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
AuthorsNom de l'autor: Cecilia Mascia
Organització: CRS4, Italy
Correu electrònic: cecilia.mascia@crs4.it
Data d'autor original: 2017-02-08
Other Details LanguageNom de l'autor: Cecilia Mascia
Organització: CRS4, Italy
Correu electrònic: cecilia.mascia@crs4.it
Data d'autor original: 2017-02-08
Other Details (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: 96CF5AA5A83A89FF4CCD34E3278102D1
  • Build Uid: d80acb5c-7ce4-4d47-991b-5e1eb8712f4d
  • Revision: 1.0.9
Keywordsgenetic findings, reference sequence, Genetic test, variant calling, genomic, variation
Lifecyclepublished
UID0d76b26d-8cbd-4e0d-a7ac-e83bf4dfcae9
Language useden
Citeable Identifier1380.146.155
Revision Number1.0.9
items
Reference genome assemblyReference genome assembly: The reference genome assembled as a representative model of the human genome.
Source nameSource name: The name of the data source containing the reference sequence.
Accession numberAccession number: A unique identifier to refer to a sequence record in a sequence repository.
Version numberVersion number: The version number of the data record of the reference sequence.
For example: 'hg38', 'hg19'.
URLURL: Network address.
Chromosome labelChromosome label: Chromosome identifier.
Elecció de:
  •  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
Other contributorsSilje 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
Translators
  • alemany: Natalia Strauch, Medizinische Hochschule Hannover, Strauch.Natalia@mh-hannover.de
  • suec: Therese Lindberg, Cambio CDS, therese.lindberg@cambio.se
  • Bokmål noruec: Vebjørn Arntzen, Liv Laugen,, Oslo University Hospital, Norway, ​Oslo University Hospital, Norway, varntzen@ous-hf.no, liv.laugen@ous-hf.no