Sequence dependencies and mutation rates of localized mutational processes in cancer [PDF]
Genome Medicine, 2023 Background Cancer mutations accumulate through replication errors and DNA damage coupled with incomplete repair. Individual mutational processes often show nucleotide sequence and functional region preferences.
Gustav Alexander Poulsgaard +4 more
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Analysis of Mutations and Dysregulated Pathways Unravels Carcinogenic Effect and Clinical Actionability of Mutational Processes [PDF]
Frontiers in Cell and Developmental Biology, 2021 Somatic mutations accumulate over time in cancer cells as a consequence of mutational processes. However, the role of mutational processes in carcinogenesis remains poorly understood.
Zedong Jiang +14 more
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Mutational processes in cancer preferentially affect binding of particular transcription factors [PDF]
Scientific Reports, 2021 Protein binding microarrays provide comprehensive information about the DNA binding specificities of transcription factors (TFs), and can be used to quantitatively predict the effects of DNA sequence variation on TF binding.
Mo Liu +4 more
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Sex differences in oncogenic mutational processes [PDF]
Nature Communications, 2020 There’s an emerging body of evidence to show how biological sex impacts cancer incidence, treatment and underlying biology. Here, using a large pan-cancer dataset, the authors further highlight how sex differences shape the cancer genome.
Constance H. Li +7 more
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Integrative analysis of mutated genes and mutational processes reveals novel mutational biomarkers in colorectal cancer [PDF]
BMC Bioinformatics, 2022 Background Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide. Recent studies have observed causative mutations in susceptible genes related to colorectal cancer in 10 to 15% of the patients.
Hamed Dashti +7 more
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MutationalPatterns: the one stop shop for the analysis of mutational processes [PDF]
BMC Genomics, 2022 Background The collective of somatic mutations in a genome represents a record of mutational processes that have been operative in a cell. These processes can be investigated by extracting relevant mutational patterns from sequencing data.
Freek Manders +9 more
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Divergent mutational processes distinguish hypoxic and normoxic tumours [PDF]
Nature Communications, 2020 Many tumours exhibit hypoxia (low oxygen) and hypoxic tumours often respond poorly to therapy. Here, the authors quantify hypoxia in 1188 tumours from 27 cancer types, showing elevated hypoxia links to increased mutational load, directing evolutionary ...
Vinayak Bhandari +4 more
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MutationalPatterns: comprehensive genome-wide analysis of mutational processes [PDF]
Genome Medicine, 2018 Background Base substitution catalogues represent historical records of mutational processes that have been active in a cell. Such processes can be distinguished by various characteristics, like mutation type, sequence context, transcriptional and ...
Francis Blokzijl +3 more
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Analysis of 7,815 cancer exomes reveals associations between mutational processes and somatic driver mutations. [PDF]
PLoS Genetics, 2018 Driver mutations are the genetic variants responsible for oncogenesis, but how specific somatic mutational events arise in cells remains poorly understood. Mutational signatures derive from the frequency of mutated trinucleotides in a given cancer sample,
Rebecca C Poulos +4 more
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The topography of mutational processes in breast cancer genomes [PDF]
Nature Communications, 2016 Mutational signatures provide evidence of the mechanism of action of a given mutagen and are found in cancer cells. Here, using 560 breast cancer genomes, the authors demonstrate that mutational signatures are frequently associated with genomic ...
Sandro Morganella +32 more
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