PanCNV-Explorer: Deciphering copy number alterations across human cancers

Abstract Copy number variants (CNVs) are major drivers of cancer progression and genetic disorders, yet their interpretation, spanning biological mechanisms, clinical relevance, and therapeutic implications, remains fragmented across disparate resources. To bridge this gap, we present PanCNV-Explorer, a unified database integrating harmonized copy number variation data across 33 cancer types, cancer cell lines, and healthy cohorts. PanCNV-Explorer provides a genome-wide atlas of CNV frequency and functional impact, quantifying tissue-specific amplifications and deletions in both cancer and non-cancer contexts through rigorous cross-dataset normalization. The interactive web interface enables researchers to dynamically query CNVs by genomic coordinates or gene symbol, visualize cancer-type-specific frequencies with real-time comparative analysis, and explore integrated genomic features including transcripts, regulatory elements, and gene expression through a zoomable genome browser. Beyond exploration, the platform offers programmatic APIs for pan-cancer CNV analysis and visualization. A public web instance of PanCNV-Explorer is available at https://mtb.bioinf.med.uni-goettingen.de/pancnv-explorer/ .