Somatic Mutations that Alter RNA Splicing in Human Cancers
summary
Uses matched exome and RNA-Seq from TCGA and JunctionBase to call unannotated splicing changes and quantify PSI, links U2AF1 S34 hotspot to altered three‑prime splice site choice and reports 131 events in lung, 369 in AML, links SF3B1 K700E to branch‑point shifts and intron retention, shows MET exon 14 skipping caused by splice‑site deletions and a Y1003 nonsense mutation that stabilizes MET and produces a clinically targetable gain‑of‑function, and flags an ERBB2 exon 16 skip (n=1) that phenocopies activating mutations.
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chapters (12)
- 0:00Intro
- 1:04Alternative splicing can result in different gene function
- 3:39The Cancer Genome Atlas TCGA data provides multiple types of genomic data for each tumor sample
- 4:48Approach to identify splicing changes associated with U2AF1 mutations
- 6:11JuncBASE quantities alternative splice variants and performs differential splicing analysis
- 11:32Approach to identify splicing changes associated with SF3B1 mutations in CLL
- 13:32In-frame deletion in DVL2 (dishevelled) is associated with SF381 mutation
- 14:31Prevalence of splicing factor mutations due to pleiotropic effects?
- 16:54Receptor tyrosine kinases are frequently activated in cancer
- 19:04An unexpected nonsense mutation is associated with MET-Rexon 14
- 21:17An ER882 exon 16 splice site mutation is associated with exon skipping in lung adenocarcinoma
- 23:12Recurrent mutations in flanking introns can be observed by whole genome sequencing
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