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A pan-cancer analysis of synonymous mutations

Author

Listed:
  • Yogita Sharma

    (University of Freiburg
    University of Freiburg
    German Cancer Consortium (DKTK))

  • Milad Miladi

    (University of Freiburg)

  • Sandeep Dukare

    (German Cancer Research Center (DKFZ)
    National Center for Tumor Diseases (NCT))

  • 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
    University of Freiburg)

  • Sven Diederichs

    (University of Freiburg
    University of Freiburg
    German Cancer Consortium (DKTK)
    German Cancer Research Center (DKFZ))

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.

Suggested Citation

  • Yogita Sharma & Milad Miladi & Sandeep Dukare & Karine Boulay & Maiwen Caudron-Herger & Matthias Groß & Rolf Backofen & Sven Diederichs, 2019. "A pan-cancer analysis of synonymous mutations," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10489-2
    DOI: 10.1038/s41467-019-10489-2
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    Cited by:

    1. Aviv A. Rosenberg & Ailie Marx & Alex M. Bronstein, 2022. "Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    2. Fabio Alfieri & Giulio Caravagna & Martin H. Schaefer, 2023. "Cancer genomes tolerate deleterious coding mutations through somatic copy number amplifications of wild-type regions," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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