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Updated: Jan 9, 2026

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A graph-based approach to variant description extraction from sequences.

Mark A Santcroos1,2, Walter A Kosters3, Mihai Lefter1

  • 1Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands.

NAR Genomics and Bioinformatics
|December 10, 2025
PubMed
Summary

This study introduces a novel graph-based method for accurately describing complex genomic variants. The approach generates more meaningful descriptions than existing methods, particularly for repeat expansions and contractions.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Accurate genomic variant description is crucial in genomics.
  • Increasingly complex variants, like multiple indels, challenge current description methods.
  • Existing methods struggle with comprehensive variant representation.

Purpose of the Study:

  • To develop a complete representation of genomic variants using a graph-based approach.
  • To create methods for deriving variant descriptions from this graph.
  • To improve variant description accuracy, especially for complex cases.

Main Methods:

  • Constructing a graph from all minimal alignments to represent variants completely.
  • Developing three complementary extraction methods to derive variant descriptions from the graph.
  • Generating HGVS nomenclature constructs from the graph.

Main Results:

  • The graph-based method provides a complete variant representation.
  • Identical HGVS descriptions for simple variants compared to dbSNP.
  • More meaningful descriptions for complex variants, including repeat expansions/contractions.

Conclusions:

  • The proposed graph-based method offers a robust way to describe complex genomic variants.
  • This approach enhances variant description accuracy and detail compared to dbSNP.
  • The methods facilitate better understanding and analysis of genomic variations.