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Generating realistic null hypothesis of cancer mutational landscapes using SigProfilerSimulator [article]

Erik N Bergstrom, Mark Barnes, Inigo Martincorena, Ludmil B Alexandrov
2020 bioRxiv   pre-print
In cancer genomics, a key challenge is the fast generation of accurate somatic mutational landscapes that can be used as a realistic null hypothesis for making biological discoveries.  ...  Here we present SigProfilerSimulator, a powerful tool that is capable of simulating the mutational landscapes of thousands of cancer genomes at different resolutions within seconds.  ...  An observation is generally considered statistically significant if it reflects an unlikely outcome of the null hypothesis.  ... 
doi:10.1101/2020.02.13.948422 fatcat:7uiduf64d5cw7ogcafxw2nnef4

Generating realistic null hypothesis of cancer mutational landscapes using SigProfilerSimulator

Erik N. Bergstrom, Mark Barnes, Iñigo Martincorena, Ludmil B. Alexandrov
2020 BMC Bioinformatics  
In cancer genomics, a key challenge is the fast generation of accurate somatic mutational landscapes that can be used as a realistic null hypothesis for making biological discoveries.  ...  Results Here we present SigProfilerSimulator, a powerful tool that is capable of simulating the mutational landscapes of thousands of cancer genomes at different resolutions within seconds.  ...  We constructed a null hypothesis by applying the tool to the 2144 PCAWG cancer genomes.  ... 
doi:10.1186/s12859-020-03772-3 pmid:33028213 fatcat:6yz3i7ufg5ccrctmvvg7ytgboq

Deficiency in DNA mismatch repair of methylation damage is a major mutational process in cancer [article]

Hu Fang, Xiaoqiang Zhu, Jieun Oh, Jayne A Barbour, Jason W. H. Wong
2020 bioRxiv   pre-print
Here, using mutation data from cancer genomes, we identify a previously unknown function of MMR, showing that the loss of non-canonical replication-independent MMR activity is a major mutational process  ...  The mechanisms underlying these mutational signatures have remained unclear despite studies using a range of in vitro and in vivo models of MMR deficiency.  ...  Generating realistic 28 null hypothesis of cancer mutational landscapes using SigProfilerSimulator. (2020). 29 51 Sloan, C. A. et al. ENCODE data at the ENCODE portal. Nucleic Acids Res 44, A. et al.  ... 
doi:10.1101/2020.11.18.388108 fatcat:z6uuj2djybdhfbimpoonbn5zfa