Abstract
Genome analysis in cancer has focused mainly on elucidating the function and regulatory mechanisms of genes that exhibit differential expression or mutation in cancer samples compared to normal samples. Recently, transcriptome analysis revealed that abnormal splicing events in cancer samples could contribute to cancer pathogenesis. Moreover, splicing variants in cancer reportedly generate diverse cancer antigens. Although abnormal splicing events are expected to be potential targets in cancer immunotherapy, the exploration of such targets and their biological significance in cancer have not been fully understood. In this study, to explore subtype-specific alternative splicing events, we conducted a comprehensive analysis of splicing events for each breast cancer subtype using large-scale splicing data derived from The Cancer Genome Atlas and found subtype-specific alternative splicing patterns. Analyses indicated that genes that produce subtype-specific alternative splicing events are potential novel targets for immunotherapy against breast cancer. The subtype-specific alternative splicing events identified in this study, which were not identified by mutation or differential expression analysis, bring new significance to previously overlooked splicing events.