Journal Article

Complex structural variant visualization with SVTopo

Saunders, Christopher T., Lake, Juniper A., Rowell, William J., Eberle, Michael A., Kronenberg, Zev, Holt, James Matthew, Belyeu, Jonathan R.

2025

Overview

Background Structural variants are genomic variants that impact at least 50 nucleotides. Structural variants can play major roles in diversity and human health. Many structural variants are difficult to interpret and understand with existing visualization tools, especially when comprised of inverted sequences or multiple breakend pairs. Results We present SVTopo, a tool to visualize germline structural variants with supporting evidence from high-accuracy long reads in easily understood figures. We include examples of 101 visually complex structural variants from seven unrelated human genomes, manually assigned to ten categories. These demonstrate a broad spectrum of rearrangement and showcase the frequency of complex structural variants in human genomes. Conclusions SVTopo shows breakpoint evidence in ways that aid reasoning about the impact of multi-breakpoint rearrangements. The images created aid human reasoning about the result of structural variation on gene and regulatory regions.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Animal Genetics and Genomics / Applications software / Biomedical and Life Sciences / Complex SV / Genetic research / Genome visualization / Genome, Human / Genomes / Genomic Structural Variation / Genomic structural variations / Genomics - methods / Haplotypes / Humans / Life Sciences / Long-read sequencing / Microarrays / Microbial Genetics and Genomics / Nucleotides / Physiological aspects / Plant Genetics and Genomics / Proteomics / Reasoning / Regulatory sequences / Software / Structural variant / Visualization