And (5) considering specific functional mutations or mutational features may improve prediction power.
In this sense, in the phylogenetic analysis, there is a potentially (partially) redundant modeling of mutational features, in having explicit parameters devoted to these, in combination with the use of the SC setting.
Additional subtle processes may exist, and sharper definition of currently characterized processes may follow refinements of NMF and inclusion of other mutational features in the models.
Some of these correspond to lowly recurrent drivers whose mutational features are not correctly computed because of the scarcity of their alterations.
Using a combination of these important mutational features, we were able to detect additional cases of aggressive disease beyond that detected by cytology alone in pancreatic masses and their associated biliary strictures.
As expected, a mutational signature with features of C > T mutations at CpG sites was identified in most samples, thus reflecting the activity of normal endogenous cellular processes.
Cancer genome sequences contain footprints of somatic mutational processes, whose analysis in large tumor sequencing datasets has revealed novel mutational signatures, correlative features of variant topography, and complex events.
Analysis of smaller, exome-derived mutational catalogs (or catalogs from other subcomponents of the genome) may also be useful in detecting biologically revealing features of mutational processes that are particular to coding, transcribed, nontranscribed, or other functionally distinct regions.
TCGA aims to comprehensively characterize the mutational landscape and genomic features of cancer.
