To infer mutational signatures, we included mutations called within the gene sequence (HIGH, MODERATE, and LOW impact) and excluded mutations with rs ID together with mutations with a quality score below 100 or a Fisher Strand score (FS) above 30.0. Finally, mutations were included if they met the following criteria: (1) alternate allele frequency (AF) > 0.15 and < 0.60; (2) number of reads > 20. Only samples with more than 100 SNVs were kept to infer the mutational signatures (n = 441). We used non-negative matrix factorization to decompose the motifs matrix into seven signatures and their corresponding weights using the R package SomaticSignatures. The similarity between the seven inferred signatures and defined COSMIC signatures was examined using the R package MutationalPatterns.

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