The dynamic usage of mRNA 3 untranslated region (3UTR) resulting from alternative polyadenylation (APA) is emerging as a pervasive mechanism to regulate approximately 70% of human genes.The importance of APA in human diseases such as cancer is only beginning to be appreciated.Current APA profiling protocols use the partitioning and fragmentation of mRNA to enrich for polyA sites followed by high throughput sequencing (polyA-seq).These polyA-seq protocols, although powerful, have not been widely adopted.Therefore, global studies of APA in cancer are very limited.In contrast, whole transcriptome RNAseq has been broadly employed in almost every large-scale genomics project, including The Cancer Genome Atlas (TCGA).We therefore developed a novel bioinformatics algorithm, termed Dynamic analysis of Alternative PolyAdenylation from RNA-Seq (DaPars), to directly infer dynamic APA events through standard RNA-seq.DaPars used a linear regression model to identify the exact location of the de novo APA site, and quantify the lengthening or shortening of 3UTRs between different conditions.