Pan-Cancer Repository of Validated Natural and Cryptic mRNA Splicing Mutations

We present a major public resource of mRNA splicing mutations validated according to multiple lines of evidence of abnormal gene expression. Likely mutations present in all tumor types reported in the Cancer Genome Atlas (TCGA) were identified based on the comparative strengths of splice sites in tumor versus normal genomes and then validated by respectively comparing counts of splice junction spanning and abundance of transcript reads in RNA-Seq data from matched tissues and tumors lacking these mutations. The comprehensive resource features 351,423 of these validated mutations, the majority of which (69.1%) are not featured in the Single Nucleotide Polymorphism Database (dbSNP 150). There are 117,951 unique mutations which weaken or abolish natural splice sites, and 244,415 mutations which strengthen cryptic splice sites (10,943 affect both simultaneously). 27,803 novel or rare flagged variants (with <1% population frequency in dbSNP) were observed in multiple tumor tissue types. Single variants or chromosome ranges can be queried using a Global Alliance for Genomics and Health (GA4GH)-compliant web Beacon, Validated Splicing Mutations, either separately or in aggregate alongside other beacons through the public Beacon Network (http://www.beacon-network.org/#/search?beacon=cytognomix), as well as through our website (https://validsplicemut.cytognomix.com/).