Mutational signature analysis is a recent computational approach for interpreting somatic mutations in the genome. Its application to cancer data has enhanced our understanding of mutational forces driving tumorigenesis and demonstrated its potential to inform prognosis and treatment decisions. However, methodological challenges remain for discovering new signatures and assigning proper weights to existing signatures, thereby hindering broader clinical applications. Here we present Mutational Signature Calculator (MuSiCal), a rigorous analytical framework with algorithms that solve major problems in the standard workflow. Our simulation studies demonstrate that MuSiCal outperforms state-of-the-art algorithms for both signature discovery and assignment. By reanalyzing more than 2,700 cancer genomes, we provide an improved catalog of signatures and their assignments, discover nine indel signatures absent in the current catalog, resolve long-standing issues with the ambiguous 'flat' signatures and give insights into signatures with unknown etiologies. We expect MuSiCal and the improved catalog to be a step towards establishing best practices for mutational signature analysis.
Music , Neoplasms , Humans , Neoplasms/genetics , Mutation , Carcinogenesis/genetics , INDEL Mutation
In this study, we present the design of a new charge exchange recombination spectroscopy (CXRS) system for Wendelstein 7-X (W7-X), which aims at measuring line radiation from highly ionized iron impurities after laser blow off injections over transport timescales. New fiber bundles with a core diameter of 600 µm have been added to one of the existing optical systems at W7-X used for CXRS. The fibers direct collected light to five newly developed single channel high frame rate F/2.8 spectrometers. The new custom-made spectrometers are built using entirely off-the-shelf and 3D printed components, and employ a round-to-linear fiber bundle, instead of an entrance slit, to maximize light throughput. The detector is an ultra-low readout noise EM-CCD camera capable of frame rates of up to 10 000 fps for about 500 consecutive frames when operated using a single readout channel. Such high frame rates will enable the study of inward convection of injected impurities. An initial sensitivity study is performed using a newly developed Markov chain Monte Carlo approach based on the pySTRAHL impurity transport code. This study indicates that, with the addition of the new CX diagnostic, impurity convection velocities can be inferred.
