Chromoscope: interactive multiscale visualization for structural variation in human genomes

Abstract

Whole genome sequencing is now routinely used to profile mutations in DNA in the soma and in the germline, informing molecular diagnoses of disease and therapeutic decisions. Structural variants (SVs) are the main new type of alterations we see more of, and they are often diagnostic, prognostic, or therapy-informing. However, the size and complexity of SV data, combined with the difficulty of obtaining accurate SV calls, pose challenges in the interpretation of SVs, requiring tedious visual inspection of potentially pathogenic variants with multiple visualization tools. To overcome the problems with the interpretation of SVs, we developed Chromoscope, an open-source web-based application for the interactive visualization of structural variants. Chromoscope has several innovative features which unlock the insights from whole genome sequencing: visualization at multiple scale levels simultaneously, effective navigation across scales; easy setup for loading users’ large datasets, and a feature to export, share, and further customize visualizations. We are hosting a freely available public instance of Chromoscope (https://chromoscope.bio) to showcase data from the ‘Pan-cancer Analysis of the Whole Genomes’ consortium, providing easy access to this reference dataset. We additionally facilitate the set up of visualizations for users’ data. We anticipate that Chromoscope will accelerate the exploration and interpretation of SVs by a broad range of scientists and clinicians, leading to new insights into genomic biomarkers.

Citation

S L’Yi, D Maziec, V Stevens, T Manz, A Veit, M Berselli, PJ Park, D Głodzik, N Gehlenborg. “Chromoscope: interactive multiscale visualization for structural variation in human genomes”, Nature Methods 20(12):1834-1835 (2023). doi:10.1038/s41592-023-02056-x