A pan-cancer analysis of synonymous mutations

Yogita Sharma, Milad Miladi, Sandeep Dukare, Karine Boulay, Maiwen Caudron-Herger, Matthias Groß, Rolf Backofen and Sven Diederichs ()
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Yogita Sharma: University of Freiburg
Milad Miladi: University of Freiburg
Sandeep Dukare: German Cancer Research Center (DKFZ)
Karine Boulay: German Cancer Research Center (DKFZ)
Maiwen Caudron-Herger: German Cancer Research Center (DKFZ)
Matthias Groß: German Cancer Research Center (DKFZ)
Rolf Backofen: University of Freiburg
Sven Diederichs: University of Freiburg

Nature Communications, 2019, vol. 10, issue 1, 1-14

Abstract: Abstract Synonymous mutations have been viewed as silent mutations, since they only affect the DNA and mRNA, but not the amino acid sequence of the resulting protein. Nonetheless, recent studies suggest their significant impact on splicing, RNA stability, RNA folding, translation or co-translational protein folding. Hence, we compile 659194 synonymous mutations found in human cancer and characterize their properties. We provide the user-friendly, comprehensive resource for synonymous mutations in cancer, SynMICdb ( http://SynMICdb.dkfz.de ), which also contains orthogonal information about gene annotation, recurrence, mutation loads, cancer association, conservation, alternative events, impact on mRNA structure and a SynMICdb score. Notably, synonymous and missense mutations are depleted at the 5'-end of the coding sequence as well as at the ends of internal exons independent of mutational signatures. For patient-derived synonymous mutations in the oncogene KRAS, we indicate that single point mutations can have a relevant impact on expression as well as on mRNA secondary structure.

Date: 2019
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DOI: 10.1038/s41467-019-10489-2

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