a, Overview of cryptic alternative splicing of GLI2, demonstrating the position of a cryptic cassette exon with the 5′ splice-site sequence. b, Sashimi plot of splicing of GLI2 in representative cases. The bar plot shows counts per million reads. Numbers are of junctional reads; reads for the mutant U1 snRNA isoform are in red. c, Scatter plot comparing detected alternatively spliced read and total junction reads that share a 3′ splice site. Jittering was performed for both values. d, Per cent spliced in values for SHHα with mutant U1 snRNA, SHHδ with mutant U1 snRNA and SHH medulloblastoma with wild-type U1 snRNA (all subtypes of SHH medulloblastoma). e, Box plot of fold changes in expression of the alternatively spliced isoform as compared to the wild-type isoform of GLI2 in subsets of SHH medulloblastoma, determined by real-time qPCR. f, Illustration of canonical and cryptic isoforms of GLI2. Translation start sites are indicated by an ATG arrow. Resulting proteins (and sizes) are displayed for each isoform. Repression and activation domains are indicated in blue and orange, respectively. g, Overview of cryptic alternative splicing of CCND2, illustrating the position of a cryptic cassette exon with the 5′ splice-site sequence. h, Sashimi plot of representative cases demonstrates alternative splicing at the CCND2 locus. Numbers illustrate junctional reads. Junctional reads specific to U1 snRNA mutants are in red. i, The canonical isoform and the cryptic isoform of CCND2. j, Scatter plot comparing detected alternatively spliced read and total junction reads that shared a 3′ splice site. Jittering was performed for both values. k, Per cent spliced in values for U1-mutant SHHα (n = 13), U1-mutant SHHδ (n = 58), and U1-wildtype SHH (all SHH subtypes, n = 104). l) Real-time qPCR comparing the expression of the cryptic isoform of CCND2 demonstrates high levels of expression of CCND2 restricted to SHHδ cases (n = 6 for SHHα with mutant U1 snRNA, n = 6 for SHHδ with mutant U1 snRNA, n = 6 for SHHα with wild-type U1 snRNA). m, Overview of cryptic alternative splicing of PAX5, illustrating the position of a cryptic cassette exon with the 5′ splice-site sequence. n, Sashimi plot of representative cases demonstrates alternative splicing at the PAX5 locus. Numbers denote junctional reads. Junctional reads specific to U1 snRNA mutants are in red. o, The canonical isoform and the cryptic isoform of PAX5. p, Scatter plot comparing detected alternatively spliced read and total junction reads that shared a 3′ splice site. Jittering was performed for both values. q, Per cent spliced in values by SHHα with mutant U1 snRNA (n = 5), SHHδ with mutant U1 snRNA (n = 27) and SHH medulloblastoma with wild-type U1 snRNA (all subtypes of SHH medulloblastoma, n = 7). In all box plots, centre lines show data median; box limits indicate the IQR from the 25th and 75th percentiles; lower and upper whiskers extend 1.5× the IQR. Outliers are represented by individual points. P values were calculated using two-sided Wilcoxon rank-sum tests. Source data