OpenEHR Master CKM Mirror
Name
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'.
Comment
For example: changing 'AGTAGAGG' to 'AGTAGatAGG'.
Keywords
insertion
variation
genetic
genomic
variant
DNA
chromosome
mutation
nucleotide
Purpose
To record the details about an insertion variant of human DNA, observed in a genomic sequence.
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.
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.
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.
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/
Archetype Id
openEHR-EHR-CLUSTER.genomic_insertion_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
|
| Name | Card | Type | Description |
|---|---|---|---|
|
Start position
|
1..1 | DV_COUNT |
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.
|
|
End position
|
1..1 | DV_COUNT |
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.
|
|
Inserted sequence
|
0..1 | DV_TEXT |
The inserted nucleotide or sequence.
Comment
For example: for a variant where the reference sequence 'AGTAGAGG' is changed to 'AGTAGatAGG', the inserted sequence is 'AT'.
|
|
Reference sequence
|
0..* | Slot (Cluster) |
The sequence file used as a reference to describe this variant.
Slot
Slot
|
archetype (adl_version=1.4; uid=d9f75b85-a5d0-4f62-80da-038c547a86c6) openEHR-EHR-CLUSTER.genomic_insertion_variant.v1 concept [at0000] -- Genomic 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"] = <"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 \"Insertion Variante\" menschlicher DNA."> use = <"Verwenden Sie diesen Archetyp, um die Details einer Insertion 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 = <"Insertion", "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 sich die zusätzliche Kopie einer erkannten Sequenz im Tandem befindet (direkt 3'-flankierend zur Originalkopie). Verwenden Sie zu diesem Zweck den Archetyp CLUSTER.genomic_duplication_variant.)"> > ["nb"] = < language = <[ISO_639-1::nb]> purpose = <"For å registrere detaljene om en insersjonvariant i humant DNA, funnet i en genomisk sekvens."> use = <"Brukes for å registrere detaljene om en insersjonvariant 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 = <"base", "DNA", "gen", "genetisk", "insersjon", "mutasjon", "nukleinsyrer", "nukleotid", "sekvens", "variant", "variasjon"> misuse = <"Skal ikke brukes til å registrere informasjon om varianter av ikke-humant DNA, eller noen form for RNA eller protein Skal ikke brukes for å registrere en endring hvis en ekstra kopi av sekvensen er en tandem (har blitt satt direkte inn i 3' (-enden) av den originale sekvenskopien), bruk da heller arketypen CLUSTER.duplication_variant til dette formålet."> > ["en"] = < language = <[ISO_639-1::en]> purpose = <"To record the details about an insertion variant of human DNA, observed in a genomic sequence."> 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."> keywords = <"insertion", "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 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."> copyright = <"© openEHR Foundation"> > > lifecycle_state = <"published"> other_contributors = <"Vebjørn Arntzen, Oslo University Hospital, Norway (openEHR Editor)", "Silje Ljosland Bakke, Nasjonal IKT HF, 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 - 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"> > definition CLUSTER[at0000] matches { -- Genomic insertion variant items cardinality matches {3..*; ordered} matches { ELEMENT[at0001] matches { -- Start position value matches { DV_COUNT matches {*} } } ELEMENT[at0003] matches { -- End position value matches { DV_COUNT matches {*} } } ELEMENT[at0006] occurrences matches {0..1} matches { -- Inserted sequence value matches { DV_TEXT matches {*} } } allow_archetype CLUSTER[at0007] 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 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'."> comment = <"For example: changing 'AGTAGAGG' to 'AGTAGatAGG'."> > ["at0001"] = < 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."> > ["at0003"] = < 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."> > ["at0006"] = < text = <"Inserted sequence"> description = <"The inserted nucleotide or sequence."> comment = <"For example: for a variant where the reference sequence 'AGTAGAGG' is changed to 'AGTAGatAGG', the inserted sequence is 'AT'."> > ["at0007"] = < text = <"Reference sequence"> description = <"The sequence file used as a reference to describe this variant."> > > > ["nb"] = < items = < ["at0000"] = < text = <"Genetisk variant - insersjon"> description = <"En endring av den humane gensekvensen hvor det settes inn en eller flere nukleotider, og innsettingen ikke er en kopi av en sekvensens umiddelbare 5 '(-ende), sammenliknet med referansesekvensen. Engelsk: Insertion."> comment = <"For eksempel: endring av 'AGTAGAGG' til 'AGTAGatAGG'."> > ["at0001"] = < text = <"Startposisjon"> description = <"Posisjonen til det første av de to flankerende nukleotidene."> comment = <"For eksempel: for en variant hvor referansesekvensen 'AGTAGAGG' er endret til 'AGTAGatAGG', er startposisjonen 5."> > ["at0003"] = < text = <"Sluttposisjon"> description = <"Posisjonen til nukleotidet etter det siste innsatte nukleotidet."> comment = <"For eksempel: for en variant hvor referansesekvensen 'AGTAGAGG' er endret til 'AGTAGatAGG', er sluttposisjonen 6."> > ["at0006"] = < text = <"Innsatt sekvens"> description = <"Nukleotidet eller sekvensen som er innsatt."> comment = <"For eksempel: for en variant hvor referansesekvensen 'AGTAGAGG' er endret til 'AGTAGatAGG' er den insatte sekvensen 'AT'."> > ["at0007"] = < text = <"Referansesekvensen"> description = <"Sekvensfilen som har blitt brukt som en referanse for å beskrive varianten."> > > > ["de"] = < items = < ["at0000"] = < text = <"Genomic insertion variant"> description = <"Eine humangenetische Sequenzänderung, bei der im Vergleich zur genomischen Referenzsequenz ein oder mehrere Nukleotide eingefügt werden und bei der die Insertion keine Kopie einer Sequenz ist, die sofort 5' ist."> comment = <"For example: changing \"AGTAGAGG\" to \"AGTAGatAGG\"."> > ["at0001"] = < 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."> > ["at0003"] = < 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."> > ["at0006"] = < text = <"Inserted sequence"> description = <"The inserted nucleotide or sequence."> comment = <"For example: for a variant where the reference sequence \"AGTAGAGG\" is changed to \"AGTAGatAGG\", the inserted sequence is \"AT\"."> > ["at0007"] = < text = <"Reference sequence"> description = <"The sequence file used as a reference to describe this variant."> > > > >