CD96 and lung cancer: To determine whether APA captures genes with clinical relevance, we performed a multivariate Cox regression correcting for patient age, sex, race, and tumor stage for each gene and identified a strong prognostic signature based on the APA usage pattern of 12 genes in lung cancer (Fig. 2f and Supplementary Data 8), including the type I transmembrane glycoprotein immunoglobulin CD96 and a key homologous recombination repair gene POLA2. Further, gene ontology analysis of APA events associated with survival revealed enrichment of cellular metabolic processes (Supplementary Data 9).