Introduction

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.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.The algorithm is accessible as an experimental service in the Mutalyzer program suite (https://mutalyzer.nl). The C++ source code and Python interface are accessible at: https://github.com/mutalyzer/description-extractor.j.k.vis@lumc.nl.

Publications

  1. An efficient algorithm for the extraction of HGVS variant descriptions from sequences.
    Cite this
    Vis JK, Vermaat M, Taschner PE, Kok JN, Laros JF, 2015-12-01 - Bioinformatics (Oxford, England)

Credits

  1. Jonathan K Vis
    Developer

    Department of Molecular Epidemiology, Leiden University Medical Center, United States of America

  2. Martijn Vermaat
    Developer

    Department of Human Genetics, Leiden University Medical Center

  3. Peter E M Taschner
    Developer

    Department of Human Genetics, Leiden University Medical Center

  4. Joost N Kok
    Developer

    Department of Molecular Epidemiology, Leiden University Medical Center, United States of America

  5. Jeroen F J Laros
    Investigator

    Department of Human Genetics, Leiden University Medical Center

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Summary
AccessionBT006705
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByJeroen F J Laros