An efficient algorithm for the extraction of HGVS variant descriptions from sequences

Jonathan K. Vis; Martijn Vermaat; Peter E.M. Taschner; Joost N. Kok; Jeroen F.J. Laros

doi:10.1093/bioinformatics/btv443

An efficient algorithm for the extraction of HGVS variant descriptions from sequences

Jonathan K. Vis, Martijn Vermaat, Peter E.M. Taschner, Joost N. Kok, Jeroen F.J. Laros

Research output: Contribution to journal › Article › Academic › peer-review

24 Citations (Scopus)

Abstract

Motivation: Unambiguous sequence variant descriptions are important in reporting the outcome of clinical diagnostic DNA tests. The standard nomenclature of the Human Genome Variation Society (HGVS) describes the observed variant sequence relative to a given reference sequence. We propose an efficient algorithm for the extraction of HGVS descriptions from two sequences with three main requirements in mind: minimizing the length of the resulting descriptions, minimizing the computation time and keeping the unambiguous descriptions biologically meaningful. Results: Our algorithm is able to compute the HGVS descriptions of complete chromosomes or other large DNA strings in a reasonable amount of computation time and its resulting descriptions are relatively small. Additional applications include updating of gene variant database contents and reference sequence liftovers.

Original language	English
Pages (from-to)	3751-3757
Number of pages	7
Journal	Bioinformatics
Volume	31
Issue number	23
DOIs	https://doi.org/10.1093/bioinformatics/btv443
Publication status	Published - 18 Jun 2015
Externally published	Yes

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© The Author 2015. Published by Oxford University Press. All rights reserved.

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abstract = "Motivation: Unambiguous sequence variant descriptions are important in reporting the outcome of clinical diagnostic DNA tests. The standard nomenclature of the Human Genome Variation Society (HGVS) describes the observed variant sequence relative to a given reference sequence. We propose an efficient algorithm for the extraction of HGVS descriptions from two sequences with three main requirements in mind: minimizing the length of the resulting descriptions, minimizing the computation time and keeping the unambiguous descriptions biologically meaningful. Results: Our algorithm is able to compute the HGVS descriptions of complete chromosomes or other large DNA strings in a reasonable amount of computation time and its resulting descriptions are relatively small. Additional applications include updating of gene variant database contents and reference sequence liftovers.",

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AU - Laros, Jeroen F.J.

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AB - Motivation: Unambiguous sequence variant descriptions are important in reporting the outcome of clinical diagnostic DNA tests. The standard nomenclature of the Human Genome Variation Society (HGVS) describes the observed variant sequence relative to a given reference sequence. We propose an efficient algorithm for the extraction of HGVS descriptions from two sequences with three main requirements in mind: minimizing the length of the resulting descriptions, minimizing the computation time and keeping the unambiguous descriptions biologically meaningful. Results: Our algorithm is able to compute the HGVS descriptions of complete chromosomes or other large DNA strings in a reasonable amount of computation time and its resulting descriptions are relatively small. Additional applications include updating of gene variant database contents and reference sequence liftovers.

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An efficient algorithm for the extraction of HGVS variant descriptions from sequences

Abstract

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