ISO_639-1 en false 2019-06-24 Aurelie Tomczak Institute of Pathology, University Hospital Heidelberg au.tomczak@yahoo.com Simon 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 in_development 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/. openEHR Foundation Sequencing assay definition adapted from Ontology for Biomedical Investigations term. Available from: http://purl.obolibrary.org/obo/OBI_0600047 org.openehr openEHR Foundation org.openehr DF6286EF2822D432D92AE88D5CC61E1B a700a9b2-39d0-4c48-938e-5173ac39140a 0.0.1-alpha

ISO_639-1 de Zur detaillierten Darstellung der Sequenzierungsanalyse an einer Probe inklusive der Aufzählung aller untersuchten Gene bei einer Panelsequenzierung. Sequenzierung Genomics Assay Panel Pathologie Sequenzierungsanalyse Panelsequenzierung Gene Probe Zur detaillierten Darstellung der Sequenzierungsanalyse an einer Probe inklusive der Aufzählung aller untersuchten Gene bei einer Panelsequenzierung. Eine oder mehrere Instanzen dieses Archetyps können im SLOT "Testdaten" in "OBSERVATION.laboratory_test_result" verschachtelt sein. *Used 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'. (en) © HiGHmed, openEHR Foundation

ISO_639-1 nb For å registrere detaljer om en gensekvensanalyse / genanalyse, inkludert en liste over alle testede gener dersom en genpaneltest ble utført. Sekvensere Genomikk Assay Panel Patologi Sekvenseringsanalyse Panelsekvensering Gen DNA Probe Nuklotid Nestegenerasjonssekvensering Bruk for å registrere detaljer om en gensekvensanalyse /genanalyse, inkludert en liste over alle testede gener hvis en genpaneltest ble utført. En eller flere forekomster av denne arketypen kan nøstes i SLOTet "Undersøkelsesdetaljer" i arketypen "OBSERVATION.laboratory_test_result" (Laboratorieresultat). *Used 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'. (en)

ISO_639-1 en To record details of the performed sequencing analysis including a list of all tested genes if panel sequencing was performed. Sequencing Genomics Panel Assay Pathology Sequencing analysis Panel sequencing Gene Specimen Use 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. Used 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'. © HiGHmed, openEHR Foundation

ISO_639-1 de Aurelie Tomczak Institute of Pathology, University Hospital Heidelberg, Uniklinikum Heidelberg au.tomczak@yahoo.com, aurelie.tomczak@med.uni-heidelberg.de ISO_639-1 nb Liv Laugen, Vebjørn Arntzen ​Oslo University Hospital, Norway liv.laugen@ous-hf.no, varntzen@ous-hf.no 80b7cd2c-11f8-429f-80a4-5c341a5b816f openEHR-EHR-CLUSTER.sequencing_assay.v0 1.4 at0000 CLUSTER true false true 0 at0000 items true true false false 1 1 ELEMENT true true false false 1 1 at0001 value true true false false 0 1 DV_TEXT true true false false 1 1 CLUSTER true false true 0 at0036 archetype_id/value matches {/openEHR-EHR-CLUSTER\.device(-[a-zA-Z0-9_]+)*\.v1/} Boolean 2007 false String archetype_id/value attribute C_STRING openEHR-EHR-CLUSTER\.device(-[a-zA-Z0-9_]+)*\.v1 constraint CLUSTER true false true 0 at0039 archetype_id/value matches {/openEHR-EHR-CLUSTER\.knowledge_base_reference(-[a-zA-Z0-9_]+)*\.v1|openEHR-EHR-CLUSTER\.device(-[a-zA-Z0-9_]+)*\.v1/} Boolean 2007 false String archetype_id/value attribute C_STRING openEHR-EHR-CLUSTER\.knowledge_base_reference(-[a-zA-Z0-9_]+)*\.v1|openEHR-EHR-CLUSTER\.device(-[a-zA-Z0-9_]+)*\.v1 constraint CLUSTER true true false false 0 1 at0038 archetype_id/value matches {/openEHR-EHR-CLUSTER\.reference_sequence(-[a-zA-Z0-9_]+)*\.v1/} Boolean 2007 false String archetype_id/value attribute C_STRING openEHR-EHR-CLUSTER\.reference_sequence(-[a-zA-Z0-9_]+)*\.v1 constraint ELEMENT true true false false 0 1 at0002 value true true false false 0 1 DV_TEXT true true false false 1 1 ELEMENT true true false false 0 1 at0003 value true true false false 0 1 DV_TEXT true true false false 1 1 DV_CODED_TEXT true true false false 1 1 defining_code true true false false 1 1 CODE_PHRASE true true false false 1 1 local at0022 at0023 at0024 CLUSTER true false true 0 at0006 items true true false false 1 1 ELEMENT true true false false 1 1 at0007 value true true false false 0 1 DV_CODED_TEXT true true false false 1 1 CLUSTER true false true 0 at0025 archetype_id/value matches {/openEHR-EHR-CLUSTER\.reference_sequence(-[a-zA-Z0-9_]+)*\.v1/} Boolean 2007 false String archetype_id/value attribute C_STRING openEHR-EHR-CLUSTER\.reference_sequence(-[a-zA-Z0-9_]+)*\.v1 constraint false false true false true 1 CLUSTER true false true 0 at0030 items true true false false 1 1 ELEMENT true true false false 1 1 at0031 value true true false false 0 1 DV_TEXT true true false false 1 1 DV_CODED_TEXT true true false false 1 1 defining_code true true false false 1 1 CODE_PHRASE true true false false 1 1 local at0064 at0065 at0066 at0067 at0068 at0069 at0070 at0071 at0072 at0073 at0074 at0075 at0076 at0077 at0078 at0079 at0080 at0081 at0082 at0083 at0084 at0085 at0086 at0087 ELEMENT true true false false 0 1 at0032 value true true false false 0 1 DV_COUNT true true false false 1 1 ELEMENT true true false false 0 1 at0033 value true true false false 0 1 DV_COUNT true true false false 1 1 CLUSTER true false true 0 at0035 archetype_id/value matches {/openEHR-EHR-CLUSTER\.reference_sequence(-[a-zA-Z0-9_]+)*\.v1/} Boolean 2007 false String archetype_id/value attribute C_STRING openEHR-EHR-CLUSTER\.reference_sequence(-[a-zA-Z0-9_]+)*\.v1 constraint false false true false true 1 CLUSTER true false true 0 at0026 archetype_id/value matches {/.*/} Boolean 2007 false String archetype_id/value attribute C_STRING .* constraint ELEMENT true true false false 0 1 at0037 value true true false false 0 1 DV_TEXT true true false false 1 1 false false true false true 1 *Sequencing assay(en) *An assay that uses sequencing technology to infer the sequence of a nucleic acid (DNA, RNA). (en) *Sequencing type (en) Technologie, die zur Sequenzierung benutzt wurde. *For example: WES, WGS, Gene panel, RNA sequencing, Fusion panel. Coding with an external terminology is preferred, where possible. (en) Kit Name Name des Kits, das für das Experiment benutzt wurde. Nukleinsäure Der Nukleinsäuretyp, z.B. DNA, RNA oder cf-DNA, der zur Sequenzierung verwendet wird. Getestete Gene Liste aller getesteten Gene, wenn eine Panel-Sequenzierung durchgeführt wurde. Gensymbol Das offizielle Gensymbol, das von der HGNC genehmigt wurde und eine Kurzform des Gennamens ist. DNA RNA cf-DNA Referenzsequenz des Gens Strukturierte Details zur Referenzsequenz des Gens. Erweiterungen Zusätzliche Details, die aufgezeichnet werden sollen. Getestete Region Liste aller getesteten Regionen, wenn eine Panel-Sequenzierung durchgeführt wurde. Chromosomale Lokalisation Chromosomale Lokalisation der getesteten Region. Start Startposition der getesteten Region. Ende Endposition der getesteten Region. Referenzsequenz der Region Strukturierte Details zur Referenzsequenz der Region. *Sequencing device (en) *The technology platform used to perform nucleic acid sequencing. (en) Kommentar Kommentar zum Sequenzierungsassay, der nicht in anderen Feldern erfasst wurde. Referenzgenom Strukturierte Details zur spezifischen Version der human sequence assembly, die für die Annotation verwendet wird. Beispiel: '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/'. Bioinformatic analysis workflow Strukturierte Details zum bioinformatischen Analyseworkflow oder zum verwendeten Protokoll. *Chromosome 1 (en) *Chromosome 1. (en) *Chromosome 2 (en) *Chromosome 2. (en) *Chromosome 3 (en) *Chromosome 3. (en) *Chromosome 4 (en) *Chromosome 4. (en) *Chromosome 5 (en) *Chromosome 5. (en) *Chromosome 6 (en) *Chromosome 6. (en) *Chromosome 7 (en) *Chromosome 7. (en) *Chromosome 8 (en) *Chromosome 8. (en) *Chromosome 9 (en) *Chromosome 9. (en) *Chromosome 10 (en) *Chromosome 10. (en) *Chromosome 11 (en) *Chromosome 11. (en) *Chromosome 12 (en) *Chromosome 12. (en) *Chromosome 13 (en) *Chromosome 13. (en) *Chromosome 14 (en) *Chromosome 14. (en) *Chromosome 15 (en) *Chromosome 15. (en) *Chromosome 16 (en) *Chromosome 16. (en) *Chromosome 17 (en) *Chromosome 17. (en) *Chromosome 18 (en) *Chromosome 18. (en) *Chromosome 19 (en) *Chromosome 19. (en) *Chromosome 20 (en) *Chromosome 20. (en) *Chromosome 21 (en) *Chromosome 21. (en) *Chromosome 22 (en) *Chromosome 22. (en) *Chromosome X (en) *Chromosome X. (en) *Chromosome Y (en) *Chromosome Y. (en) Sequencing assay An assay that uses sequencing technology to infer the sequence of a nucleic acid (DNA, RNA). Sequencing 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. Kit name Name of the kit used for the experiment. For example Oncomine Comprehensive Panel V3. Nucleic acid Type of nucleic acid used for sequencing, e.g. DNA, RNA or cf-DNA. Tested Gene List of all tested genes, if panel sequencing was performed. Gene symbol The official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name. DNA RNA cf-DNA Gene 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) Extensions Additional details to be captured. Tested 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 label The chromosome of the tested region. Start Start position of the tested region. End End position of the tested region. Reference sequence of region Structured details on the reference sequence of the region. Sequencing device The technology platform used to perform nucleic acid sequencing. Comment Comment on the sequencing assay that was not captured in other fields. Reference 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/'. Bioinformatic 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 Chromosome 1 Chromosome 1. Chromosome 2 Chromosome 2. Chromosome 3 Chromosome 3. Chromosome 4 Chromosome 4. Chromosome 5 Chromosome 5. Chromosome 6 Chromosome 6. Chromosome 7 Chromosome 7. Chromosome 8 Chromosome 8. Chromosome 9 Chromosome 9. Chromosome 10 Chromosome 10. Chromosome 11 Chromosome 11. Chromosome 12 Chromosome 12. Chromosome 13 Chromosome 13. Chromosome 14 Chromosome 14. Chromosome 15 Chromosome 15. Chromosome 16 Chromosome 16. Chromosome 17 Chromosome 17. Chromosome 18 Chromosome 18. Chromosome 19 Chromosome 19. Chromosome 20 Chromosome 20. Chromosome 21 Chromosome 21. Chromosome 22 Chromosome 22. Chromosome X Chromosome X. Chromosome Y Chromosome Y. *Sequencing assay (en) *An assay that uses sequencing technology to infer the sequence of a nucleic acid (DNA, RNA). (en) *Sequencing type (en) Teknologi brukt til gensekvensanalysen. *For example: WES, WGS, Gene panel, RNA sequencing, Fusion panel. Coding with an external terminology is preferred, where possible. (en) Navn på Kit Navnet på kitet som ble brukt til eksperimentet. Nukleinsyre Type nukleinsyre som er brukt til sekvensanalysen, f.eks. DNA, RNA eller cf-DNA. Testede gener Liste over alle gener som ble testet hvis det ble utført en genpaneltest. Gensymbol Det offisielle gensymbolet godkjent av HGNC, som er en kortform for gennavnet. DNA RNA cfDNA Referansesekvens for genet Strukturerte detaljer om referansesekvensen til genet. Tilleggsinformasjon Ytterligere informasjon som ikke er registrert andre steder. Testet genregion Liste over alle de testede regionene hvis det ble utført en genpaneltest. Kromosomal lokalisasjon Lokalisasjonen til kromosomet i den testede regionen. Start Startposisjon for det testede området. Slutt Sluttposisjonen til det testede området. Referansesekvens for regionen Strukturerte detaljer om referansesekvensen til regionen. *Sequencing device (en) *The technology platform used to perform nucleic acid sequencing. (en) Kommentar Ytterligere fritekst om analyseresultatet som ikke fanges opp av andre elementer. Referansegenom * Strukturerte detaljer om den spesifikke versjonen av XXXXXXXXX som er brukt for kommentar. *For eksempel: Navn på kilde: 'NCBI'. Accession number: 'GCF_000001405'. Versjonsnummer: 'GCF_000001405.38'. URL: 'https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.38/'. Bioinformatisk analyseprosess Strukturerte detaljer om den bioinformatiske analyseprosessen eller protokollen som er brukt. *Chromosome 1 (en) *Chromosome 1. (en) *Chromosome 2 (en) *Chromosome 2. (en) *Chromosome 3 (en) *Chromosome 3. (en) *Chromosome 4 (en) *Chromosome 4. (en) *Chromosome 5 (en) *Chromosome 5. (en) *Chromosome 6 (en) *Chromosome 6. (en) *Chromosome 7 (en) *Chromosome 7. (en) *Chromosome 8 (en) *Chromosome 8. (en) *Chromosome 9 (en) *Chromosome 9. (en) *Chromosome 10 (en) *Chromosome 10. (en) *Chromosome 11 (en) *Chromosome 11. (en) *Chromosome 12 (en) *Chromosome 12. (en) *Chromosome 13 (en) *Chromosome 13. (en) *Chromosome 14 (en) *Chromosome 14. (en) *Chromosome 15 (en) *Chromosome 15. (en) *Chromosome 16 (en) *Chromosome 16. (en) *Chromosome 17 (en) *Chromosome 17. (en) *Chromosome 18 (en) *Chromosome 18. (en) *Chromosome 19 (en) *Chromosome 19. (en) *Chromosome 20 (en) *Chromosome 20. (en) *Chromosome 21 (en) *Chromosome 21. (en) *Chromosome 22 (en) *Chromosome 22. (en) *Chromosome X (en) *Chromosome X. (en) *Chromosome Y (en) *Chromosome Y. (en) LOINC(2.80) 48018-6 LOINC(2.80) LA21254-0 LOINC(2.80) LA21255-7 LOINC(2.80) LA21256-5 LOINC(2.80) LA21257-3 LOINC(2.80) LA21258-1 LOINC(2.80) LA21259-9 LOINC(2.80) LA21260-7 LOINC(2.80) LA21261-5 LOINC(2.80) LA21262-3 LOINC(2.80) LA21263-1 LOINC(2.80) LA21264-9 LOINC(2.80) LA21265-6 LOINC(2.80) LA21266-4 LOINC(2.80) LA21267-2 LOINC(2.80) LA21268-0 LOINC(2.80) LA21269-8 LOINC(2.80) LA21270-6 LOINC(2.80) LA21271-4 LOINC(2.80) LA21272-2 LOINC(2.80) LA21273-0 LOINC(2.80) LA21274-8 LOINC(2.80) LA21275-5 LOINC(2.80) LA21276-3 LOINC(2.80) LA21277-1