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.

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.
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.
Example 4
Generic abbreviated form NPU57724 DNA(spec.)—FMR1 gene(NG_007529.1:g.5102GGC); seq.var. = ?
Full form with a result NPU57724 DNA(specification)—FMR1 gene(NG_007529.1:g.5102GGC); sequence variation = NG_007529.1:g.5102GGC [20];[40]
Abbreviated form with a result NPU57724 DNA(spec.)—FMR1 gene(NG_007529.1:g.5102GGC); seq.var. = NG_007529.1:g.5102GGC [20];[40]
Written expression The sequence variation of FMR1 gene(NG_007529.1:g.5102GGC 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.

Reference

  • 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.