Journal Article

SigsPack, a package for cancer mutational signatures

Schumann, Franziska, Beule, Dieter, Blanc, Eric, Blankenstein, Thomas, Busse, Antonia, Messerschmidt, Clemens

2019

Overview

Background Mutational signatures are specific patterns of somatic mutations introduced into the genome by oncogenic processes. Several mutational signatures have been identified and quantified from multiple cancer studies, and some of them have been linked to known oncogenic processes. Identification of the processes contributing to mutations observed in a sample is potentially informative to understand the cancer etiology. Results We present here SigsPack , a Bioconductor package to estimate a sample’s exposure to mutational processes described by a set of mutational signatures. The package also provides functions to estimate stability of these exposures, using bootstrapping. The performance of exposure and exposure stability estimations have been validated using synthetic and real data. Finally, the package provides tools to normalize the mutation frequencies with respect to the tri-nucleotide contents of the regions probed in the experiment. The importance of this effect is illustrated in an example. Conclusion SigsPack provides a complete set of tools for individual sample exposure estimation, and for mutation catalogue & mutational signatures normalization.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algorithms / Bioconductor / Bioinformatics / Biomedical and Life Sciences / Cancer / Cancer genetics / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Etiology / Etiology (Medicine) / Exposure / Genomes / Genomics / Health aspects / Life Sciences / Microarrays / Mutation / Mutational signatures / Nucleotides / Scientific software / Sequence analysis / Signatures / Software / Stability / Technology application