TEMPLATE Genomics example template (Genomics example template)

Name: Genomics example template
License: http://creativecommons.org/licenses/by-sa/3.0/

TEMPLATE ID	Genomics example template
Concept	Genomics example template
Description	Example of how the genomics archetypes are intended to be used together and within the OBSERVATION.laboratory_test_result archetype.
Use	Only for example use.
Purpose	Example of how the genomics archetypes are intended to be used together and within the OBSERVATION.laboratory_test_result archetype.
References
Authors	date: 2019-04-25; name: Silje Ljosland Bakke; organisation: Nasjonal IKT HF; email: silje.ljosland.bakke@nasjonalikt.no
Other Details Language	date: 2019-04-25; name: Silje Ljosland Bakke; organisation: Nasjonal IKT HF; email: silje.ljosland.bakke@nasjonalikt.no
Other Details (Language Independent)	Licence: This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/. Custodian Organisation: openEHR Foundation Original Namespace: org.openehr Original Publisher: openEHR Foundation Custodian Namespace: org.openehr MD5-CAM-1.0.1: a65f8cbb6cb304350447072509dda27b PARENT:MD5-CAM-1.0.1: C73B6234DE67D5588E6486968624168B Original Language: ISO_639-1::en
Language used	en
Citeable Identifier	1013.26.223
Root archetype id	openEHR-EHR-OBSERVATION.laboratory_test_result.v1
Laboratory test result	Laboratory test result: 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
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)'.
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
Overall test status timestamp	Overall test status timestamp: The date and/or time that ‘Overall test status’ was issued.
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.
Genomic variant result	Genomic variant result: Result of a genomic test for one variant in a human individual.
Knowledge base reference	Knowledge base reference: 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.
Knowledge base name	Knowledge base name: The name of the knowledge base. For example: Galaxy/Snakemake; dbSNP; or CADD.
Knowledge base version	Knowledge base version: The version of the referenced knowledge base.
Knowledge base URI	Knowledge base URI: The hyperlink to the referenced knowledge base.
Item name	Item name: The name of the referenced item within the knowledge base. For example: rs139581412.
Item version	Item version: The version of the referenced item within the knowledge base.
Item publication	Item publication: Date and/or time when the item within the database was published.
Item URI	Item URI: The hyperlink to the referenced item within the knowledge base.
Comment	Comment: Additional narrative about the knowledge base, not captured in other fields.
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.
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
Knowledge base reference (2)	Knowledge base reference (2): 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.
Knowledge base name	Knowledge base name: The name of the knowledge base. For example: Galaxy/Snakemake; dbSNP; or CADD.
Knowledge base version	Knowledge base version: The version of the referenced knowledge base.
Knowledge base URI	Knowledge base URI: The hyperlink to the referenced knowledge base.
Item name	Item name: The name of the referenced item within the knowledge base. For example: rs139581412.
Item version	Item version: The version of the referenced item within the knowledge base.
Item publication	Item publication: Date and/or time when the item within the database was published.
Item URI	Item URI: The hyperlink to the referenced item within the knowledge base.
Comment	Comment: Additional narrative about the knowledge base, not captured in other fields.
Variant	Variant: 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.
Genomic conversion variant	Genomic conversion variant: A human genetic sequence change where, compared to a genomic reference sequence, a range of nucleotides are replaced by a sequence from elsewhere in the genome.
Start converted position	Start converted position: The position of the first nucleotide of the converted range.
End converted position	End converted position: The position of the last nucleotide of the converted range.
Replacing sequence start position	Replacing sequence start position: The position of the first nucleotide of the replacing sequence.
Replacing sequence end position	Replacing sequence end position: The position of the last nucleotide of the replacing sequence.
Genomic copy number variant	Genomic copy number variant: A human genetic sequence change where, compared to a genomic reference sequence, a DNA segment, that is 1 kilobases (kb) or larger, 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. >1
Copy number change type	Copy number change type: Type of sequence alteration. Different type of impact, such as low-level amplification or whole gene deletion, should be recorded using the Reported impact Cluster within the CLUSTER.genetic_variant.v0 archetype. Gain Loss
Genomic deletion variant	Genomic deletion variant: A human sequence change where, compared to a genomic reference sequence, one or more nucleotides are not present (deleted). For example: changing 'AGAAtCACA' to 'AGAA_CACA'.
Start position	Start position: Position of the deleted nucleotide or the first nucleotide of the deleted range. For example: for a variant where the reference sequence 'AGAatcACA' is changed to 'AGA___ACA' the start position is 4.
End position	End position: Position of the last nucleotide of the deleted range. For example: for a variant where the reference sequence 'AGAatcACA' is changed to 'AGA___ACA' the end position is 6.
Deleted sequence	Deleted sequence: The deleted nucleotide or sequence. For example: for a variant where the reference sequence 'AGAatcACA' is changed to 'AGA___ACA' the deleted sequence is 'ATC'.
Genomic deletion-insertion variant	Genomic deletion-insertion variant: A human genetic sequence change where, compared to a genomic reference sequence, one or more nucleotides are replaced by one or more other nucleotides and which is not a substitution, inversion or conversion. For example: changing 'AGGCtcaTT' to 'AGGCcTT'.
Start position	Start position: Position of the deleted nucleotide or the first nucleotide of the deleted range. For example: for a variant where the reference sequence 'AGGCtcaTT' is changed to 'AGGCcTT', the start position is 5.
End position	End position: Position of the last nucleotide of the deleted range. For example: for a variant where the reference sequence 'AGGCtcaTT' is changed to 'AGGCcTT', the end position is 7.
Deleted sequence	Deleted sequence: The deleted nucleotide or sequence. For example: for a variant where the reference sequence 'AGGCtcaTT' is changed to 'AGGCcTT', the deleted sequence is 'TCA'.
Inserted sequence	Inserted sequence: The inserted nucleotide or sequence. For example: for a variant where the reference sequence 'AGGCtcaTT' is changed to 'AGGCcTT', the inserted nucleotide is 'C'.
Genomic duplication variant	Genomic duplication variant: A human genetic sequence change where, compared to a genomic reference sequence, a copy of one or more nucleotides are inserted directly 3' of the original copy of that sequence. For example: changing 'AGtagaGG' to 'AGtagatagaGG'.
Start position	Start position: Position of the duplicated nucleotide or the first nucleotide of the duplicated range. For example: for a variant where the reference sequence 'AGtagaGG' is changed to 'AGtagatagaGG', the start position is 3.
End position	End position: Position of the last nucleotide of the duplicated range. For example: for a variant where the reference sequence 'AGtagaGG' is changed to 'AGtagatagaGG', the end position is 6.
Duplicated sequence	Duplicated sequence: The duplicated nucleotide or sequence. For example: for a variant where the reference sequence 'AGtagaGG' is changed to 'AGtagatagaGG', the duplicated sequence is 'TAGA'.
Genomic insertion variant	Genomic insertion variant: A human genetic sequence change where, compared to the genomic reference sequence, one or more nucleotides are inserted and where the insertion is not a copy of a sequence immediately 5'. For example: changing 'AGTAGAGG' to 'AGTAGatAGG'.
Start position	Start position: The position of the first of the two flanking nucleotides. For example: for a variant where the reference sequence 'AGTAGAGG' is changed to 'AGTAGatAGG', the start position is 5.
End position	End position: The position of the last of the two flanking nucleotides. For example: for a variant where the reference sequence 'AGTAGAGG' is changed to 'AGTAGatAGG', the end position is 6.
Inserted sequence	Inserted sequence: The inserted nucleotide or sequence. For example: for a variant where the reference sequence 'AGTAGAGG' is changed to 'AGTAGatAGG', the inserted sequence is 'AT'.
Genomic inversion variant	Genomic inversion variant: A human genetic sequence change where more than one nucleotide replaces the original sequence with the reverse complement of the original sequence, compared to a genomic reference sequence. For example: changing 'TCAG' to 'CTGA'.
Start position	Start position: Position of the first nucleotide of the inverted range, in relation to the reference sequence. For example: for a variant where the reference sequence 'CAtcagCCT' is changed to 'CActgaCCT', the start position is 3.
End position	End position: Position of the last nucleotide of the inverted range, in relation to the reference sequence. For example: for a variant where the reference sequence 'CAtcagCCT' is changed to 'CActgaCCT', the end position is 6.
Inverted sequence	Inverted sequence: The inverted sequence. For example: for a variant where the reference sequence 'CAtcagCCT' is changed to 'CActgaCCT', the inverted sequence is 'TCAG'.
Genomic repeated sequence variant	Genomic repeated sequence variant: A human genetic sequence change where, compared to a genomic reference sequence, a segment of one or more nucleotides (the repeat unit) is present several times, one after the other. For example: changing 'CACGGCCT' to 'CACGGcggcggCCT'. For example: changing 'CGG' to 'CGGCGGCGG'.
Start position	Start position: Position of the first nucleotide of the repeated range, in relation to the reference sequence. For example: for a variant where the reference sequence 'CACGGCCT' is changed to 'CACGGcggcggCCT', the start position is 3.
End position	End position: Position of the last nucleotide of the repeated range, in relation to the reference sequence. For example: for a variant where the reference sequence 'CACGGCCT' is changed to 'CACGGcggcggCCT', the end position is 5.
Repeat unit	Repeat unit: A repeated unit consisting of a repeated sequence and a copy number. This cluster is repeatable to allow for mixed repeats. For example: for a variant where the reference sequence is 'GGC[9]GGA[1]GGC[10]', a mixed repeat could be 'GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]'. The numbers in brackets in the example are the copy numbers.
Repeat order	Repeat order: The intended position of this repeat unit within the overall sequence of repeat units. This element is only relevant for mixed repeats. For example: for a variant where the reference sequence is 'GGC[9]GGA[1]GGC[10]' and the mixed repeat is 'GGC[10]GGA[1]GGC[9]GGA[2]GGC[11]', the 'Repeat order' for 'GGC[10]' is 1, for 'GGA[1]' 2, for 'GGC[9]' 3, and so on.
Repeated sequence	Repeated sequence: The sequence of nucleotides that has been repeated. For example: for a variant where the reference sequence 'CACGGCCT' is changed to 'CACGGcggcggCT', the repeated sequence is 'CGG'.
Copy number	Copy number: The total number of times the 'Repeated sequence' was repeated. For example: for a variant where the reference sequence 'CACGGCCT' is changed to 'CACGGcggcggCCT', the copy number is 3. >=2
Genomic substitution variant	Genomic substitution variant: A human genetic sequence change where, compared to a genomic reference sequence, one nucleotide is replaced by one other nucleotide. For example: changing 'AGTAgAGG' to 'AGTAtAGG'.
Position substituted	Position substituted: The position of the sustituted nucleotide. For example: for a variant where the reference sequence 'AGTAgAGG' is changed to 'AGTAtAGG', the position substituted is 5.
Reference nucleotide	Reference nucleotide: The nucleotide at reference position. For example: for a variant where the reference sequence 'AGTAgAGG' is changed to 'AGTAtAGG', the reference nucleotide is 'G'.
New nucleotide	New nucleotide: Substituted nucleotide. For example: for a variant where the reference sequence 'AGTAgAGG' is changed to 'AGTAtAGG', the new nucleotide is 'T'.
Genetic translocation variant	Genetic translocation variant: Translocation variant.
Breakpoint position 1	Breakpoint position 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".
Breakpoint position 2	Breakpoint position 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".
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.
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
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.
DNA change	DNA change: Description of the variation at the DNA level following the HGVS nomenclature. For example: 'c.5249C>T'.
Amino acid change	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.
Knowledge base reference	Knowledge base reference: 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.
Knowledge base name	Knowledge base name: The name of the knowledge base. For example: Galaxy/Snakemake; dbSNP; or CADD.
Knowledge base version	Knowledge base version: The version of the referenced knowledge base.
Knowledge base URI	Knowledge base URI: The hyperlink to the referenced knowledge base.
Item name	Item name: The name of the referenced item within the knowledge base. For example: rs139581412.
Item version	Item version: The version of the referenced item within the knowledge base.
Item publication	Item publication: Date and/or time when the item within the database was published.
Item URI	Item URI: The hyperlink to the referenced item within the knowledge base.
Comment	Comment: Additional narrative about the knowledge base, not captured in other fields.
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	Impact: 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 symbol	Gene symbol: 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 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.
Part of fusion	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
ACMG classification	ACMG classification: The clinical significance according to the ACMG recommendations. Pathogenic Likely pathogenic Uncertain significance Likely benign Benign
Fusion exon	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'.
Conservation	Conservation: Structured details about the evolutionary conservation.
Knowledge base reference	Knowledge base reference: 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.
Knowledge base name	Knowledge base name: The name of the knowledge base. For example: Galaxy/Snakemake; dbSNP; or CADD.
Knowledge base version	Knowledge base version: The version of the referenced knowledge base.
Knowledge base URI	Knowledge base URI: The hyperlink to the referenced knowledge base.
Item name	Item name: The name of the referenced item within the knowledge base. For example: rs139581412.
Item version	Item version: The version of the referenced item within the knowledge base.
Item publication	Item publication: Date and/or time when the item within the database was published.
Item URI	Item URI: The hyperlink to the referenced item within the knowledge base.
Comment	Comment: Additional narrative about the knowledge base, not captured in other fields.
Score	Score: The conservation score. Units: (UCUM: 1)
Read depth	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.
Knowledge base reference	Knowledge base reference: 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.
Knowledge base name	Knowledge base name: The name of the knowledge base. For example: Galaxy/Snakemake; dbSNP; or CADD.
Knowledge base version	Knowledge base version: The version of the referenced knowledge base.
Knowledge base URI	Knowledge base URI: The hyperlink to the referenced knowledge base.
Item name	Item name: The name of the referenced item within the knowledge base. For example: rs139581412.
Item version	Item version: The version of the referenced item within the knowledge base.
Item publication	Item publication: Date and/or time when the item within the database was published.
Item URI	Item URI: The hyperlink to the referenced item within the knowledge base.
Comment	Comment: Additional narrative about the knowledge base, not captured in other fields.
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.
Specimen identifier	Specimen identifier: Identification of the specimen used for the genomic result. In some situations, a single OBSERVATION.laboratory_test_result archetype will contain multiple CLUSTER.specimen archetypes and multiple CLUSTER.genomic_variant_result archetypes. In these situations, this 'Specimen identifier' data element is needed to be able to connect the results with the correct specimens. Identifier URI
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'.
Comment	Comment: Additional narrative about the test result not captured in other fields.
State
Confounding factors	Confounding factors: Issues or circumstances that impact on the accurate interpretation of the measurement or test result. 'Confounding factors' should be reserved for uncontrolled/unplanned issues of patient state/physiology that might affect interpretation, for example 'recent exercise' or 'recent tobacco smoking'. Known or required preconditions, such as 'fasting' should be carried in the 'Sampling conditions' element within the CLUSTER.specimen archetype . In some cases preconditions are captured as part of the test name, for example 'Fasting blood glucose'. Known issues with specimen collection or handling, such as 'prolonged use of tourniquet' or 'sample haemolysed', should be carried in the 'Specimen quality' elements within CLUSTER.specimen archetype. Coding with a terminology is desirable, where possible.
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
Point-of-care test	Point-of-care test: This indicates whether the test was performed directly at Point-of-Care (POCT) as opposed to a formal result from a laboratory or other service delivery organisation. True if the test was performed directly at Point-of-Care (POCT).