Copy number variations (CNVs) within non-coding RNA loci may affect RNA biogenesis, expression, and function, thereby contributing to disease pathogenesis. To systematically investigate CNVs within circRNA loci, we collected somatic copy number segments from the TCGA Pan-Cancer cohort, covering 33 cancer types and 11,084 samples. Absolute integer copy numbers were inferred using the ABSOLUTE algorithm, and all genomic coordinates were mapped to the GRCh37/hg19 reference assembly. By intersecting these copy number segments with circBase circRNA loci, we identified 2,962,504 circRNA–copy number alteration associations across 33 cancer types. For each circRNA, Circ2CNV summarizes the per-cancer distribution of copy number states, including homozygous deletion, loss, normal, gain, and amplification, as well as loss of heterozygosity (LOH) status.

Circ2CNV is a newly developed module designed to retrieve copy number alterations within circRNA loci and explore their potential relevance across cancer types.