ARCHETYPE Reference sequence (openEHR-EHR-CLUSTER.reference_sequence.v1)

ARCHETYPE IDopenEHR-EHR-CLUSTER.reference_sequence.v1
ConceptReference sequence
DescriptionA sequence file that is used as a reference to describe genetic variants that are present in an analysed sequence.
UseThis archetype has been specifically designed to be used in the 'Reference Genome' and in the 'Transcript reference sequence' SLOTs within the CLUSTER.genomic_variant_result archetype and in the 'Reference sequence' SLOT within other specific genetic variant archetypes, such as the CLUSTER.genomic_insertion_variant and the CLUSTER.genomic_deletion_variant. Itt can also be used within other ENTRY or CLUSTER archetypes, where clinically appropriate.
PurposeTo record details about the reference sequence used to describe variants.
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.
Copyright© openEHR Foundation
AuthorsAuthor name: Cecilia Mascia
Organisation: CRS4, Italy
Email: cecilia.mascia@crs4.it
Date originally authored: 2017-02-08
Other Details LanguageAuthor name: Cecilia Mascia
Organisation: CRS4, Italy
Email: cecilia.mascia@crs4.it
Date originally authored: 2017-02-08
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., original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=A435C094BF5B5FE9FD6F95D477E4A4AB, build_uid=9735cea1-302d-47d4-9d0f-02827743873f, revision=1.0.8}
Keywordsgenetic findings, reference sequence, Genetic test, variant calling, genomic, variation
Lifecyclepublished
UID0d76b26d-8cbd-4e0d-a7ac-e83bf4dfcae9
Language useden
Citeable Identifier1246.145.400
Revision Number1.0.8
AllArchetype [runtimeNameConstraintForConceptName=null, archetypeConceptBinding=null, archetypeConceptDescription=A sequence file that is used as a reference to describe genetic variants that are present in an analysed sequence., archetypeConceptComment=null, otherContributors=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
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
Aurelie Tomczak, Uniklinikum Heidelberg, Germany
Paolo Uva, CRS4, Italy
Gianluigi Zanetti, CRS4, Italy, originalLanguage=en, translators=German: Natalia Strauch, Medizinische Hochschule Hannover, Strauch.Natalia@mh-hannover.de
Norwegian Bokmål: Vebjørn Arntzen, Liv Laugen,, Oslo University Hospital, Norway, ​Oslo University Hospital, Norway, varntzen@ous-hf.no, liv.laugen@ous-hf.no
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  •  Coded Text
    • Chromosome 1 [Chromosome 1.]
      [LOINC(2.65)::LA21254-0]
    • Chromosome 2 [Chromosome 2.]
      [LOINC(2.65)::LA21255-7]
    • Chromosome 3 [Chromosome 3.]
      [LOINC(2.65)::LA21256-5]
    • Chromosome 4 [Chromosome 4.]
      [LOINC(2.65)::LA21257-3]
    • Chromosome 5 [Chromosome 5.]
      [LOINC(2.65)::LA21258-1]
    • Chromosome 6 [Chromosome 6.]
      [LOINC(2.65)::LA21259-9]
    • Chromosome 7 [Chromosome 7.]
      [LOINC(2.65)::LA21260-7]
    • Chromosome 8 [Chromosome 8.]
      [LOINC(2.65)::LA21261-5]
    • Chromosome 9 [Chromosome 9.]
      [LOINC(2.65)::LA21262-3]
    • Chromosome 10 [Chromosome 10.]
      [LOINC(2.65)::LA21263-1]
    • Chromosome 11 [Chromosome 11.]
      [LOINC(2.65)::LA21264-9]
    • Chromosome 12 [Chromosome 12.]
      [LOINC(2.65)::LA21265-6]
    • Chromosome 13 [Chromosome 13.]
      [LOINC(2.65)::LA21266-4]
    • Chromosome 14 [Chromosome 14.]
      [LOINC(2.65)::LA21267-2]
    • Chromosome 15 [Chromosome 15.]
      [LOINC(2.65)::LA21268-0]
    • Chromosome 16 [Chromosome 16.]
      [LOINC(2.65)::LA21269-8]
    • Chromosome 17 [Chromosome 17.]
      [LOINC(2.65)::LA21270-6]
    • Chromosome 18 [Chromosome 18.]
      [LOINC(2.65)::LA21271-4]
    • Chromosome 19 [Chromosome 19.]
      [LOINC(2.65)::LA21272-2]
    • Chromosome 20 [Chromosome 20.]
      [LOINC(2.65)::LA21273-0]
    • Chromosome 21 [Chromosome 21.]
      [LOINC(2.65)::LA21274-8]
    • Chromosome 22 [Chromosome 22.]
      [LOINC(2.65)::LA21275-5]
    • Chromosome X [Chromosome X.]
      [LOINC(2.65)::LA21276-3]
    • Chromosome Y [Chromosome Y.]
      [LOINC(2.65)::LA21277-1]
  •  Text
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  •  Coded Text
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    • Chromosome 2 [Chromosome 2.]
      [LOINC(2.65)::LA21255-7]
    • Chromosome 3 [Chromosome 3.]
      [LOINC(2.65)::LA21256-5]
    • Chromosome 4 [Chromosome 4.]
      [LOINC(2.65)::LA21257-3]
    • Chromosome 5 [Chromosome 5.]
      [LOINC(2.65)::LA21258-1]
    • Chromosome 6 [Chromosome 6.]
      [LOINC(2.65)::LA21259-9]
    • Chromosome 7 [Chromosome 7.]
      [LOINC(2.65)::LA21260-7]
    • Chromosome 8 [Chromosome 8.]
      [LOINC(2.65)::LA21261-5]
    • Chromosome 9 [Chromosome 9.]
      [LOINC(2.65)::LA21262-3]
    • Chromosome 10 [Chromosome 10.]
      [LOINC(2.65)::LA21263-1]
    • Chromosome 11 [Chromosome 11.]
      [LOINC(2.65)::LA21264-9]
    • Chromosome 12 [Chromosome 12.]
      [LOINC(2.65)::LA21265-6]
    • Chromosome 13 [Chromosome 13.]
      [LOINC(2.65)::LA21266-4]
    • Chromosome 14 [Chromosome 14.]
      [LOINC(2.65)::LA21267-2]
    • Chromosome 15 [Chromosome 15.]
      [LOINC(2.65)::LA21268-0]
    • Chromosome 16 [Chromosome 16.]
      [LOINC(2.65)::LA21269-8]
    • Chromosome 17 [Chromosome 17.]
      [LOINC(2.65)::LA21270-6]
    • Chromosome 18 [Chromosome 18.]
      [LOINC(2.65)::LA21271-4]
    • Chromosome 19 [Chromosome 19.]
      [LOINC(2.65)::LA21272-2]
    • Chromosome 20 [Chromosome 20.]
      [LOINC(2.65)::LA21273-0]
    • Chromosome 21 [Chromosome 21.]
      [LOINC(2.65)::LA21274-8]
    • Chromosome 22 [Chromosome 22.]
      [LOINC(2.65)::LA21275-5]
    • Chromosome X [Chromosome X.]
      [LOINC(2.65)::LA21276-3]
    • Chromosome Y [Chromosome Y.]
      [LOINC(2.65)::LA21277-1]
  •  Text
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