A graph-based approach to variant description extraction from sequences
NAR Genomics and Bioinformatics, vol. 7, pp. 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.
Authors 4
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Leiden University Medical Center
Affiliation as printed
Department of Clinical Genetics, Leiden University Medical Center , 2333 ZC Leiden ,
Department of Human Genetics, Leiden University Medical Center , 2333 ZC Leiden,
Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
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Affiliation as printed
Leiden Institute of Advanced Computer Science, Leiden University , 2333 CC Leiden ,
Leiden Institute of Advanced Computer Science, Leiden University, 2333 CC Leiden, the Netherlands
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Leiden University Medical Center · National Institute for Public Health and the Environment
Affiliation as printed
Department of Human Genetics, Leiden University Medical Center , 2333 ZC Leiden,
National Institute for Public Health and the Environment (RIVM) , 3721 MA Bilthoven ,
Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, the Netherlands
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Leiden University · Leiden University Medical Center
Affiliation as printed
Department of Human Genetics, Leiden University Medical Center , 2333 ZC Leiden,
Leiden Institute of Advanced Computer Science, Leiden University , 2333 CC Leiden ,
Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
Leiden Institute of Advanced Computer Science, Leiden University, 2333 CC Leiden, the Netherlands
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