CNAScope: pan-cancer copy number aberration database with functional annotation and interactive visualization

Nucleic Acids Res. 2025 Nov 20:gkaf1242. doi: 10.1093/nar/gkaf1242. Online ahead of print.

ABSTRACT

Copy number aberrations (CNAs) are critical drivers of genomic diversity in oncology, where recurrent CNAs frequently underlie tumorigenesis. However, existing public resources are limited in their somatic CNA specificity, breadth across multiple data modalities, and support for recurrent CNAs with online functional annotation and interactive visualization. Here, we present CNAScope (https://cna.fengslab.com/), a database that curates and functionally annotates over 3 954 361 CNA profiles and 3 946 319 metadata from 810 datasets, 174 464 samples, 3 018 672 single cells, and 764 232 spatial cells/spots, spanning 77 cancer subtypes from eight data sources and 55 cancer initiatives and institutions. CNAScope offers downloadable CNA annotations and interactive visualizations at bin, gene, and pathway term levels, including phylogenetic inference, clustering, dimension reduction, and focal/consensus CNA detection. Users can explore data through interactive heatmaps, phylogenetic trees, embedding plots, CN charts, and focal/consensus plots, or upload and annotate their own CNAs in real time. In all, with its large curated data volume and rich annotation capabilities, CNAScope serves as a vital resource for accelerating cancer research.

PMID:41263112 | DOI:10.1093/nar/gkaf1242