| ARCHETYPE ID | openEHR-EHR-CLUSTER.sequencing_assay.v0 |
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| Concept | Sequencing assay |
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| Description | To record details of the sequencing analysis including a list of all tested genes if panel sequencing was performed. |
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| Use | One or more instances of this archetype may be nested within the 'Testing details' SLOT in the OBSERVATION.laboratory_test_result. |
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| Misuse | Used only to document the analysis protocol but not to document the results of the sequence analysis. The results are documented with the archetype 'genetic variant'. |
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| Purpose | To record details of the performed sequencing analysis including a list of all tested genes if panel sequencing was performed. |
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| References | |
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| Copyright | © HiGHmed, openEHR Foundation, openEHR Foundation |
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| Authors | Author name: Aurelie Tomczak
Organisation: Institute of Pathology, University Hospital Heidelberg
Email: au.tomczak@yahoo.com
Date originally authored: 2019-06-24
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| Other Details Language | Author name: Aurelie Tomczak
Organisation: Institute of Pathology, University Hospital Heidelberg
Email: au.tomczak@yahoo.com
Date originally authored: 2019-06-24
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| Other Details (Language Independent) | - Licence: This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/.
- Custodian Organisation: Ocean Informatics
- Original Namespace: com.oceaninformatics
- Original Publisher: Ocean Informatics
- Custodian Namespace: com.oceaninformatics
- MD5-CAM-1.0.1: 6DB57FE3BECC443D3BCE4ED5AE054B5E
- Build Uid: d63f49cd-fed8-4416-bc08-a580cc43cc31
- Revision: 0.0.1-alpha
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| Keywords | Sequencing, Genomics, Panel, Assay, Pathology, Sequencing analysis, Panel sequencing, Gene, Specimen |
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| Lifecycle | in_development |
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| UID | 20311eb5-8d7b-407f-8fcc-6b2a15833438 |
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| Language used | en |
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| Citeable Identifier | 1013.1.2348 |
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| Revision Number | 0.0.1-alpha |
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| items | |
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| Sequencing technology | Sequencing technology: Name of the technology used for sequencing analysis.
Choice of:
 Coded Text
- at0010::NGS (hybrid-capture) [*]
- at0011::NGS (amplicon) [*]
- at0012::Genome sequencing [*]
- at0013::Array-CGH [*]
- at0014::MLPA [*]
- at0015::Sanger sequencing [*]
- at0016::Fragment analysis [*]
- at0017::Methylation assay [*]
- at0018::Miscellaneous [*]
 Text
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| Sequencing or analysis device | Sequencing or analysis device: Used to specify devices and tools used for the sequencing analysis or result annotation.
e.g. Sequencing device, alignment method, variant caller
Include:
openEHR-EHR-CLUSTER.device.v1 and specialisations |
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| Kit name | Kit name: Name of the kit used for the experiment.
Choice of:
- Text
- Coded Text
- at0021::Oncomine Comprehensive Panel V3 [*]
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| Nucleic acid | Nucleic acid: Type of nucleic acid used for sequencing, e.g. DNA, RNA oder cf-DNA.
Choice of:
- Text
- Coded Text
- at0022::DNA [*]
- at0023::RNA [*]
- at0024::cf-DNA [*]
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| Tumor cell percentage | Tumor cell percentage: To record the tumor cell content in percent.
min: >=0; max: <=100
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| Tested Genes | Tested Genes: List of all tested genes, if panel sequencing was performed. |
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| Gen symbol | Gen symbol: The official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name. |
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| Gen name | Gen name: The full gene name approved by the HGNC that convey the character or function of the gene. |
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| Gene reference sequence | Gene reference sequence: Structured details on the reference sequence of the gene.
Include:
openEHR-EHR-CLUSTER.reference_sequence.v1 and specialisations |
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| Tested Region | Tested Region: List of all tested regions, if panel sequencing was performed. |
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| Chromosomal location | Chromosomal location: Chromosomal location of tested region.
Choice of:
- Text
- Coded Text
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| Start | Start: Start position of the tested region. |
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| End | End: End position of the tested region. |
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| Reference sequence of region | Reference sequence of region: Structured details on the reference sequence of the region.
Include:
openEHR-EHR-CLUSTER.reference_sequence.v1 and specialisations |
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| Extensions | Extensions: Additional details to be captured.
Include:
All not explicitly excluded archetypes |
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| Comment | Comment: Comment on the sequencing assay that was not captured in other fields. |
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| Other contributors | 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 |
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| Translators | English: Aurelie Tomczak, Institute of Pathology, University Hospital Heidelberg, au.tomczak@yahoo.com
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