IPScan: Detecting novel intronic PolyAdenylation events with RNA-seq data

Intronic PolyAdenylation (IPA) is an important post-transcriptional mechanism that can alter transcript coding potential by truncating translation regions, thereby increasing transcriptome and proteome diversity. This process generates novel protein isoforms with altered peptide sequences, some of which are implicated in disease progression, including cancer. Truncated proteins may lose tumor-suppressive functions, contributing to oncogenesis. Despite advancements in Alternative PolyAdenylation (APA) analysis using RNA-seq, detecting and quantifying novel IPA events remains challenging. To address this, we developed IPScan, a computational pipeline for precise IPA event identification, quantification, and visualization. IPScan has been benchmarked against existing methods using simulated data, different human and mouse cell lines, and TCGA (The Cancer Genome Atlas) breast cancer datasets. Differential IPA events under different biological conditions were quantified and validated via qPCR.