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Somatic base substitutions were classified into 96 mutation trinucleotides and the somatic mutation rate of each type of substitutions was calculated to generate a context-specific mutation profile. Mutational signatures were extracted from the context-specific mutation profile by using NMF algorithm (“MutationalPatterns” package). Consensus clustering (“CancerSubtypes” package; clusterAlg = “hc”, distance = “pearson”, innerLinkage = “ward.D2”) was performed on contribution of each mutational signature among all samples.
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