ARCHETYPE Sequencing assay (openEHR-EHR-CLUSTER.sequencing_assay.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.sequencing_assay.v0
ConceptSequencing assay
DescriptionAn assay that uses sequencing technology to infer the sequence of a nucleic acid (DNA, RNA).
UseUse to record details of the performed sequencing analysis including a list of all tested genes if panel sequencing was performed. One or more instances of this archetype may be nested within the 'Testing details' SLOT in the OBSERVATION.laboratory_test_result.
MisuseUsed only to document the analysis protocol but not to document the results of the sequence analysis. The results are documented with the archetype 'CLUSTER.genomic_variant_result'.
PurposeTo record details of the performed sequencing analysis including a list of all tested genes if panel sequencing was performed.
ReferencesSequencing assay definition adapted from Ontology for Biomedical Investigations term. Available from: http://purl.obolibrary.org/obo/OBI_0600047
Copyright© HiGHmed, openEHR Foundation
AuthorsAuthor name: Aurelie Tomczak
Organisation: Institute of Pathology, University Hospital Heidelberg
Email: au.tomczak@yahoo.com
Date originally authored: 2019-06-24
Other Details LanguageAuthor name: Aurelie Tomczak
Organisation: Institute of Pathology, University Hospital Heidelberg
Email: au.tomczak@yahoo.com
Date originally authored: 2019-06-24
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: Sequencing assay definition adapted from Ontology for Biomedical Investigations term. Available from: http://purl.obolibrary.org/obo/OBI_0600047
  • Original Namespace: org.openehr
  • Original Publisher: openEHR Foundation
  • Custodian Namespace: org.openehr
  • MD5-CAM-1.0.1: DF6286EF2822D432D92AE88D5CC61E1B
  • Build Uid: a700a9b2-39d0-4c48-938e-5173ac39140a
  • Revision: 0.0.1-alpha
KeywordsSequencing, Genomics, Panel, Assay, Pathology, Sequencing analysis, Panel sequencing, Gene, Specimen
Lifecyclein_development
UID80b7cd2c-11f8-429f-80a4-5c341a5b816f
Language useden
Citeable Identifier1013.1.4256
Revision Number0.0.1-alpha
items
Sequencing typeSequencing type: Name of the technology used for sequencing analysis.
For example: WES, WGS, Gene panel, RNA sequencing, Fusion panel. Coding with an external terminology is preferred, where possible.
Sequencing deviceSequencing device: The technology platform used to perform nucleic acid sequencing.
Include:
openEHR-EHR-CLUSTER.device.v1 and specialisations
Bioinformatic analysisBioinformatic analysis: Structured details about the bioinformatic analysis workflow steps or the protocols that is used (e.g., devices, software, pipelines).
This slot can be used to record tools used to perform the different steps of the analysis (e.g., alignment, annotation, filtration, preprocessing, QC, variant calling) or whole pipelines. Alignment, Annotation, Filtration, Preprocessing, QC, Variant Calling
Include:
openEHR-EHR-CLUSTER.knowledge_base_reference.v1 and specialisations or
openEHR-EHR-CLUSTER.device.v1 and specialisations
Reference genomeReference genome: Structured details about the specific version of the human sequence assembly used for annotation.
For example: 'GCF_000001405.38'. Source name: 'NCBI'. Accession number: 'GCF_000001405'. Version number: 'GCF_000001405.38'. URL: 'https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.38/'.
Include:
openEHR-EHR-CLUSTER.reference_sequence.v1 and specialisations
Kit nameKit name: Name of the kit used for the experiment.
For example Oncomine Comprehensive Panel V3.
Nucleic acidNucleic acid: Type of nucleic acid used for sequencing, e.g. DNA, RNA or cf-DNA.
Choice of:
  •  Text
  •  Coded Text
    • DNA
    • RNA
    • cf-DNA
Tested GeneTested Gene: List of all tested genes, if panel sequencing was performed.
Gene symbolGene symbol: The official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name.
Gene reference sequenceGene reference sequence: Structured details on the reference sequence of the gene.
This slot is repeating to allow the description of the reference sequence using different vocabularies as source (e.g., RefSeq and Ensembl)
Include:
openEHR-EHR-CLUSTER.reference_sequence.v1 and specialisations
Tested RegionTested Region: If panel sequencing was performed, this cluster is used to report the region(s) of interest for sequencing studies as one genomic range that identifies the parts of the reference sequence that are sequenced.
Chromosome labelChromosome label: The chromosome of the tested region.
Choice of:
  •  Text
  •  Coded Text
    • Chromosome 1 [Chromosome 1.]
      [LOINC(2.80)::LA21254-0]
    • Chromosome 2 [Chromosome 2.]
      [LOINC(2.80)::LA21255-7]
    • Chromosome 3 [Chromosome 3.]
      [LOINC(2.80)::LA21256-5]
    • Chromosome 4 [Chromosome 4.]
      [LOINC(2.80)::LA21257-3]
    • Chromosome 5 [Chromosome 5.]
      [LOINC(2.80)::LA21258-1]
    • Chromosome 6 [Chromosome 6.]
      [LOINC(2.80)::LA21259-9]
    • Chromosome 7 [Chromosome 7.]
      [LOINC(2.80)::LA21260-7]
    • Chromosome 8 [Chromosome 8.]
      [LOINC(2.80)::LA21261-5]
    • Chromosome 9 [Chromosome 9.]
      [LOINC(2.80)::LA21262-3]
    • Chromosome 10 [Chromosome 10.]
      [LOINC(2.80)::LA21263-1]
    • Chromosome 11 [Chromosome 11.]
      [LOINC(2.80)::LA21264-9]
    • Chromosome 12 [Chromosome 12.]
      [LOINC(2.80)::LA21265-6]
    • Chromosome 13 [Chromosome 13.]
      [LOINC(2.80)::LA21266-4]
    • Chromosome 14 [Chromosome 14.]
      [LOINC(2.80)::LA21267-2]
    • Chromosome 15 [Chromosome 15.]
      [LOINC(2.80)::LA21268-0]
    • Chromosome 16 [Chromosome 16.]
      [LOINC(2.80)::LA21269-8]
    • Chromosome 17 [Chromosome 17.]
      [LOINC(2.80)::LA21270-6]
    • Chromosome 18 [Chromosome 18.]
      [LOINC(2.80)::LA21271-4]
    • Chromosome 19 [Chromosome 19.]
      [LOINC(2.80)::LA21272-2]
    • Chromosome 20 [Chromosome 20.]
      [LOINC(2.80)::LA21273-0]
    • Chromosome 21 [Chromosome 21.]
      [LOINC(2.80)::LA21274-8]
    • Chromosome 22 [Chromosome 22.]
      [LOINC(2.80)::LA21275-5]
    • Chromosome X [Chromosome X.]
      [LOINC(2.80)::LA21276-3]
    • Chromosome Y [Chromosome Y.]
      [LOINC(2.80)::LA21277-1]
StartStart: Start position of the tested region.
EndEnd: End position of the tested region.
Reference sequence of regionReference sequence of region: Structured details on the reference sequence of the region.
Include:
openEHR-EHR-CLUSTER.reference_sequence.v1 and specialisations
ExtensionsExtensions: Additional details to be captured.
Include:
All not explicitly excluded archetypes
CommentComment: Comment on the sequencing assay that was not captured in other fields.
Other contributorsSimon Schumacher, HiGHmed, Germany
Christina Jaeger-Schmidt, Heidelberg University Hospital, Germany
Gideon Giacomelli, Charité Berlin, Germany
Florian Kaercher, Charité Berlin, Germany
Heather Leslie, Atomica Informatics, Australia (openEHR Editor)
Ian McNicoll, freshEHR Clinical Informatics, United Kingdom (openEHR Editor)
Silje Ljosland Bakke, Nasjonal IKT HF, Norway (openEHR Editor)
Francesca Frexia, CRS4 - Center for advanced studies, research and development in Sardinia, Italy
Cecilia Mascia, CRS4, Italy (openEHR Editor)
Paolo Uva, CRS4, Italy
Gianluigi Zanetti, CRS4, Italy
Translators
  • German: Aurelie Tomczak, Institute of Pathology, University Hospital Heidelberg, Uniklinikum Heidelberg, au.tomczak@yahoo.com, aurelie.tomczak@med.uni-heidelberg.de
  • Norwegian Bokmål: Liv Laugen, Vebjørn Arntzen, ​Oslo University Hospital, Norway, liv.laugen@ous-hf.no, varntzen@ous-hf.no