Development of a bioinformatics pipeline for the detection and visualization of mutational signatures in next-generation-sequencing data

Abstract

Cancer is predominantly caused by genetic mutations resulting from exogenous or endogenous processes. Mutational signatures are characteristic patterns of somatic mutations that can indicate the underlying process and thus the etiology of the tumor, such as ultraviolet light, tobacco smoking or defective DNA repair processes and many others. Single base substitutions (SBS) are the most studied mutational signatures. There are 96 SBS categories resulting from the six substitution subtypes: C>A, C>G, C>T, T>A, T>C, and T>G including the immediately neighboring nucleotides (Alexandrov et al., 2020). Detection of mutational signatures in targeted sequencing is much more challenging than in whole genome sequencing data due many times fewer variants present (Lee et al., 2023). Reference signatures can be used to map mutational signatures of tumors.