Microsatellite unstable gastric cancer were observed to have a hi

Microsatellite unstable gastric cancer were observed to have a higher mutation prevalence of both C > T transitions and C > A transversions [71]. Examining the cancer exomes of patients with urothelial carcinoma (of the upper urinary tract) revealed a large number of somatic mutations with an unique pattern of T > A transversions predominately located at CpTpG

sites and possessing a very strong transcription strand Alectinib research buy bias [81]. This pattern of mutations was associated with exposure to aristolochic acid. In oesophageal cancer, a high prevalence of T > G transversions was observed [40] while certain breast cancer genomes were found to be overwhelmed with C > T and C > G mutations at TpC sites [35]. These next generation sequencing

studies provided an unbiased look into the patterns of DNA changes across cancer genomes. While they resolved some of the previous limitations from TP53 studies (mostly by examining large portions of the human genome which are usually not under selection selleck and which have a nucleotide context that is representative of the whole human genome) they still did not address the important issue of examining mixtures of mutations generated by different mutational processes. The somatic mutations in a cancer genome are the cumulative result of the mutational processes that have been operative since the very first division of the fertilized egg, from which the cancer cell was derived [21 and 22]. Each of these mutations was caused by the activity of endogenous and/or exogenous mutational processes with different strengths (Figure 1). Some of these processes have been active throughout the whole lifetime of the cancer patient while others have been sporadically triggered, for example, due to lifestyle choices (Figure 1). While examining patterns of somatic mutations can provide an indication

of the aetiology of the operative mutational processes, it does not allow deciphering the individual mutational signatures that are operative in each sample as usually the pattern of a sequenced cancer genome does Decitabine cell line not resemble any of the operative mutational processes (Figure 1). Recently, a theoretical model and computational framework that allows decomposing distinct patterns of somatic mutations from a set of cancer samples was developed [20••]. The mathematical model was an extension of the well-known blind source separation problem, in which original signals need to be separated from a set of mixed signals [82], and the algorithm was based on a method used in face recognition software that allows meaningfully learning distinct parts of objects [83]. The algorithm deciphers the minimal set of mutational signatures that optimally explains the proportion of each mutation type found in each cancer sample and then the method estimates the contribution of each signature to each cancer sample (see Ref.

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