| TEMPLATE ID | Molecular Pathology Report |
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| Concept | Molecular Pathology Report |
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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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| 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: 55DB2D45BC470E831EE8C905348471E4
- Build Uid: 049f2a54-38cd-40a4-ab98-a8bb28653e4c
- MD5-CAM-1.0.1: c2b22b7d52343b4f5dd68eaccd105be3
|
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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 | 1013.26.249 |
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| Revision | 1 |
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| Root archetype id | openEHR-EHR-COMPOSITION.report.v1 |
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| Molecular Pathology Report | Molecular Pathology Report: 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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| 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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| Molecular Pathology Report | Molecular Pathology Report: 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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| Test name | Test name: 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: Molekularpathologische Begutachtung |
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| Specimen | Specimen: A physical sample for investigation, examination or analysis, collected from or related to an individual.
For example: Tissue, body fluid or food. |
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| Specimen type | Specimen type: The type of specimen.
For example: Venous blood, bacterial culture, cytology, or prostatic biopsy. Coding of the specimen type with a terminology is preferred, where possible.
Optional[{fhir_mapping=Specimen.type}]
Annotations- Fhir Mapping: Specimen.type
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| Laboratory specimen identifier | Laboratory specimen identifier: 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}]
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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| Specimen preparation | Specimen preparation: To record details of laboratory specimen processing. |
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| Specific preparation | Specific preparation: Details of the specific preparation carried out during a single processing step. |
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| Fixative | Fixative: The fixative used.
- fixiert (FFPE)
- Kryofixation
- nicht fixiert
- sonstiges
Default value: fixiert (FFPE) |
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| Comment on Specimen | Comment on Specimen: Additional narrative about the specimen not captured in other fields.
Optional[{fhir_mapping=Specimen.note}] |
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| Overall test status | Overall test status: The status of the laboratory test result as a whole.
The values have been specifically chosen to match those in the HL7 FHIR Diagnostic report, historically derived from HL7v2 practice. Other local codes/terms can be used via the Text 'choice'.
This element is multiple occurrence to cater for the use cases where statuses for different aspects of the result have been split into several elements.
 Coded Text- Registered
- Partial
- Preliminary
- Final
- Amended
- Corrected
- Appended
- Cancelled
- Entered in error
 Text
|
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| Overall test status timestamp | Overall test status timestamp: The date and/or time that ‘Overall test status’ was issued. |
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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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| Clinical information provided | Clinical information provided: 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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| Genetic variant | Genetic variant: Result of a genetic test for a single variant. |
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| Reference sequence | Reference sequence: A sequence file that is used as a reference to describe variants that are present in an analysed sequence. |
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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 |
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| URL | URL: Network address. |
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| Variant identifier | Variant identifier: A reference to a specific variation recorded into a biological variation database. |
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| Source name | Source name: The name of the public data source that gives the variant identification. |
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| Identification | Identification: The ID of a variation record. |
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| Conversion variant | Conversion variant: A sequence change where, compared to a reference sequence, a range of nucleotides are replaced by a sequence from elsewhere in the genome. |
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| Start converted position | Start converted position: The position of the first nucleotide of the converted range. |
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| End converted position | End converted position: The position of the last nucleotide of the converted range. |
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| Replacing sequence start position | Replacing sequence start position: The position of the first nucleotide of the replacing sequence. |
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| Replacing sequence end position | Replacing sequence end position: The position of the last nucleotide of the replacing sequence. |
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| Reference sequence | Reference sequence: A sequence file that is used as a reference to describe variants that are present in an analysed sequence. |
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| Source name | Source name: The name of the data source containing the reference sequence. |
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| Accession number | Accession number: A unique identifier to refer to a sequence record in a sequence repository. |
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| Version number | Version number: An attribute that provides a specific indication of the sequence used for annotation. |
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| URL | URL: Network address. |
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| 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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| Genetic deletion variant | Genetic deletion variant: A sequence change where, compared to a reference sequence, one or more nucleotides are not present (deleted). |
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| Start position | Start position: Position of the deleted nucleotide or the first nucleotide of the deleted range. |
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| End position | End position: Position of the last nucleotide of the deleted range. |
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| Deleted nucleotide(s) | Deleted nucleotide(s): The deleted nucleotide or the sequence deleted. |
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| Reference sequence | Reference sequence: A sequence file that is used as a reference to describe variants that are present in an analysed sequence. |
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| Source name | Source name: The name of the data source containing the reference sequence. |
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| Accession number | Accession number: A unique identifier to refer to a sequence record in a sequence repository. |
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| Version number | Version number: An attribute that provides a specific indication of the sequence used for annotation. |
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| URL | URL: Network address. |
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| 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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| Genetic copy number variant | Genetic copy number variant: Describes a copy number variant, where any part of a genome was deleted or duplicated (gain or loss of an allele). |
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| Start position | Start position: Start position on the given reference sequence.
Number should not be treated as an absolute more as an estimation. |
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| End position | End position: End position on the given reference sequence.
Number should not be treated as an absolute more as an estimation. |
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| Allelzahl (Total copy number) | Allelzahl (Total copy number): Number of appearance of the allele. |
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| Copy number change type | Copy number change type: Any copy number variant results in a gain or loss of the region e.g. a loss could result that a hetergozygous locus becomes homozygous since one gene was deleted.
|
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| Reference sequence | Reference sequence: A sequence file that is used as a reference to describe variants that are present in an analysed sequence. |
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| Source name | Source name: The name of the data source containing the reference sequence. |
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| Accession number | Accession number: A unique identifier to refer to a sequence record in a sequence repository. |
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| Version number | Version number: An attribute that provides a specific indication of the sequence used for annotation. |
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| URL | URL: Network address. |
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| 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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| Genetic duplication variant | Genetic duplication variant: A genetic sequence change where, compared to a reference sequence, a copy of one or more nucleotides are inserted directly 3' of the original copy of that sequence. |
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| Start position | Start position: Position of the duplicated nucleotide or the first nucleotide of the duplicated range. |
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| End position | End position: Position of the last nucleotide of the duplicated range. |
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| Duplicated nucletide(s) | Duplicated nucletide(s): The nucleotide or the sequence duplicated. |
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| Reference sequence | Reference sequence: A sequence file that is used as a reference to describe variants that are present in an analysed sequence. |
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| Source name | Source name: The name of the data source containing the reference sequence. |
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| Accession number | Accession number: A unique identifier to refer to a sequence record in a sequence repository. |
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| Version number | Version number: An attribute that provides a specific indication of the sequence used for annotation. |
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| URL | URL: Network address. |
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| 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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| Genetic inversion variant | Genetic inversion variant: A genetic sequence change where, compared to a reference sequence, more than one nucleotide replacing the original sequence are the reverse complement of the original sequence. |
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| Start position | Start position: Position of the first nucleotide of the inverted range. |
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| End position | End position: Position of the last nucleotide of the inverted range. |
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| Inverted sequence | Inverted sequence: The nucleotide sequence of the reference sequence at th given positions. |
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| Reference sequence | Reference sequence: A sequence file that is used as a reference to describe variants that are present in an analysed sequence. |
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| Source name | Source name: The name of the data source containing the reference sequence. |
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| Accession number | Accession number: A unique identifier to refer to a sequence record in a sequence repository. |
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| Version number | Version number: An attribute that provides a specific indication of the sequence used for annotation. |
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| URL | URL: Network address. |
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| 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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| Genetic repeated sequence variant | Genetic repeated sequence variant: A genetic sequence where, compared to a reference sequence, a segment of one or more nucleotides (the repeat unit) is present several times, one after the other. |
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| Start position | Start position: Position of the first nucleotide of the repeated range. |
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| End position | End position: Position of the last nucleotide of the repeated range. |
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| Repeated sequence | Repeated sequence: The sequence of nucleotides that has been repeated. |
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| Copy number | Copy number: Number of repeat units. |
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| Reference sequence | Reference sequence: A sequence file that is used as a reference to describe variants that are present in an analysed sequence. |
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| Source name | Source name: The name of the data source containing the reference sequence. |
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| Accession number | Accession number: A unique identifier to refer to a sequence record in a sequence repository. |
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| Version number | Version number: An attribute that provides a specific indication of the sequence used for annotation. |
|---|
| URL | URL: Network address. |
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| 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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| Genetic substitution variant | Genetic substitution variant: A genetic sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide. |
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| Position substituted (Genomposition (aus vcf-File)) | Position substituted (Genomposition (aus vcf-File)): The position of the sustituted nucleotide. |
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| Reference nucleotide ("ref") | Reference nucleotide ("ref"): The nucleotide at reference position. |
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| New nucleotide ("alt") | New nucleotide ("alt"): Substituted nucleotide. |
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| Reference sequence | Reference sequence: A sequence file that is used as a reference to describe variants that are present in an analysed sequence. |
|---|
| Source name | Source name: The name of the data source containing the reference sequence. |
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| Accession number | Accession number: A unique identifier to refer to a sequence record in a sequence repository. |
|---|
| Version number | Version number: An attribute that provides a specific indication of the sequence used for annotation. |
|---|
| 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
|
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| Genetic translocation variant | Genetic translocation variant: Translocation variant. |
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| Breakpoint position 1 | Breakpoint position 1: Position of first breakpoint relative to start of "Chromosome 1". |
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| 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". |
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| Reference sequence | Reference sequence: A sequence file that is used as a reference to describe variants that are present in an analysed sequence. |
|---|
| 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: An attribute that provides a specific indication of the sequence used for annotation. |
|---|
| 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
|
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| Breakpoint position 2 | Breakpoint position 2: Position of second breakpoint relative to start of "Chromosome 2". |
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| 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". |
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| Reference sequence (2) | Reference sequence (2): A sequence file that is used as a reference to describe variants that are present in an analysed sequence. |
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| Source name | Source name: The name of the data source containing the reference sequence. |
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| Accession number | Accession number: A unique identifier to refer to a sequence record in a sequence repository. |
|---|
| Version number | Version number: An attribute that provides a specific indication of the sequence used for annotation. |
|---|
| URL | URL: Network address. |
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| 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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| HGVS term | HGVS term: The description of the variant using the recommendations of the accepted HGVS nomeclature named extension ISCN. |
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| Genetic deletion-insertion variant | Genetic deletion-insertion variant: A genetic sequence change where, compared to a reference sequence, one or more nucleotides are replaced by one or more other nucleotides and which is not a substitution, inversion or conversion. |
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| Start position | Start position: Position of the deleted nucleotide or the first nucleotide of the deleted range. |
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| End position | End position: Position of the last nucleotide of the deleted range. |
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| Deleted nucleotide(s) | Deleted nucleotide(s): The deleted nucleotide or sequence. |
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| Inserted nucleotide(s) | Inserted nucleotide(s): The sequence inserted. |
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| Reference sequence | Reference sequence: A sequence file that is used as a reference to describe variants that are present in an analysed sequence. |
|---|
| 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: An attribute that provides a specific indication of the sequence used for annotation. |
|---|
| 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
|
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| Insertion variant | Insertion variant: A sequence change where, compared to the reference sequence, one or more nucleotides are inserted and where the insertion is not a copy of a sequence immediately 5'. |
|---|
| Start position | Start position: The position of the first of the two flanking nucleotides. |
|---|
| End position | End position: The position of the last of the two flanking nucleotides. |
|---|
| Inserted nucleotide(s) | Inserted nucleotide(s): The sequence inserted between the two flanking nucleotides. |
|---|
| Reference sequence | Reference sequence: A sequence file that is used as a reference to describe variants that are present in an analysed sequence. |
|---|
| 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: An attribute that provides a specific indication of the sequence used for annotation. |
|---|
| 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
|
|---|
| 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 variants that are present in an analysed sequence. |
|---|
| 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.
Value set: terminology://www.hgvs.org/mutnomen/refseq.html#standard |
|---|
| URL | URL: Network address. |
|---|
| DNARegionName | DNARegionName: A human readable name for the region of interest. Typically Exon #, Intron # or other. |
|---|
| 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"
NC_000023.10:g.33038255C>A |
|---|
| 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
|
|---|
| Predicted impact | Predicted impact: Estimate of the effects that each variant may have on the transcript.
Calculation is based on a precise data source and only done by software. |
|---|
| Score | Score: The calculated value.
Units: (UCUM: 1) |
|---|
| Qualitative prediction | Qualitative prediction: Human readable version of the predicted impact. |
|---|
| Reported impact | Reported impact: Intepretation of the Mutation linked to a specific paper (e.g. activation, deactivating, dysfunction…). |
|---|
| 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. |
|---|
| Impact / Variantenklassifikation | Impact / Variantenklassifikation: Interpretative data about the specific variant.
- Aktivierende Mutation
- Vermutlich Aktivierende Mutation
- Vermutlich Deletär
- Deletär
- Variante unbekannter Signifikanz
- Polymorphismus
- Vermutlicher Polymorphismus
- Resistenzmutation
- [...]
|
|---|
| Gene | Gene: Structured details about the gene harboring the variant. |
|---|
| Gen-Name | Gen-Name: The official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name.
For example "CHD5". |
|---|
| Full name | Full name: The full gene name approved by the HGNC that convey 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): Single DNA marker or individual allele interpretation in the context of the assessed genetic disease according to the ACMG recommendations.
- Pathogenic
- Likely pathogenic
- Uncertain significance
- Likely benign
- Benign
|
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| Fusionstranskript-Name 2 (Fusion exon) | Fusionstranskript-Name 2 (Fusion exon): The number of the exon which is either the end or the beginning of the fusion. |
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| Best transcript candidate | Best transcript candidate: The ID of the transcript with the highest predicted impact. |
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| Lesetiefe an Variantenposition (Read depth) | Lesetiefe an Variantenposition (Read depth): Total number of reads mapped at this specific location. |
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| Allele depth | Allele depth: The number of reads that support the reported variant. |
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| Allelfrequenz (Allele frequency) | Allelfrequenz (Allele frequency): The relative frequency of an allele at a particular locus, expressed as a number from 0 to 1.
0..1 (UCUM: 1) |
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| Population allele frequency details | Population allele frequency details: The relative frequency of a particular allele in the population, expressed as a number from 0 to 1. |
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| Population allele frequency | Population allele frequency: The population allele frequency.
0..1 (UCUM: 1) |
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| 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. |
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| Filter name | Filter name: Name of the quality filter.
For example "q10". |
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| Description | Description: Quality filter extended description.
For example "at this site the quality is below 10". |
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| Filter passed | Filter passed: Whether the variant passed the quality filter. |
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| Strand bias ratio | Strand bias ratio: The ratio of the strand bias.
Units: (UCUM: 1) |
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| Strand bias p-value | Strand bias p-value: The Phred-scaled p-value of the strand bias.
Units: (UCUM: 1) |
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| Genotype | Genotype: Genotype encoded as allele values separated by either of / or | (0 for the reference allele, 1 for the first alternate, etc.). |
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| 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
|
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| Genotype quality | Genotype quality: Conditional genotype quality, encoded as a phred quality. |
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| 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. |
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| Genetic Variant Assessment | Genetic Variant Assessment: Assessment of the presence or absence of a specific DNA variants.
'No Call' is different from 'Absent', because 'No Call' did not result in the determination of the marker's presence or absence. This may be due to test failure or specimen specific context which renders the test ineffective.
- Present
- Absent
- No call
- Indeterminate
|
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| 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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| Analyse-ID / Laborinterne Kennzeichnung | Analyse-ID / Laborinterne Kennzeichnung: 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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| 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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| Sequencing technology | Sequencing technology: 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
|
|---|
| 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. |
|---|
| 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. |
|---|
| Kit name | Kit name: Name of the kit used for the experiment.
- Text
- Coded Text
- Oncomine Comprehensive Panel V3
|
|---|
| Nucleic acid | Nucleic acid: Type of nucleic acid used for sequencing, e.g. DNA, RNA oder cf-DNA.
- Text
- Coded Text
|
|---|
| Tumor cell percentage | Tumor cell percentage: To record the tumor cell content in percent.
0..100 |
|---|
| Tested Genes | Tested Genes: List of all tested genes, if panel sequencing was performed. |
|---|
| Gen symbol | Gen symbol: The official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name. |
|---|
| Gen name | Gen name: The full gene name approved by the HGNC that convey the character or function of the gene. |
|---|
| Tested Region | Tested Region: List of all tested regions, if panel sequencing was performed. |
|---|
| 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. |
|---|
| Comment | Comment: Comment on the sequencing assay that was not captured in other fields. |
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