Alternative splicing of the TERT gene was analysed using Leafcutter 91, which focuses on introns and quantifies both known and novel alternative splicing events by quantifying reads mapping to exon-exon junctions. Annotations were derived from Gencode v19. Introns supported by fewer than 30 reads (-m 30; default) across all samples were removed. We obtained quantifications for eight intron clusters within TERT. After removing individual introns with a mean intron usage of zero, we had a total of 22 introns to test. We used the intron excision proportions to assess genotype-dependent effect of rs10069690 on TERT splicing (linear model between genotype and excision proportion, Bonferroni correction of P-values for the total number of introns tested). One intron showed evidence of a splicing-QTL effect (P < 0.05, Bonferroni adjusted; Extended Data Fig. 10).
