ArticleNature genetics2024
Accurate and sensitive mutational signature analysis with MuSiCal.
Article in Nature genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Identification and validation of a previously missed mutational signature in colorectal cancer.Nature communications · 2026Article
- Topographical archetypes of somatic mutagenesis in cancer.bioRxiv : the preprint server for biology · 2026Article
- Combined inference of known and novel mutational signatures with ReDeNovo.bioRxiv : the preprint server for biology · 2026Article
- Non-negative matrix factorization and deconvolution as a dual simplex problem.Genome biology · 2026Article
- Mutational signatures in hematological malignancies.Einstein (Sao Paulo, Brazil) · 2026Review
- Benchmarking of duplex sequencing approaches to reveal somatic mutation landscapes.bioRxiv : the preprint server for biology · 2025Article
- The Impact of Variant Calling on Substitution Mutational Signature Inference.bioRxiv : the preprint server for biology · 2025Article
- Enabling whole genome sequencing analysis from FFPE specimens in clinical oncology.Nature communications · 2025Article
- Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data.bioRxiv : the preprint server for biology · 2025Article
- Natural history of liver fluke infection underpins epidemiological patterns of biliary cancer.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Divergent somatic mutation patterns among human cerebellar neuron types.bioRxiv : the preprint server for biology · 2025Article
- Collateral mutagenesis funnels multiple sources of DNA damage into a ubiquitous mutational signature.bioRxiv : the preprint server for biology · 2025Article
- Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules.bioRxiv : the preprint server for biology · 2025Article
- Joint inference of mutational signatures from indels and single-nucleotide substitutions reveals prognostic impact of DNA repair deficiencies.Genome medicine · 2025Article
- A Thiopurine-like Mutagenic Process Defines TGCT Subtypes.bioRxiv : the preprint server for biology · 2025Article
- A macrophage-predominant immunosuppressive microenvironment and therapeutic vulnerabilities in advanced salivary gland cancer.Nature communications · 2025Article
- Explainable AI Model Reveals Informative Mutational Signatures for Cancer-Type Classification.Cancers · 2025Article
- A redefined InDel taxonomy provides insights into mutational signatures.Nature genetics · 2025Article
- Error-corrected flow-based sequencing at whole-genome scale and its application to circulating cell-free DNA profiling.Nature methods · 2025Article
- Nonhypermutator Cancers Access Driver Mutations Through Reversals in Germline Mutational Bias.Molecular biology and evolution · 2025Article
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Authors and funding
7 authors.
Funding
Abstract
Mutational signature analysis is a recent computational approach for interpreting somatic mutations in the genome. Its application to cancer data has enhanced our understanding of mutational forces driving tumorigenesis and demonstrated its potential to inform prognosis and treatment decisions. However, methodological challenges remain for discovering new signatures and assigning proper weights to existing signatures, thereby hindering broader clinical applications. Here we present Mutational Signature Calculator (MuSiCal), a rigorous analytical framework with algorithms that solve major problems in the standard workflow. Our simulation studies demonstrate that MuSiCal outperforms state-of-the-art algorithms for both signature discovery and assignment. By reanalyzing more than 2,700 cancer genomes, we provide an improved catalog of signatures and their assignments, discover nine indel signatures absent in the current catalog, resolve long-standing issues with the ambiguous 'flat' signatures and give insights into signatures with unknown etiologies. We expect MuSiCal and the improved catalog to be a step towards establishing best practices for mutational signature analysis.
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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.