Structural variation (struc.var.) - Dynamic NPU Manual

Structural variation (struc.var.)

by | Feb 4, 2020 | List of kinds-of-property, Narrative kind-of-property

Structural variation (struc.var.)

Abbreviation

 Struc.var.

Definition in words

Kind-of-property designating sequence variation consisting of deviations in the position of one or more parts of the sequence from a reference sequence of the same kind.

Note: Used to describe position changes (inversions, translocations, insertions, deletions) of  large regions of DNA (approximately 1 kb and larger in size)

Systematic terms

 Structural variation of component B in system 1

Result type

 Narrative description
  • Value sets are structural sentences with two or more values
  • 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 NPU58070 DNA(spec.)—CYP2D6 gene(NG_008376.3:g.1_8953del); struc.var.(proc.) = ?
Full form with a result NPU58070 DNA(specification)—CYP2D6 gene(NG_008376.3:g.1_8953del); structure variation(procedure) = NG_008376.3:g.1_8953[Del)];[Del]
Abbreviated form with a result NPU58070 DNA(spec.)—CYP2D6 gene(NG_008376.3:g.1_8953del); struc.var.(proc.) = NG_008376.3:g.1_8953[Del)];[Del]
Written expression The structural variation of CYP2D6 gene(NG_008376.3:g.1_8953del) of DNA from leukocytes derived in Mr. Smith’s blood is [NG_008376.3:g.1_8953[Del)];[Del]]. The examination is performed according to procedure defined by the laboratory.
Notes
  1. The specification to system is specified as “leukocytes derived from Mr. Smith’s blood” by the laboratory.
  2. The value set should always be stated by Sequence Variant Nomenclature (HGVS-nomenclature).
  3. The NPU code is established according to model of Molecular biology and Genetics
Example 2
Generic abbreviated form NPU58075 DNA(spec.)—CYP2D6 gene(NG_008376.3:g.1_8953dup); struc.var.(proc.) = ?
Full form with a result NPU58075 DNA(specification)—CYP2D6 gene(NG_008376.3:g.1_8953dup); structural variation(procedure) = NG_008376.3:g.1_8953[Dup)];[Dup]
Abbreviated form with a result NPU58075 DNA(spec.)—CYP2D6 gene(NG_008376.3:g.1_8953dup); struc.var.(proc.) = NG_008376.3:g.1_8953[Dup)];[Dup]
Written expression The structural variation of CYP2D6 gene(NG_008376.3:g.1_8953dup) of DNA from leukocytes derived in Mr. Smith’s blood is [NG_008376.3:g.1_8953[Dup)];[Dup]]. The examination is performed according to procedure defined by the laboratory.
Notes
  1. The specification to system is specified as “leukocytes derived from Mr. Smith’s blood” by the laboratory.
  2. The value set should always be stated by Sequence Variant Nomenclature (HGVS-nomenclature).
  3. The NPU code is established according to model of Molecular biology and Genetics

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

      • Sequence variation

        • Structural 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 Structural 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

 QU104024