Copy number variation (cnv) - Dynamic NPU Manual

Copy number variation (cnv)

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

Abbreviation

 Cnv

Definition in words

Kind-of-property designating structural variation in the number of copies of one or more specific sequences from a reference sequence of the same kind.(Ref 1)

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

Systematic terms

 Copy number 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 NPUxxxxx DNA(B)—LDLR gene(LRG_274t1); cnv(proc.) = ?
Full form with a result NPUxxxxx DNA(Blood)—LDLR gene(LRG_274t1); copy number variation (procedure) = LRG_274t1:c.(2311+1_2312-1)_(∗807_?)del
Abbreviated form with a result NPUxxxxx DNA(Blood)—LDLR gene(LRG_274t1); cnv (proc.) = LRG_274t1:c.(2311+1_2312-1)_(∗807_?)del
Written expression The copy number variation of LDLR gene(LRG_274t1) of DNA in Mr. Smith’s blood is [ LRG_274t1:c.(2311+1_2312-1)_(∗807_?)del]. The examination is performed according to procedure defined by the laboratory.
Notes The NPU code is established according to model of Molecular biology and Genetics
Example 2
Generic abbreviated form NPUxxxxx DNA(spec.)—DMD gene; cnv(proc.) = ?
Full form with a result NPUxxxxx DNA(spec.)—DMD gene; copy number variation(procedure) = NG_012232.1(NM_004006.1):c.4072-1234_5155-246del
Abbreviated form with a result NPUxxxxx DNA(spec.)—DMD gene; cnv(proc.) = NG_012232.1(NM_004006.1):c.4072-1234_5155-246del
Written expression The copy number variation of DMD gene of DNA in Mr. Smith’s Plasma is [LRG_304:g.6529_6530AC[11];[19]]. 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 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

        • Copy number variation
Date Term Note Reference
2016-06-21 Copy number 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

 QU103472
Date Notes

Example
2019-12-04 This kind-of-property may be used for repeat expansion disorders