Sequence variation (seq.var.) - Dynamic NPU Manual

Sequence variation (seq.var.)

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

Sequence variation (seq.var.)

Abbreviation

 Seq.var.

Definition in words

Kind-of property designating variation consisting in deviations from a specified part of a reference sequence of the same kind. (Ref 1.)

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

Note: The sequences are assumed to be fully investigated (sequenced), even if only clinically relevant deviations are reported.

Systematic terms

 Sequence 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 values (a=b; a≠b)

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

Clinical Immunology

 Example 1
Generic abbreviated form NPU27995 DNA(spec.)—UGT1A1 gene; seq.var. = ?
Full form with a result NPU27995 DNA(specification)—UGT1A1 gene; sequence variation = LRG_733:g.8721[G>T];[=]
Abbreviated form with a result NPU27995 DNA(spec.)—UGT1A1 gene; seq.var. = LRG_733:g.8721[G>T];[=]
Written expression The sequence variation of UGT1A1 gene of DNA from leukocytes in Mr. Smith’s blood is LRG_733:g.8721[G>T];[=].
Notes
  1. The specification to system is specified as “leukocytes derived from Mr. Smith’s blood” by the laboratory.
  2. A full sequence of the UGT1A1 gene has been examined. The laboratory has decided to report only one variant.
  3. The NPU code is established according to model of Molecular biology and Genetics

Molecular Biology and Genetics

 

 

 Example 2
Generic abbreviated form NPU19240 DNA(spec.)—BCHE gene; seq.var. = ?
Full form with a result NPU19240 DNA(specification)—BCHE gene; sequence variation = NG_009031.1:g.56211[A>T];[A>T]
Abbreviated form with a result NPU19240 DNA(spec.)—BCHE gene; sequence variation = NG_009031.1:g.56211[A>T];[A>T]
Written expression The sequence variation of BCHE gene of DNA from leukocytes in Mr. Smith’s blood is [NG_009031.1:g.56211[A>T];[A>T]].
Notes
  1. The specification to system is specified as “leukocytes derived from Mr. Smith’s blood” by the laboratory.
  2. A full sequence of the BCHR gene has been examined. The laboratory has decided to report only one variant.
  3. The NPU code is established according to model of Molecular biology and Genetics
Example 3
Generic abbreviated form NPU54619 DNA(Marrow)—ASXL1 gene(LRG_630t1:c.1720_4626); seq.var. = ?
Full form with a result NPU54619 DNA(Marrow)—ASXL1 gene(LRG_630t1:c.1720_4626); sequence variation = LRG_630t1:c.1934[dupG]
Abbreviated form with a result NPU54619 DNA(Marrow)—ASXL1 gene(LRG_630t1:c.1720_4626); seq.var. = LRG_630t1:c.1934[dupG]
Written expression The sequence variation of ASXL1 gene(LRG_630t1:c.1720_4626) of DNA in Mr. Smith’s marrow is LRG_630t1:c.1934[dupG].
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
Example 4
Generic abbreviated form NPU57724 DNA(spec.)—FMR1 gene(NG_007529.1:g.5102GGC[size]); seq.var. = ?
Full form with a result NPU57724 DNA(specification)—FMR1 gene(NG_007529.1:g.5102GGC[size]); sequence variation = NG_007529.1:g.5102GGC [20];[40]
Abbreviated form with a result NPU57724 DNA(spec.)—FMR1 gene(NG_007529.1:g.5102GGC[size]); seq.var. = NG_007529.1:g.5102GGC [20];[40]
Written expression The sequence variation of FMR1 gene(NG_007529.1:g.5102GGC[size] of DNA in leukocytes derived from Mr. Smith’s marrow is NG_007529.1:g.5102GGC [20];[40] .
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

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
1996-01-01 Sequence variation Term established

NPU term identifier

 QU71310
Date Notes

Example
2019-12-02

This k-o-p was designed for reporting substitutions, small deletions, small insertions or small duplications. Hence, any small variations that are detected by sequencing the DNA.