SpliceHarmonization: an integrated method for identifying RNA splicing events in therapeutics for splicing modulation.

Abstract

Splicing, a critical co-transcriptional process in eukaryotes, enhances transcriptome diversity by generating isoforms specific to cell types, tissues, or developmental stages. Recent advancements in splicing modulators have opened new avenues for targeting previously undruggable genes by inducing significant perturbations in splicing events. These developments underscore the need for comprehensive methods to accurately identify and compare splicing events. While several tools have been developed to detect local splice variants, inconsistencies across methods remain a significant challenge. To address this, we present SpliceHarmonization, an integrated approach that combines the strengths of rMATS, LeafCutter, and MAJIQ, enabling robust and reliable splicing analysis with event type annotations. In a comprehensive evaluation using diverse simulated datasets, SpliceHarmonization streamlined and standardized the outputs from three detection methods into a unified format, thereby improving splicing detection with event type annotation and outperforming individual methods. By integrating the outputs from rMATS, LeafCutter, and MAJIQ, our approach not only enhanced identification of a wide range of splicing events but also effectively mitigated method-specific discrepancies. This integration led to an accuracy exceeding 0.8 and a recall of up to 0.5, with an observed increase in AUC of up to 10%. Furthermore, SpliceHarmonization demonstrated high sensitivity in detecting low-abundance and complex splicing events, providing annotations including genomic coordinates and event type. SpliceHarmonization is available at https://github.com/interactivereport/SpliceHarmonization.