SF3B1 and breast carcinoma: We used RNA-sequencing data from SF3B1 mutated and SF3B1 wild-type chronic lymphocytic leukemia (CLL; seven mutant, nine wild-type), breast cancer (BRCA; 14 mutant, 18 wild-type), and uveal melanoma (UM; four mutant, four wild-type) samples (S1 Fig., S1 File) to test 219,476 splice junctions present in the Gencode v14 gene annotation [19] along with 87,941 novel splice junctions (not annotated in Gencode) for differential usage by comparing junction-spanning reads using a generalized linear model as implemented in DEXSeq [20].