| TEMPLATE ID | Molekulargenetischer Befund |
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| Concept | Molekulargenetischer Befund |
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| Description | Wird verwendet, um Beobachtungen und Annotationen zu den im Genom gefundenen Mutationen aus einem Sequenzierungstest zu berichten. |
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| Use | Zur Beschreibung der Ergebnisse einer Panelsequenzierung. |
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| Misuse | Nicht zur Repräsentation anderer pathologischer Befunde bestimmt. Es wird z.B. ein anderes Template für den Histopathologischen Befund benötigt. |
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| Purpose | Wird verwendet, um Beobachtungen und Annotationen zu den im Genom gefundenen Mutationen aus einem Sequenzierungstest zu berichten. |
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| References | |
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| Authors | date: 2019-10-22; name: Aurelie Tomczak; organisation: Institute of Pathology, University Hospital Heidelberg, Germany; email: au.tomczak@yahoo.com |
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| Other Details Language | date: 2019-10-22; name: Aurelie Tomczak; organisation: Institute of Pathology, University Hospital Heidelberg, Germany; email: au.tomczak@yahoo.com |
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| 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
- Original Namespace: org.openehr
- Original Publisher: openEHR Foundation
- Custodian Namespace: org.openehr
- PARENT:MD5-CAM-1.0.1: A60D0B7F52F1F9C3C9B3518DB83ACDAE
- Build Uid: 049f2a54-38cd-40a4-ab98-a8bb28653e4c
- MD5-CAM-1.0.1: c3130323c5ce64179490ed0972d73870
- Original Language: ISO_639-1::de
- Sem Ver: 5.0.0
|
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| Keywords | Report; Befund; Molekularpathologie; Variante; genetisch; genomisch; Variation; Genom |
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| Language used | en |
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| Citeable Identifier | 1246.169.236 |
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| Root archetype id | openEHR-EHR-COMPOSITION.report.v1 |
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| Molekulargenetischer Befund | Molekulargenetischer Befund: Document to communicate information to others, commonly in response to a request from another party. |
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| Other Context | |
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| Report ID | Report ID: Identification information about the report. |
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| Status | Status: The status of the entire report. Note: This is not the status of any of the report components.
|
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| Case identification | Case identification: To record case identification details for public health purposes. |
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| Case identifier | Case identifier: The identifier of this case. |
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| Molekulargenetische Begutachtung | Molekulargenetische Begutachtung: The result, including findings and the laboratory's interpretation, of an investigation performed on specimens collected from an individual or related to that individual. |
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| Data | |
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| Any event | Any event: Default, unspecified point in time or interval event which may be explicitly defined in a template or at run-time. |
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| Data | |
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| Analyseart | Analyseart: Name of the laboratory investigation performed on the specimen(s).
A test result may be for a single analyte, or a group of items, including panel tests. It is strongly recommended that 'Test name' be coded with a terminology, for example LOINC or SNOMED CT. For example: 'Glucose', 'Urea and Electrolytes', 'Swab', 'Cortisol (am)', 'Potassium in perspiration' or 'Melanoma histopathology'. The name may sometimes include specimen type and patient state, for example 'Fasting blood glucose' or include other information, as 'Potassium (PNA blood gas)'.
Default value: Molekulargenetische Begutachtung |
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| Specimen | Specimen: A physical sample collected from, or related to, an individual for the purpose of investigation, examination or analysis.
For example: Tissue or body fluid. |
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| Probenmaterial | Probenmaterial: The type of specimen.
For example: Venous blood, bacterial culture, cytology, or tissue sample. Coding of the specimen type with a terminology is preferred, where possible.
Optional[{fhir_mapping=Specimen.type}]
- Tumor
- Blut (EDTA)
- Blut (für cf-DNS-Extraktion)
- Mundschleimhautabstrich
- DNS
- RNA
- Normalgewebe
- Liquor
- [...]
Annotations- Fhir Mapping: Specimen.type
|
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| Laborprobenidentifikator (Blocknummer) | Laborprobenidentifikator (Blocknummer): A unique identifier of the specimen, normally assigned by the laboratory.
Sometimes called the Accession Identifier. Specimen containers, for example vacuum vials or tissue cassettes, have their own identitiers which may be recorded in the 'Container identifier' element in the 'Specimen container' archetype.
Optional[{fhir_mapping=Specimen.accessionIdentifier}]
 Identifier Text
Annotations- Fhir Mapping: Specimen.accessionIdentifier
|
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| Date/time received | Date/time received: The date and time that the sample was received at the laboratory.
Optional[{fhir_mapping=Specimen.receivedTime}]
Annotations- Fhir Mapping: Specimen.receivedTime
|
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| Collection date/time | Collection date/time: The date and time that collection has been ordered to take place or has taken place.
This datetime will be captured primarily in the INSTRUCTION timing, ACTION time or OBSERVATION times. However, as this is a critical piece of information, it can be useful to also associate it directly with the specimen itself.
 Date/Time Interval of Date/Time
|
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| Specimen processing | Specimen processing: Details about the processing or preparation of a specimen. |
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| Process name | Process name: The name of the processing activity.
For example: preparation for microscopic examination, sperm preparation for IVF treatment, fixation, dehydration, paraffin infiltration, centrifugation.
Default value: Fixierung |
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| Fixierungsmittel | Fixierungsmittel: A narrative description of the processing activity.
For example: 'Centrifuged EDTA plasma, separated the plasma from the cells by hand using a single channel pipette, froze the plasma within 2 hours.'
- fixiert (FFPE)
- Kryofixation
- nicht fixiert
- sonstiges
|
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| Parent specimen identifier | Parent specimen identifier: Unique identifier of the parent specimen, where the specimen is split into sub-samples.
For example: A specific histology slide specimen can have a specific paraffin wax block as its parent specimen.
- Identifier
- Text
|
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| Kommentar zur Probe | Kommentar zur Probe: Additional narrative about the specimen not captured in other fields.
Optional[{fhir_mapping=Specimen.note}]
Annotations- Fhir Mapping: Specimen.note
|
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| Diagnostic service category | Diagnostic service category: The diagnostic service or discipline that is responsible for the laboratory test result.
This is intended to be a general categorisation and not to capture the organisational name of the laboratory. For example: anatomical pathology, immunology and transfusion medicine, medical microbiology, clinical pharmacology, medical genetics, medical biochemistry. Alternatively more granular sub categories or sub disciplines, such as endocrinology, haematology, and allergology services, may be used. This may assist clinicians in filtering between categories of results. Coding with a terminology is desirable, where possible. |
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| Zusätzliche klinische Information | Zusätzliche klinische Information: Description of clinical information available at the time of interpretation of results.
This data element may include a link to the original clinical information provided in the test request. |
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| Sequencing result | Sequencing result: Cluster to combine sequencing assay, General sequencing parameters and all variant results of a single analysis. |
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| Analysis-ID/Labinternal Identifier | Analysis-ID/Labinternal Identifier: A local identifier that is assigned by the receiving laboratory information system (LIS) in order to track the test process. |
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| General sequencing result parameter | General sequencing result parameter: General sequencing result parameter. |
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| Tumor cell content (pathologic/histologic) | Tumor cell content (pathologic/histologic): Tumor cell content determinded by pathologic/histologic methods.
Units: % |
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| Tumor cell content (bioinformatic) | Tumor cell content (bioinformatic): Tumor cell content determinded by bioinformatic methods.
Units: % |
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| Microsatellite instability (MSI) | Microsatellite instability (MSI): Microsatellite instability (MSI).
 Count0..2 Quantity
|
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| Tumor Mutational Burden (TMB) per Mb | Tumor Mutational Burden (TMB) per Mb: Tumor Mutational Burden (TMB) per Megabase.
- Count
- Quantity
|
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| BRCAness | BRCAness: BRCAness is defined as a phenotypic copy of germline BRCA mutations.
0..1 |
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| Sequencing assay | Sequencing assay: To record details of the sequencing analysis including a list of all tested genes if panel sequencing was performed. |
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| Sequenzierungstechnologie / Analysetechnologie | Sequenzierungstechnologie / Analysetechnologie: Name of the technology used for sequencing analysis.
 Coded Text- NGS (hybrid-capture)
- NGS (amplicon)
- Genome sequencing
- Array-CGH
- MLPA
- Sanger sequencing
- Fragment analysis
- Methylation assay
- Miscellaneous
- Text
|
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| Medical device | Medical device: An instrument, apparatus, implant, material or similar, used in the provision of healthcare. In this context, a medical device includes a broad range of devices which act through a variety of physical, mechanical, thermal or similar means but specifically excludes devices which act through medicinal means such as pharmacological, metabolic or immunological methods. The scope is inclusive of disposable devices as well as durable or persisting devices that require tracking, maintenance activities or regular calibration, recognising that each type of device has specific data recording requirements. |
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| Device name | Device name: Identification of the medical device, preferably by a common name, a formal fully descriptive name or, if required, by class or category of device.
This data element will capture the term, phrase or category used in clinical practice. For example: <brand name><machine> (XYZ Audiometer); <size> <brand name> <intravenous catheter> (14G Jelco IV catheter); or <brand name/type> <implant>. Coding with a terminology is desirable, where possible, although this may be local and depending on local supplies available. |
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| Manufacturer | Manufacturer: Name of manufacturer. |
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| Catalogue number | Catalogue number: The exact number assigned by the manufacturer, as it appears in the manufacturer's catalogue, device labeling, or accompanying packaging. |
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| Software version | Software version: Identification of the version of software being used in the medical device.
When the medical device is an actual software application, record the version of the software using this data element. When the medical device has multiple software applications embedded within it, record each software component in a separate CLUSTER archetype within the Components SLOT - either as a nested instance of another CLUSTER.device archetype or using a CLUSTER archetype designed specifically for recording software details (but not yet available at time of this archetype development). |
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| Comment | Comment: Additional narrative about the device not captured in other fields. |
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| Kit name | Kit name: Name of the kit used for the experiment.
- Text
- Coded Text
- 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.
- Text
- Coded Text
|
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| Tested Genes | Tested Genes: List of all tested genes, if panel sequencing was performed. |
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| Gene symbol | Gene symbol: The official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name. |
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| Gene name | Gene name: The full gene name approved by the HGNC that convey the character or function of the gene. |
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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.
- Text
- Coded Text
|
|---|
| Start | Start: Start position of the tested region. |
|---|
| End | End: End position of the tested region. |
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| Kommentar zur Qualität der Analyse | Kommentar zur Qualität der Analyse: Comment on the sequencing assay that was not captured in other fields.
- Gute Qualität
- Eingeschränkte Qualität
- Kommentar
- [...]
|
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| Genomic variant result | Genomic variant result: Findings and annotations related to one variant found in a human individual by a sequencing test. |
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| Reference sequence | Reference sequence: A sequence file that is used as a reference to describe genetic variants that are present in an analysed sequence. |
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| Reference genome assembly | Reference genome assembly: The reference genome assembled as a representative model of the human genome. |
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| Source name | Source name: The name of the data source containing the reference sequence. |
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| Reference Genome Accession | Reference Genome Accession: A unique identifier to refer to a sequence record in a sequence repository.
- GRCh37/hg19
- GRCh38/hg38
- NCBI36/hg18
- [...]
Default value: GRCh37/hg19 |
|---|
| URL | URL: Network address. |
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| Database variant identification | Database variant identification: A citation of a digital resource used as an source of authoritative or expert information, and/or to items contained within the resource.
For example: a genomics pipeline history, a database of genomic variants, or a database of healthcare procedure guidelines. |
|---|
| Source Name | Source Name: The name of the knowledge base.
For example: Galaxy/Snakemake; dbSNP; or CADD. |
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| Identification | Identification: The name of the referenced item within the knowledge base.
For example: rs139581412. |
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| Indentification Version | Indentification Version: The version of the referenced item within the knowledge base. |
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| Variant / Genomposition aus vcf-File nach HGVS (g.*) | Variant / Genomposition aus vcf-File nach HGVS (g.*): Description of the variation at the genomic level following the HGVS nomenclature.
For example: 'g.33038255C>A'.
If both this element and the 'Structured variant' SLOT are used simultaneously, they need to represent identical data. |
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| Simple genetic variant | Simple genetic variant: A sequence change where, compared to a reference sequence, a one or more nucleotides are changed. |
|---|
| Chromosome label | Chromosome label: Chromosome identifier.
- Coded Text
- Chromosome 1
- Chromosome 2
- Chromosome 3
- Chromosome 4
- Chromosome 5
- Chromosome 6
- Chromosome 7
- Chromosome 8
- Chromosome 9
- Chromosome 10
- Chromosome 11
- Chromosome 12
- Chromosome 13
- Chromosome 14
- Chromosome 15
- Chromosome 16
- Chromosome 17
- Chromosome 18
- Chromosome 19
- Chromosome 20
- Chromosome 21
- Chromosome 22
- Chromosome X
- Chromosome Y
- Text
|
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| Startposition der Variante / Genomposition (aus vcf-File) | Startposition der Variante / Genomposition (aus vcf-File): The position of the first nucleotide of the changed range for a simple variant. ("Start" in vcf-file). |
|---|
| Endposition der Variant / Genomposition (aus vcf-File) | Endposition der Variant / Genomposition (aus vcf-File): The position of the last nucleotide of the changed range for a simple variant. ("End" in vcf-file). |
|---|
| Alternative Nukleotidsequenz (Alt) | Alternative Nukleotidsequenz (Alt): The observed alternate nucleotide or nucleotide sequence ("Alt" in vcf-file). |
|---|
| Referenznukleotidsequenz (Ref) | Referenznukleotidsequenz (Ref): The reference nucleotide or nucleotide sequence. ("Ref" in vcf-file). |
|---|
| Transkript Referenz | Transkript Referenz: A sequence file that is used as a reference to describe genetic variants that are present in an analysed sequence. |
|---|
| Reference genome assembly | Reference genome assembly: The reference genome assembled as a representative model of the human genome. |
|---|
| Source name | Source name: The name of the data source containing the reference sequence. |
|---|
| Accession number | Accession number: A unique identifier to refer to a sequence record in a sequence repository. |
|---|
| Version number | Version number: The version number of the data record of the reference sequence.
For example: 'hg38', 'hg19'. |
|---|
| URL | URL: Network address. |
|---|
| Genomic copy number variant | Genomic copy number variant: A human genetic sequence change where, compared to a genomic reference sequence, a DNA segment, usually larger than 1 kilobase (kb), was deleted or duplicated. |
|---|
| Start | Start: Position or range of possible positions of the first nucleotide of the CNV.
- Count
 Interval of Count
|
|---|
| End | End: Position or range of possible positions of the last nucleotide of the CNV.
- Count
- Interval of Count
|
|---|
| Allelzahl (Total copy number) | Allelzahl (Total copy number): Number of appearance of the allele.
>=0 |
|---|
| Copy number change type | Copy number change type: Type of sequence alteration.
Different types of impact, such as low-level amplification or whole gene deletion, should be recorded using the 'Functional impact' Cluster within the CLUSTER.genomic_variant_result archetype.
|
|---|
| Transkript Referenz | Transkript Referenz: A sequence file that is used as a reference to describe genetic variants that are present in an analysed sequence. |
|---|
| Reference genome assembly | Reference genome assembly: The reference genome assembled as a representative model of the human genome. |
|---|
| Source name | Source name: The name of the data source containing the reference sequence. |
|---|
| Accession number | Accession number: A unique identifier to refer to a sequence record in a sequence repository. |
|---|
| Version number | Version number: The version number of the data record of the reference sequence.
For example: 'hg38', 'hg19'. |
|---|
| URL | URL: Network address. |
|---|
| Chromosome label | Chromosome label: Chromosome identifier.
- Coded Text
- Chromosome 1
- Chromosome 2
- Chromosome 3
- Chromosome 4
- Chromosome 5
- Chromosome 6
- Chromosome 7
- Chromosome 8
- Chromosome 9
- Chromosome 10
- Chromosome 11
- Chromosome 12
- Chromosome 13
- Chromosome 14
- Chromosome 15
- Chromosome 16
- Chromosome 17
- Chromosome 18
- Chromosome 19
- Chromosome 20
- Chromosome 21
- Chromosome 22
- Chromosome X
- Chromosome Y
- Text
|
|---|
| Genetic translocation variant | Genetic translocation variant: Translocation variant. |
|---|
| Breakpoint position (or closest approximation by exon border if no WGS data) 1 | Breakpoint position (or closest approximation by exon border if no WGS data) 1: Position of first breakpoint relative to start of "Chromosome 1". |
|---|
| Strand 1 | Strand 1: A value of "+" indicates that the chromosomal segment at the second breakpoint is connected to the chromosomal segment at the first breakpoint right of "Breakpoint position 1". A value of "-" indicates that the chromosomal segment at the second breakpoint is connected to the chromosomal segment of the first breakpoint left of "Breakpoint position 1". |
|---|
| Transkript Referenz 1 | Transkript Referenz 1: A sequence file that is used as a reference to describe genetic variants that are present in an analysed sequence. |
|---|
| Reference genome assembly | Reference genome assembly: The reference genome assembled as a representative model of the human genome. |
|---|
| Source name | Source name: The name of the data source containing the reference sequence. |
|---|
| Accession number | Accession number: A unique identifier to refer to a sequence record in a sequence repository. |
|---|
| Version number | Version number: The version number of the data record of the reference sequence.
For example: 'hg38', 'hg19'. |
|---|
| URL | URL: Network address. |
|---|
| Chromosome label | Chromosome label: Chromosome identifier.
- Coded Text
- Chromosome 1
- Chromosome 2
- Chromosome 3
- Chromosome 4
- Chromosome 5
- Chromosome 6
- Chromosome 7
- Chromosome 8
- Chromosome 9
- Chromosome 10
- Chromosome 11
- Chromosome 12
- Chromosome 13
- Chromosome 14
- Chromosome 15
- Chromosome 16
- Chromosome 17
- Chromosome 18
- Chromosome 19
- Chromosome 20
- Chromosome 21
- Chromosome 22
- Chromosome X
- Chromosome Y
- Text
|
|---|
| Breakpoint position (or closest approximation by exon border if no WGS data) 2 | Breakpoint position (or closest approximation by exon border if no WGS data) 2: Position of second breakpoint relative to start of "Chromosome 2". |
|---|
| Strand 2 | Strand 2: A value of "+" indicates that the chromosomal segment at the first breakpoint is connected to the chromosomal segment at the second breakpoint right of "Breakpoint position 2". A value of "-" indicates that the chromosomal segment at the first breakpoint is connected to the chromosomal segment of the second breakpoint left of "Breakpoint position 2". |
|---|
| Transkript Referenz 2 | Transkript Referenz 2: A sequence file that is used as a reference to describe genetic variants that are present in an analysed sequence. |
|---|
| Reference genome assembly | Reference genome assembly: The reference genome assembled as a representative model of the human genome. |
|---|
| Source name | Source name: The name of the data source containing the reference sequence. |
|---|
| Accession number | Accession number: A unique identifier to refer to a sequence record in a sequence repository. |
|---|
| Version number | Version number: The version number of the data record of the reference sequence.
For example: 'hg38', 'hg19'. |
|---|
| URL | URL: Network address. |
|---|
| Chromosome label | Chromosome label: Chromosome identifier.
- Coded Text
- Chromosome 1
- Chromosome 2
- Chromosome 3
- Chromosome 4
- Chromosome 5
- Chromosome 6
- Chromosome 7
- Chromosome 8
- Chromosome 9
- Chromosome 10
- Chromosome 11
- Chromosome 12
- Chromosome 13
- Chromosome 14
- Chromosome 15
- Chromosome 16
- Chromosome 17
- Chromosome 18
- Chromosome 19
- Chromosome 20
- Chromosome 21
- Chromosome 22
- Chromosome X
- Chromosome Y
- Text
|
|---|
| HGVS term | HGVS term: The description of the variant using the recommendations of the accepted HGVS nomeclature named extension ISCN. |
|---|
| Transcript | Transcript: Structured details about the transcript which is potentially affected by the variant. |
|---|
| Reference sequence | Reference sequence: A sequence file that is used as a reference to describe genetic variants that are present in an analysed sequence. |
|---|
| Reference genome assembly | Reference genome assembly: The reference genome assembled as a representative model of the human genome. |
|---|
| Source name | Source name: The name of the data source containing the reference sequence. |
|---|
| Referenztranskript (Accession number) | Referenztranskript (Accession number): A unique identifier to refer to a sequence record in a sequence repository. |
|---|
| URL | URL: Network address. |
|---|
| DNA region name | DNA region name: The human readable name for the region of interest.
For example: 'exon number', 'intron number', 'splice site' or other. |
|---|
| Distance from splicing site | Distance from splicing site: Distance in nucleotides between mutation and exon–intron junction. |
|---|
| cDNA Nomenklatur Variante (DNA change) | cDNA Nomenklatur Variante (DNA change): Description of the variation at the DNA level following the HGVS nomenclature.
For example: 'c.5249C>T'. |
|---|
| Proteinebene Nomenklatur Variante (Amino Acid Change) | Proteinebene Nomenklatur Variante (Amino Acid Change): Description of the variation at the protein level following the HGVS nomenclature.
For example: 'p.T1750M'. |
|---|
| Amino acid change type | Amino acid change type: Codified type for associated amino acid marker.
- Coded Text
- Wild type
- Deletion
- Duplication
- Frameshift
- Initiating methionine
- Insertion
- Insertion and deletion
- Missense
- Nonsense
- Silent
- Stop codon mutation
- Text
|
|---|
| RNA change | RNA change: Description of the variation at the RNA level following the HGVS nomenclature.
For example: 'r.76a>u'. |
|---|
| Predicted impact | Predicted impact: Estimate of the effects that the variant may have on the transcript. |
|---|
| Score | Score: The calculated value.
For example: '30.2'.
Units: (UCUM: 1) |
|---|
| Qualitative prediction | Qualitative prediction: Human readable version of the predicted impact.
For example: 'probably damaging'. |
|---|
| Functional impact | Functional impact: Interpretation of the variation linked to a specific paper. |
|---|
| Impact / Variantenklassifikation | Impact / Variantenklassifikation: Single word or phrase describing the reported impact of the specific variant.
For example: 'activating', 'deactivating', 'dysfunction', 'gain of function'. Coding with a terminology is preferred, where possible. |
|---|
| Citation | Citation: Reference to information held elsewhere, in the same EHR or external to the EHR. |
|---|
| Description | Description: Description about the citation. |
|---|
| Citation | Citation: Representation of the citation.
 Parsable Multimedia
|
|---|
| URI to original data | URI to original data: Link to the original data. |
|---|
| Comment | Comment: Comment about the citation. |
|---|
| Gene | Gene: Structured details about the gene carrying the variant. |
|---|
| Gen-Name (HGNC) | Gen-Name (HGNC): The official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name.
For example 'CHD5'. |
|---|
| Full gene name | Full gene name: The full gene name approved by the HGNC that conveys the character or function of the gene.
For example 'Chromodomain helicase DNA binding protein 5'. |
|---|
| Copy number overlap | Copy number overlap: The fraction of gene region covered by copy number. |
|---|
| Fusionstranskript-Name 1 (Part of fusion) | Fusionstranskript-Name 1 (Part of fusion): States if the gene is part of a fusion gene and if it is the first or second part of the fusion gene.
|
|---|
| Pathogenitätsklasse/Variantenklassifikation (ACMG classification) | Pathogenitätsklasse/Variantenklassifikation (ACMG classification): The clinical significance according to the ACMG recommendations.
- Pathogenic
- Likely pathogenic
- Uncertain significance
- Likely benign
- Benign
|
|---|
| Fusionstranskript-Name 2 (Fusion exon) | Fusionstranskript-Name 2 (Fusion exon): The number of the exon which is part of the fusion.
>0 |
|---|
| Best transcript candidate | Best transcript candidate: The ID of the transcript with the highest predicted impact.
For example: 'ENST00000413998.7'. |
|---|
| Lesetiefe an Variantenposition (Median read depth) | Lesetiefe an Variantenposition (Median read depth): The total number of reads mapped at this specific location.
>=0 |
|---|
| Allele depth | Allele depth: The number of reads that support the reported variant.
>=0 |
|---|
| Allelfrequenz (Allele frequency) | Allelfrequenz (Allele frequency): The relative frequency of an allele at a particular locus.
For example: '0.63'.
0..1 (UCUM: 1) |
|---|
| Population allele frequency details | Population allele frequency details: The relative frequency of a particular allele in the population. |
|---|
| Population allele frequency | Population allele frequency: The population allele frequency.
For example: '0.43'.
0..1 (UCUM: 1) |
|---|
| VCF quality filter | VCF quality filter: Structured details about the quality filters that have been applied to the data.
This field is derived from the FILTER column of VCF. |
|---|
| Filter name | Filter name: Name of the quality filter.
For example: 'q10'. |
|---|
| Description | Description: Quality filter extended description.
For example: 'at this site the quality is below 10'. |
|---|
| Filter passed | Filter passed: Did the variant pass the quality filter?
Record as 'True' if the filter was passed. |
|---|
| Strand bias ratio | Strand bias ratio: The ratio of the strand bias.
Units: (UCUM: 1) |
|---|
| Strand bias p-value | Strand bias p-value: The Phred-scaled p-value of the strand bias.
Units: (UCUM: 1) |
|---|
| Genotype | Genotype: Genotype encoded as allele values.
The format for the genotype should be value separated by either of / or | (0 for the reference allele, 1 for the first alternate, etc.). For example: '1 | 0' or '0/0/1'. |
|---|
| Allelic state | Allelic state: The level of occurrence of a single DNA marker within a set of chromosomes.
This is the human readable version of genotype, e.g.: 'Heterozygous', 'Homozygous'.
- Coded Text
- Heteroplasmic
- Homoplasmic
- Homozygous
- Heterozygous
- Hemizygous
- Text
|
|---|
| Genotype quality | Genotype quality: Conditional genotype quality, encoded as a Phred quality.
>=0 |
|---|
| Genotype probability | Genotype probability: A comma separated list of the log10-scaled genotype likelihoods for all possible genotypes, given the reference and the alternate alleles. |
|---|
| Conclusion | Conclusion: Narrative description of the key findings.
For example: 'Pattern suggests significant renal impairment'. The content of the conclusion will vary, depending on the investigation performed. This conclusion should be aligned with the coded 'Test diagnosis'. |
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| Testdiagnose / Ergebnis | Testdiagnose / Ergebnis: Single word, phrase or brief description that represents the clinical meaning and significance of the laboratory test result.
For example: 'Severe hepatic impairment', 'Salmonella contamination'. Coding of the diagnosis with a terminology is strongly recommended, where possible. This diagnosis should be aligned with the narrative in the 'Conclusion'.
- keine/benigne Variante identifiziert
- Analyse erfolgt, aber nicht auswertbar
- potentiell patogene Variante identifiziert
- [...]
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| Comment | Comment: Additional narrative about the test result not captured in other fields. |
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| Protocol | |
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| Laboratory internal identifier | Laboratory internal identifier: A local identifier assigned by the receiving Laboratory Information System (LIS) to track the test process.
This identifier is an internal tracking number assigned by the LIS, and it not intended to be the name of the test.
- Identifier
- Text
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| Test request details | Test request details: Details about the test request.
In most situations there is one test request and a single corresponding test result, however this repeating cluster allows for the situation where there may be multiple test requests reported using a single test result.
As an example: 'a clinician asks for blood glucose in one request and Urea/electrolytes in a second request, but the lab analyser does both and the lab wishes to report these together'. |
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| Original test requested name | Original test requested name: Name of the original laboratory test requested.
This data element is to be used when the test requested differs from the test actually performed by the laboratory. |
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| Requester order identifier | Requester order identifier: The local identifier assigned by the requesting clinical system.
Equivalent to the HL7 Placer Order Identifier.
- Identifier
- Text
|
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| Receiver order identifier | Receiver order identifier: The local identifier assigned to the test order by the order filler, usually by the Laboratory Information System (LIS).
Assigning an identifier to a request by the Laboratory lnformation System (LIS) enables tracking progress of the request and enables linking results to requests. It also provides a reference to assist with enquiries and it is usually equivalent to the HL7 Filler Order Identifier.
- Identifier
- Text
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| Tumordiagnose_section | Tumordiagnose_section: Framework for consistent modelling of content within a template for a Problem list.
Intended to be used within the COMPOSITION.problem_list. |
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| Tumordiagnose | Tumordiagnose: Details about a single identified health condition, injury, disability or any other issue which impacts on the physical, mental and/or social well-being of an individual.
Clear delineation between the scope of a problem versus a diagnosis is not easy to achieve in practice. For the purposes of clinical documentation with this archetype, problem and diagnosis are regarded as a continuum, with increasing levels of detail and supportive evidence usually providing weight towards the label of 'diagnosis'. |
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| Data | |
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| Diagnose Name (ICD-10) | Diagnose Name (ICD-10): Identification of the problem or diagnosis, by name.
Coding of the name of the problem or diagnosis with a terminology is preferred, where possible. |
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| Diagnose Beschreibung | Diagnose Beschreibung: Narrative description about the problem or diagnosis.
Use to provide background and context, including evolution, episodes or exacerbations, progress and any other relevant details, about the problem or diagnosis. |
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| Seitenlokalisation | Seitenlokalisation: Identification of a simple body site for the location of the problem or diagnosis.
Coding of the name of the anatomical location with a terminology is preferred, where possible.
Use this data element to record precoordinated anatomical locations. If the requirements for recording the anatomical location are determined at run-time by the application or require more complex modelling such as relative locations then use the CLUSTER.anatomical_location or CLUSTER.relative_location within the 'Structured anatomical location' SLOT in this archetype. Occurrences for this data element are unbounded to allow for clinical scenarios such as describing a rash in multiple locations but where all of the other attributes are identical. If the anatomical location is included in the Problem/diagnosis name via precoordinated codes, this data element becomes redundant.
- Links (L)
- Rechts (R)
- Multilokuär (X)
- Beidseitig (B)
- Mittellinie/ Mittig (M)
- Unbekannt (U)
- Trifft nicht zu (T; Seitenangabe nicht sinnvoll, einschließlich Systemerkrankungen)
|
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| Erstdiagnosedatum | Erstdiagnosedatum: Estimated or actual date/time that signs or symptoms of the problem/diagnosis were first observed.
Data captured/imported as "Age at onset" should be converted to a date using the subject's date of birth. |
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| Tumor classification ICD-O | Tumor classification ICD-O: International Classification of Diseases for Oncology.
ICD-O-3 is a dual classification. It contains both a topographical code and a histological code for each neoplasm.
The topographical describes the site of the neoplasm; in general, it uses the same three- or four-character codes as used in ICD-10 for malignant neoplasms. This results in a greater accuracy in the encoding of the topography of benign tumors than achieved in ICD-10.
The morphological code describes the cell type of the neoplasm and its biological behaviour. It thus characterises the neoplasm itself. |
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| Morphological Code ICD-O | Morphological Code ICD-O: To record the type of cell that has become neoplastic and its biologic activity with the morphology code according to the International classification of diseases for oncology (ICD-O).
There are three parts to a complete morphology code:
4 digits – Cell type (histology)
1 digit – Behavior
1 digit – Grade, differentiation or phenotype
In ICD-O morphology codes, a common root codes the cell type of a given tumor, while an additional digit codes the behavior. The grade, differentiation, or phenotype code provides supplementary information about the tumor. |
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| Morphologie Beschreibung | Morphologie Beschreibung: To record the term (narrative description/synonyms) of the morphology code according to the International classification of diseases for oncology (ICD-O). |
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| Topography Code ICD-O | Topography Code ICD-O: The topographical describes the site of the neoplasm.
In general, it uses the same three- or four-character codes as used in ICD-10 for malignant neoplasms. |
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| Topographie Beschreibung | Topographie Beschreibung: To record the term (narrative description/synonyms) of the topography code according to the "International classification of diseases for oncology (ICD-O-3)". |
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| Protocol | |
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| Tumor ID | Tumor ID: To display the ID of the tumor. |
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| Tumor ID | Tumor ID: The ID/identifier of the tumor. |
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