A graph-based approach to variant description extraction from sequences
Santcroos, Mark A Kosters, Walter A Lefter, Mihai Laros, Jeroen FJ Vis, Jonathan K
Santcroos, Mark A
Kosters, Walter A
Lefter, Mihai
Laros, Jeroen FJ
Vis, Jonathan K
Series / Report no.
Open Access
Type
Journal Article
Article
Article
Language
en
Date of publication
2025-12-08
Year of publication
Research Projects
Organizational Units
Journal Issue
Title
A graph-based approach to variant description extraction from sequences
Translated Title
Published in
NAR Genom Bioinform 2025; 7(4):lqaf173
Abstract
Accurate variant descriptions are of paramount importance in the field of genomics. The domain is confronted with increasingly complex variants, e.g. combinations of multiple indels, making it challenging to generate proper variant descriptions directly from chromosomal sequences. We present a graph based on all minimal alignments that is a complete representation of a variant, which gives insight into the nature of a variant compared to a single variant description. We provide three complementary extraction methods to derive variant descriptions from this graph, including one that yields domain-specific constructs from the HGVS nomenclature. Our experiments show that our methods in comparison with dbSNP, the authoritative variant database from the NCBI, result in identical HGVS descriptions for simple variants and more meaningful descriptions for complex variants, in particular for repeat expansions and contractions.