, Italy", "Gunnar Houge, Haukeland University Hospital, Norway", "Gyri Aasland Gradek, Haukeland University Hospital, Norway", "Asbjørg Stray-Pedersen, Oslo University Hospital, Norway", "Toril Fagerheim, University Hospital of North Norway, Norway", "Camilla F. Skjelbred, Telemark HF Hospital, Norway", "Dag Erik Undlien, Oslo University Hospital, Norway", "Rune Østern, St Olavs Hospital, Norway"> 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"] = <"Avgrenet fra: https://ckm.openehr.org/ckm/archetypes/1013.1.3752 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 - Duplication Variant [Internet]. Human Genome Variation Society. [2019] - [cited 2020-02-26]. Available from: https://varnomen.hgvs.org/recommendations/DNA/variant/duplication/"> ["original_namespace"] = <"org.openehr"> ["original_publisher"] = <"openEHR Foundation"> ["custodian_namespace"] = <"org.openehr"> ["MD5-CAM-1.0.1"] = <"B5D9F2D8575ABDC15B30828F5A0597D0"> ["build_uid"] = <"e83638d6-7666-4bdb-8f97-c5c812b2fe9f"> ["revision"] = <"1.0.0"> > definition CLUSTER[at0000] matches { -- Genomic duplication variant items cardinality matches {1..*; 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 { -- Duplicated sequence value matches { DV_TEXT matches {*} } } allow_archetype CLUSTER[at0006] 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 duplication variant"> description = <"A human genetic sequence change where, compared to a genomic reference sequence, a copy of one or more nucleotides are inserted directly 3' of the original copy of that sequence."> comment = <"For example: changing 'AGtagaGG' to 'AGtagatagaGG'."> > ["at0001"] = < text = <"Start position"> description = <"Position of the duplicated nucleotide or the first nucleotide of the duplicated range."> comment = <"For example: for a variant where the reference sequence 'AGtagaGG' is changed to 'AGtagatagaGG', the start position is 3."> > ["at0003"] = < text = <"End position"> description = <"Position of the last nucleotide of the duplicated range."> comment = <"For example: for a variant where the reference sequence 'AGtagaGG' is changed to 'AGtagatagaGG', the end position is 6."> > ["at0005"] = < text = <"Duplicated sequence"> description = <"The duplicated nucleotide or sequence."> comment = <"For example: for a variant where the reference sequence 'AGtagaGG' is changed to 'AGtagatagaGG', the duplicated sequence is 'TAGA'."> > ["at0006"] = < text = <"Reference sequence"> description = <"The sequence file used as a reference to describe this variant."> > > > ["de"] = < items = < ["at0000"] = < text = <"Genomic duplication variant"> description = <"Eine humangenetische Sequenzänderung, bei der im Vergleich zu einer genomischen Referenzsequenz eine Kopie eines oder mehrerer Nukleotide direkt 3' der Originalkopie dieser Sequenz eingefügt wird."> comment = <"For example: changing \"AGtagaGG\" to \"AGtagatagaGG\"."> > ["at0001"] = < text = <"Start position"> description = <"Position of the duplicated nucleotide or the first nucleotide of the duplicated range."> comment = <"For example: for a variant where the reference sequence \"AGtagaGG\" is changed to \"AGtagatagaGG\", the start position is 3."> > ["at0003"] = < text = <"End position"> description = <"Position of the last nucleotide of the duplicated range."> comment = <"For example: for a variant where the reference sequence \"AGtagaGG\" is changed to \"AGtagatagaGG\", the end position is 6."> > ["at0005"] = < text = <"Duplicated sequence"> description = <"The duplicated nucleotide or sequence."> comment = <"For example: for a variant where the reference sequence \"AGtagaGG\" is changed to \"AGtagatagaGG\", the duplicated sequence is \"TAGA\"."> > ["at0006"] = < text = <"Reference sequence"> description = <"The sequence file used as a reference to describe this variant."> > > > ["nb"] = < items = < ["at0000"] = < text = <"Genetisk variant - duplikasjon"> description = <"En endring av den humane gensekvensen hvor en kopi av en eller flere nuklotider har blitt satt direkte inn i 3' (-enden) av den originale sekvenskopien, sammenliknet med referansesekvensen (tandem duplisering). Engelsk: duplication."> comment = <"For eksempel: endring av 'AGtagaGG' til 'AGtagatagaGG'."> > ["at0001"] = < text = <"Startposisjon"> description = <"Posisjonen til det dupliserte nukleotidet eller det første nukleotidet av det dupliserte området."> comment = <"For eksempel: for en variant hvor referansesekvensen 'AGtagaGG' er endret til 'AGtagatagaGG' er startposisjonen 3."> > ["at0003"] = < text = <"Sluttposisjon"> description = <"Posisjonen til det siste nukleotidet av det dupliserte området."> comment = <"For eksempel: for en variant hvor referansesekvensen 'AGtagaGG' er endret til 'AGtagatagaGG' er sluttposisjonen 6."> > ["at0005"] = < text = <"Duplisert sekvens"> description = <"Nukleotidet eller sekvensen som er duplisert."> comment = <"For eksempel: for en variant hvor referansesekvensen 'AGtagaGG' er endret til 'AGtagatagaGG' er den dupliserte nukleotiden 'TAGA'."> > ["at0006"] = < text = <"Referansesekvens"> description = <"Sekvensfilen som har blitt brukt som en referanse for å beskrive varianten."> > > > >