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Current somatic mutation callers are biased against repetitive regions, preventing the identification of potential driver alterations in these loci. We developed a mutation caller for repetitive regions, and applied it to study repetitive non protein-coding genes in more than 2200 whole-genome cases. We identified a recurrent mutation at position c.28 in the gene encoding the snRNA  U2 . This mutation is present in B-cell derived tumors, as well as in prostate and pancreatic cancer, suggesting  U2  c.28 constitutes a driver candidate associated with worse prognosis. We showed that the GRCh37 reference genome is incomplete, lacking the  U2  cluster in chromosome 17, preventing the identification of mutations in this gene. Furthermore, the 5′-flanking region of  WDR74 , previously described as frequently mutated in cancer, constitutes a functional copy of  U2 . These data reinforce the relevance of non-coding mutations in cancer, and highlight current challenges of cancer genomic research in characterizing mutations affecting repetitive genes.

PanCancer analysis of somatic mutations in repetitive regions reveals recurrent mutations in snRNA U2