No abstract

Mutational signature analysis is commonly performed in genomic studies surveying cancer and normal somatic tissues. Here we present SigProfilerExtractor, an automated tool for accurate de novo extraction of mutational signatures for all types of somatic mutations. Benchmarking with a total of 33 distinct scenarios encompassing 1,106 simulated signatures operative in more than 200,000 synthetic genomes demonstrates that SigProfilerExtractor outperforms ten other tools across all datasets with and without noise. For simulations with 5% noise, reflecting high-quality genomic datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true positive signatures while yielding more than 5-fold less false positive signatures. Applying SigProfilerExtractor to 2,778 whole-genome sequenced cancers reveals three previously missed mutational signatures. Two of the signatures are confirmed in independent cohorts with one of these signatures associating with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting mutational signatures, and several novel mutational signatures including a signature putatively attributed to direct tobacco smoking mutagenesis in bladder cancer and in normal bladder epithelium.

The physical origin of charged interfaces involving electrolyte solutions is in the thermodynamic equilibrium between the surface reactive groups and certain dissolved ionic species in the bulk. This equilibrium is very strongly dependent on the precise local density of these species, also known as potential determining ions in the solution. The latter, however, is determined by the overall solution structure, which is dominated by the large number of solvent molecules relative to all solutes. Hence, the solvent contribution to the molecular structure is a crucial factor that determines the properties of electric double layers. Models that explicitly account for the solvent structure are often referred to as "civilized" as opposed to the "primitive" ones that consider the solvent as a structureless continuum. In the present paper, we demonstrate that for a physically correct description of charged interfaces that involve electrolyte solutions (electric double layers), the full solution structure needs to be taken into account in conjunction with the precise surface chemistry governed by the thermodynamic equilibrium. The analysis shows how the surface charge depends on various experimentally relevant parameters, many of which are outside the realm of simple electrostatics. We present results on the effects of solvent molecular dimensions, ionic solvation, surface chemistry, solvophilicity and solvophobicity.