Circular RNAs (circRNAs) are an intriguing class of RNA due to their covalently closed
structure, high stability, and implicated roles in gene regulation. Here, we used
an exome capture RNA sequencing protocol to detect and characterize circRNAs across
>2,000 cancer samples. When compared against Ribo-Zero and RNase R, capture sequencing
significantly enhanced the enrichment of circRNAs and preserved accurate circular-to-linear
ratios. Using capture sequencing, we built the most comprehensive catalog of circRNA
species to date: MiOncoCirc, the first database to be composed primarily of circRNAs
directly detected in tumor tissues. Using MiOncoCirc, we identified candidate circRNAs
to serve as biomarkers for prostate cancer and were able to detect circRNAs in urine.
We further detected a novel class of circular transcripts, termed read-through circRNAs,
that involved exons originating from different genes. MiOncoCirc will serve as a valuable
resource for the development of circRNAs as diagnostic or therapeutic targets across
cancer types.