TEMPLATE Molecular genetic findings (Molecular genetic findings)

Name: Molecular genetic findings
License: http://creativecommons.org/licenses/by-sa/4.0/

TEMPLATE ID	Molecular genetic findings
Concept	Molecular genetic findings
Description	Not Specified
Purpose	Not Specified
References
Authors	date: 2019-10-22; name: Aurelie Tomczak; organisation: Institute of Pathology, University Hospital Heidelberg, Germany; email: au.tomczak@yahoo.com
Other Details Language	date: 2019-10-22; name: Aurelie Tomczak; organisation: Institute of Pathology, University Hospital Heidelberg, Germany; email: au.tomczak@yahoo.com
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: 005501C1FA493A4838F5F1121F2870EC Build Uid: 049f2a54-38cd-40a4-ab98-a8bb28653e4c MD5-CAM-1.0.1: 4758ece0af6f88d805c8aaff53d83678 Original Language: ISO_639-1::en Sem Ver: 6.0.0
Language used	en
Citeable Identifier	1246.169.3399
Root archetype id	openEHR-EHR-COMPOSITION.report.v1
Molecular genetic findings	Molecular genetic findings: Document to communicate information to others, commonly in response to a request from another party.
Other Context
Report ID	Report ID: Identification information about the report.
Status	Status: The status of the entire report. Note: This is not the status of any of the report components. preliminarily final corrected
Case identification	Case identification: To record case identification details for public health purposes.
Case identifier	Case identifier: The identifier of this case.
Molecular genetic assessment	Molecular genetic assessment: The result, including findings and the laboratory's interpretation, of an investigation performed on specimens collected from an individual or related to that individual.
Data
Any event	Any event: Default, unspecified point in time or interval event which may be explicitly defined in a template or at run-time.
Data
Type of analysis	Type of analysis: 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: Molecular genetic assessment
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.
Specimen type	Specimen type: 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 Blood (EDTA) Blood (for cf-DNA extraction) Oral mucosa swab DNS RNA Normal tissue CSF [...] Annotations Fhir Mapping: Specimen.type
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}] Identifier Text Annotations Fhir Mapping: Specimen.accessionIdentifier
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
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
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
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
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.
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.
Sequencing result	Sequencing result: Cluster to combine sequencing assay, General sequencing parameters and all variant results of a single analysis.
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.
General sequencing result parameter	General sequencing result parameter: General sequencing result parameter.
Tumor cell content (pathologic/histologic)	Tumor cell content (pathologic/histologic): Tumor cell content determinded by pathologic/histologic methods. Units: %
Tumor cell content (bioinformatic)	Tumor cell content (bioinformatic): Tumor cell content determinded by bioinformatic methods. Units: %
Microsatellite instability (MSI)	Microsatellite instability (MSI): Microsatellite instability (MSI). 0..2
Tumor Mutational Burden (TMB) per Mb	Tumor Mutational Burden (TMB) per Mb: Tumor Mutational Burden (TMB) per Megabase.
BRCAness	BRCAness: BRCAness is defined as a phenotypic copy of germline BRCA mutations. 0..1
Sequencing assay	Sequencing assay: To record details of the sequencing analysis including a list of all tested genes if panel sequencing was performed.
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.
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.
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.
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).
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 DNA RNA cf-DNA
Tested Genes	Tested Genes: List of all tested genes, if panel sequencing was performed.
Gene symbol	Gene symbol: The official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name.
Gene name	Gene 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 on the quality of the analysis	Comment on the quality of the analysis: Comment on the sequencing assay that was not captured in other fields. Gute Qualität Eingeschränkte Qualität Kommentar [...]
Genomic variant result	Genomic variant result: Findings and annotations related to one variant found in a human individual by a sequencing test.
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.
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.
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.
Identification	Identification: The name of the referenced item within the knowledge base. For example: rs139581412.
Indentification Version	Indentification Version: The version of the referenced item within the knowledge base.
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.
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
Starting position of the variant / genome position (from vcf file)	Starting position of the variant / genome position (from vcf file): The position of the first nucleotide of the changed range for a simple variant. ("Start" in vcf-file).
End position of the variant / genome position (from vcf file)	End position of the variant / genome position (from vcf file): The position of the last nucleotide of the changed range for a simple variant. ("End" in vcf-file).
Alternative nucleotide sequence (Alt)	Alternative nucleotide sequence (Alt): The observed alternate nucleotide or nucleotide sequence ("Alt" in vcf-file).
Reference nucleotide sequence (Ref)	Reference nucleotide sequence (Ref): The reference nucleotide or nucleotide sequence. ("Ref" in vcf-file).
Transcript Reference	Transcript Reference: 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
Total copy number	Total copy number: Number of appearance of the allele. Count>=0 QuantityUnits: (UCUM: 1)
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. Gain Loss
Transcript Reference	Transcript Reference: 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".
Transcript Reference 1	Transcript Reference 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".
Transcript Reference 2	Transcript Reference 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.
Accession number	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 nomenclature variant (DNA change)	cDNA nomenclature variant (DNA change): Description of the variation at the DNA level following the HGVS nomenclature. For example: 'c.5249C>T'.
Protein level nomenclature variant (amino acid change)	Protein level nomenclature variant (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 / variant classification	Impact / variant classification: 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.
Gene name (HGNC)	Gene 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.
Fusion transcript name 1 (Part of fusion)	Fusion transcript 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. First Second
Pathogenicity class/variant classification (ACMG classification)	Pathogenicity class/variant classification (ACMG classification): The clinical significance according to the ACMG recommendations. Pathogenic Likely pathogenic Uncertain significance Likely benign Benign
Fusion transcript name 2 (fusion exon)	Fusion transcript 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'.
Read depth at variant position (median read depth)	Read depth at variant position (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
Allele frequency	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'.
Test diagnosis	Test diagnosis: 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'. no/benign variant identified Analysis takes place, but cannot be evaluated potentially pathogenic variant identified [...]
Comment	Comment: Additional narrative about the test result not captured in other fields.
Protocol
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
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'.
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.
Requester order identifier	Requester order identifier: The local identifier assigned by the requesting clinical system. Equivalent to the HL7 Placer Order Identifier. Identifier Text
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
Tumordiagnosis_section	Tumordiagnosis_section: Framework for consistent modelling of content within a template for a Problem list. Intended to be used within the COMPOSITION.problem_list.
Tumordiagnosis	Tumordiagnosis: 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'.
Data
Diagnosis name (ICD-10)	Diagnosis 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.
Variant	Variant: Specific variant or subtype of the Diagnosis, if relevant. For example: 'acute motor axonal neuropathy' as a variant of Guillain-Barre Syndrome. Coding of the name of the variant with a terminology is preferred, where possible.
Clinical description	Clinical description: 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.
Cause	Cause: A cause, set of causes, or manner of causation of the problem or diagnosis. Also known as 'aetiology' or 'etiology'. Coding with an external terminology is preferred, where possible.
Date/time of onset	Date/time of onset: 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.
Protocol
Tumor ID	Tumor ID: To display the ID of the tumor.
Tumor ID	Tumor ID: The ID/identifier of the tumor.
Anatomical location	Anatomical location: A physical site on or within the human body.
Body site name	Body site name: Identification of a single physical site either on, or within, the human body. This data element is the only mandated data point in this archetype and should be used as the primary data point to record an anatomical location with a commonly used name. It is strongly recommended that 'Body site name' be recorded as specifically as is anatomically possible. For example: record 'upper eyelid' rather than recording 'eyelid' with 'upper' as a qualifier; 'fifth rib' rather than 'rib' with a numeric qualifier. Use the other data elements for laterality, aspect, region and anatomical line to provide more detail. This data element should be coded with a terminology capable of triggering decision support, where possible - an appropriate termset for use here could comprise individual concepts or a list of precoordinated terms. Free text should be used only if there is no appropriate terminology available. If body site name is already identified in the parent archetype, then this data element may be redundant. Alternatively, a use case has been identified where the value may be duplicated into this element to support semantic querying using this archetype, rather than the data element within the parent.
Specific site	Specific site: Additional detail using a specific region or a point on, or within, the identified body site. Use to increase precision of identification of the body site, if required. For example, the upper right quadrant or McBurney's point on the abdominal wall or interphalangeal joint of the great toe. If the 'Body site name' data element uses pre-coordinated terms that include the specific site, then this data element is redundant. Left (L) Right (R) Multilocuary (X) Both sides (B) Centerline/Center (M) Unknown (U) Does not apply (T; page number not useful, including systemic diseases)

TEMPLATE Molecular genetic findings (Molecular genetic findings)

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