Variation (var.) - Dynamic NPU Manual

Variation (var.)

by | Jan 31, 2020 | List of kinds-of-property, Narrative kind-of-property

Variation (var.)

Abbreviation

 Var.

Definition in words

 Kind-of-property of entitic sequences (of DNA, chromosomes, genes, RNA, proteins) consisting in deviations from parts of a reference sequence of the same kind. (Ref 1.)

Systematic terms

 Variation of component B in system 1

Result type

 Narrative description
  • Value set is presented in a standardized and structural format
  • Value set comprises of two or more values

Note: Value sets for genetic or (protein sequence) examination are expressed by Sequence Variant Nomenclature (HGVS-nomenclature).
  • Algebraic operations are not allowed
  • Possible comparison of value sets (a=b; a≠b)

Special rule(s) in the NPU syntax 

“Procedure” is stated in the specification to the kind-of-property in the NPU definition

“Procedure” indicates that the measurement procedure must be stated somewhere else than the NPU code and there may be difficulties in comparing values for the same NPU code.

Reference
  1. Ulla M. Petersen, Ariadna Padró-Miquel, Graham Taylor, Jens Michael Hertz, Rebecca Ceder, Xavier Fuentes-Arderiu, Johan T. den Dunnen,
    Properties and units in the clinical laboratory sciences part XXIV. Properties and units in clinical molecular genetics (technical report 2017),
    Clinica Chimica Acta, Volume 484,2018,Pages 122-131,ISSN 0009-8981, https://doi.org/10.1016/j.cca.2018.05.028.
  2. Ferard G, Dybkaer R, Fuentes-Arderiu X. Compendium of Terminology and Nomenclature of Properties in Clinical Laboratory Sciences : Recommendations 2016. 1 ed: Royal Society of Chemistry; 2016. 182 p. Doi:10.1039/9781782622451.

Laboratory field

Examples

Molecular Biology and Genetics

 

 

 Example 1
Generic abbreviated form NPU57374 DNA(spec.)—FSHR gene(LRG_536:g.5046); variation(proc.) = ?
Full form with a result NPU57374 DNA(specification)—FSHR gene(LRG_536:g.5046); variation(procedure) = LRG_536:g.5046[G>A];[?]
Abbreviated form with a result NPU57374 DNA(spec.)—FSHR gene(LRG_536:g.5046); variation(proc.) = LRG_536:g.5046[G>A];[?]
Written expression The variation of FSHR gene(LRG_536:g.5046) of DNA from leukocytes derived in Mr. Smith’s blood is [LRG_536:g.5046[G>A];[?]]. The examination is performed according to procedure defined by the laboratory.
Notes
  1. The NPU code is established according to model of Molecular biology and Genetics
Example 2
Generic abbreviated form NPU58150 DNA(P)—ABO gene(NG_006669.1:g.21594); variation(proc.) = ?
Full form with a result NPU58150 DNA(Plasma)—ABO gene(NG_006669.1:g.21594); variation(procedure) = NG_006669.1:g.21594[=];[G>T]
Abbreviated form with a result NPU58150 DNA(P)—ABO gene(NG_006669.1:g.21594); variation(proc.) = NG_006669.1:g.21594[=];[G>T]
Written expression The variation of ABO gene(NG_006669.1:g.21594) of DNA in Mrs. Smith’s Plasma is [NG_006669.1:g.21594[=];[G>T]]. The examination is performed according to procedure defined by the laboratory.
Notes
  1. The NPU code is established according to model of Molecular biology and Genetics
Example 3
Generic abbreviated form NPU58404 DNA(P)—EGFR gene; variation(proc.) = ?
Full form with a result NPU58404 DNA(Plasma)—EGFR gene; variation(procedure) = LRG_304:g.159983[G>T];[=],  LRG_304:g.160745_160757[delinsC];[delinsC], LRG_304:g.167347[C>T][=]
Abbreviated form with a result NPU58404 DNA(P)—EGFR gene; variation(proc.) = LRG_304:g.159983[G>T];[=],  LRG_304:g.160745_160757[delinsC];[delinsC], LRG_304:g.167347[C>T];[=]
Written expression The variation of EFGR gene of DNA in Mr. Smith’s Plasma is [LRG_304:g.159983[G>T];[=],  LRG_304:g.160745_160757[delinsC];[delinsC], LRG_304:g.167347[C>T][=]]. The examination is performed according to procedure defined by the laboratory.
Notes
  1. The NPU code is established according to model of Molecular biology and Genetics
  2. The laboratory has examined for more than one variant in several locations of the EGFR gene

Reference

 NPU database, https://www.ifcc.org/ifcc-scientific-division/sd-committees/c-npu/npusearch/ and http://www.labterm.dk/default.aspx

  • Kind-of-property

    • Variation

Reference
  • Dybkaer R. Concept system on ‘quantity’: formation and terminology. Accredit Qual Assur. 2013;18(3):253-60.
  • Dybkaer R. ISO terminological analysis of the VIM3 concepts ‘quantity’ and ‘kind-of-quantity’. Metrologia. 2010;47(3):127-34.
Date Term Note Reference
2017-03-27 Variation Term established

Ulla M. Petersen, Ariadna Padró-Miquel, Graham Taylor, Jens Michael Hertz, Rebecca Ceder, Xavier Fuentes-Arderiu, Johan T. den Dunnen,
Properties and units in the clinical laboratory sciences part XXIV. Properties and units in clinical molecular genetics (technical report 2017),
Clinica Chimica Acta, Volume 484,2018,Pages 122-131,ISSN 0009-8981, https://doi.org/10.1016/j.cca.2018.05.028.

NPU term identifier

 QU104023
Date Notes

Example
2019-12-02

This k-o-p was designed to characterize examinations of unspecified variant sets by various variation related kinds-of-property (e.g. copy number variation, sequence variation, etc).