MutationalPatterns: comprehensive genome-wide analysis of mutational processes
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Abstract
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 replicative strand bias, genomic distribution and association with (epi)-genomic features. RESULTS: We have created MutationalPatterns, an R/Bioconductor package that allows researchers to characterize a broad range of patterns in base substitution catalogues to dissect the underlying molecular mechanisms. Furthermore, it offers an efficient method to quantify the contribution of known mutational signatures within single samples. This analysis can be used to determine whether certain DNA repair mechanisms are perturbed and to further characterize the processes underlying known mutational signatures. CONCLUSIONS: MutationalPatterns allows for easy characterization and visualization of mutational patterns. These analyses willsupport fundamental research into mutational mechanisms and may ultimately improve cancer diagnosis and treatment strategies. MutationalPatterns is freely available at http://bioconductor.org/packages/MutationalPatterns .
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To assess the genome-wide off-target effects of base editor activity in intestinal organoids, we compared culture-related (SBS1, SBS5, SBS18), as well as APOBEC-related (SBS2, SBS13) mutational signatures to the overall mutational profile using the Bioconductor R package MutationalPatterns v.3.2.0.
“To assess the genome-wide off-target effects of base editor activity in intestinal organoids, we compared culture-related (SBS1, SBS5, SBS18), as well as APOBEC-related (SBS2, SBS13) mutational signatures to the overall mutational profile using the Bioconductor R package MutationalPatterns v.3.2.056,58,59.”
From One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids (2023) · cites this paper as [59]
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- Authors
- Blokzijl, F., Janssen, R., van Boxtel, R., & Cuppen, E.
- Affiliations
- Utrecht University (NL)
- Corresponding author
- Blokzijl, Francis
- Janssen, Roel
- Cuppen, Edwin
- Venue
- Genome Medicine
- Published
- 2018-04-25
- Volume
- 10
- Issue
- 1
- Pages
- 33-33
- ISSN
- 1756-994X (ISSN-L)
- PMC
- PMC5922316
- OpenAlex
- W2800002600
- Cited by
- 660
- References
- 8
- Citations by year
- 2026: 29 · 2025: 62 · 2024: 66 · 2023: 109 · 2022: 104 · 2021: 128 · 2020: 96 · 2019: 51 · 2018: 11 · 2017: 4
- FWCI
- 23.05
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genome Medicine (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Funders
- ZonMw (Zenith 93512003)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Zwaartekracht Cancer Genomics)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Keywords
- mutational signatures, mutational processes, R/Bioconductor package, sequence context, strand bias, DNA repair, mutational mechanisms, cancer genomics
- MeSH terms
- Adult, Humans, Mutation, Software, Transcription, Genetic, Genome, Human, Adult Stem Cells
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