ArticleBMC genomics2023
Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator.
Article in BMC genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Variable latency between the founder genetic event and rhabdoid tumor expansion.bioRxiv : the preprint server for biology · 2026Article
- PULPO: pipeline of understanding large-scale patterns of oncogenomic signatures.Bioinformatics (Oxford, England) · 2026Article
- Benzo[b]fluoranthene Induces Mutation Accumulation and Cancer-Relevant Mutational Signatures in Mouse Lung Alongside Steady State Levels of Chromosome Damage in Blood.Environmental and molecular mutagenesis · 2026Article
- Comparative whole-genome analyses of articular chondrocytes and skin fibroblasts reveal distinct genome instability landscapes in mesenchymal cell types.PLoS genetics · 2026Article
- Comparative whole-genome analyses of articular chondrocytes and skin fibroblasts reveal distinct genome instability landscapes in mesenchymal cell types.bioRxiv : the preprint server for biology · 2026Article
- Consensus Copy-Number Alteration Signatures from Clinical Panels Enable Pan-Cancer Risk Stratification and Therapy Response Association.International journal of molecular sciences · 2026Article
- Endogenous Processes Underlying Clock-Like Mutational Signatures.Genes, chromosomes & cancer · 2026Article
- Article
- Uncovering minimal pathways in melanoma initiation.Nature communications · 2025Article
- Evaluating topography of mutational signatures with SigProfilerTopography.Genome biology · 2025Article
- Geographic and age-related variations in mutational processes in colorectal cancer.medRxiv : the preprint server for health sciences · 2025Article
- Investigating the origins of the mutational signatures in cancer.Nucleic acids research · 2025Review
- MutSeqR: an open source R package for standardized analysis of error-corrected next-generation sequencing data in genetic toxicology.Bioinformatics advances · 2025Article
- A review on trends in development and translation of omics signatures in cancer.Computational and structural biotechnology journal · 2024Review
- Molecular classification of ovarian high-grade serous/endometrioid carcinomas through multi-omics analysis: JGOG3025-TR2 study.British journal of cancer · 2024Article
- Constitutional mismatch repair deficiency mimicking Lynch syndrome is associated with hypomorphic mismatch repair gene variants.NPJ precision oncology · 2024Article
- Genome-wide somatic mutation analysis of sinonasal adenocarcinoma with and without wood dust exposure.Genes and environment : the official journal of the Japanese Environmental Mutagen Society · 2024Article
- Arsenic is a potent co-mutagen of ultraviolet light.Communications biology · 2023Article
- Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment.bioRxiv : the preprint server for biology · 2023Article
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Abstract
backgroundAll cancers harbor somatic mutations in their genomes. In principle, mutations affecting between one and fifty base pairs are generally classified as small mutational events. Conversely, large mutational events affect more than fifty base pairs, and, in most cases, they encompass copy-number and structural variants affecting many thousands of base pairs. Prior studies have demonstrated that examining patterns of somatic mutations can be leveraged to provide both biological and clinical insights, thus, resulting in an extensive repertoire of tools for evaluating small mutational events. Recently, classification schemas for examining large-scale mutational events have emerged and shown their utility across the spectrum of human cancers. However, there has been no computationally efficient bioinformatics tool that allows visualizing and exploring these large-scale mutational events.
resultsHere, we present a new version of SigProfilerMatrixGenerator that now delivers integrated capabilities for examining large mutational events. The tool provides support for examining copy-number variants and structural variants under two previously developed classification schemas and it supports data from numerous algorithms and data modalities. SigProfilerMatrixGenerator is written in Python with an R wrapper package provided for users that prefer working in an R environment.
conclusionsThe new version of SigProfilerMatrixGenerator provides the first standardized bioinformatics tool for optimized exploration and visualization of two previously developed classification schemas for copy number and structural variants. The tool is freely available at https://github.com/AlexandrovLab/SigProfilerMatrixGenerator with an extensive documentation at https://osf.io/s93d5/wiki/home/ .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.