Signatures of mutational processes in human cancer
Open accessAbstract
All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, 'kataegis', is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy.
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GBM has a low mutational burden, and patients' tumours express only few tumour-specific antigens.
“The use of TAA-derived epitopes has the advantage of allowing development of an off-the-shelf product for a tumour indication with low mutational burden such as GBM, where patients’ tumours express only few tumour-specific antigens [38].”
From Preclinical development of an mRNA-based multiepitope immunotherapeutic for glioblastoma (2025) · cites this paper as [38]
The Results section ('Mutational catalogues'; page unavailable) reports that certain childhood cancers had the fewest mutations, but does not identify GBM as one of them. Searches for GBM, glioblastoma, and tumour-specific antigens found no passage addressing GBM’s mutational burden or the number of antigens its tumours express. (LLM, conf=0.74)
Experimental — accuracy not yet measuredIn MM, SBS9 was strongly linked with Q61H.
“In MM, SBS9, associated with mutations introduced by polymerase η repair of activation-induced deaminase (AID) activity26,31,32, was strongly linked with Q61H”
From The origins and genetic interactions of KRAS mutations are allele- and tissue-specific (2021) · cites this paper as [26]
Five substitution signatures and five rearrangement signatures were detected.
“Five substitution and five rearrangement signatures [8, 9] were identified”
From Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers (2019) · cites this paper as [8]
Some non-BRCA1/2 tumours had a high single nucleotide variant burden linked to the APOBEC substitution signature.
“a high SNV burden associated with APOBEC substitution signature [8]”
From Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers (2019) · cites this paper as [8]
The pol η mutational signature known as Signature 9 occurs in chronic lymphocytic leukemia and malignant B-cell lymphoma genomes.
“It has also been noted that the 'pol h mutational signature' (Signature 9; http://cancer.sanger.ac.uk/cosmic/sig natures) occurs in chronic lymphocytic leukemia and malignant Bcell lymphoma genomes 6,26,27 .”
From DNA polymerase <b>η</b> mutational signatures are found in a variety of different types of cancer (2018) · cites this paper as [6]
Several distinct mutational signatures sculpt the genome of NSCLC, including signatures of tobacco exposure and APOBEC-mediated cytidine deamination.
“Several distinct mutational signatures sculpt the genome of NSCLC – including signatures of tobacco exposure and APOBEC-mediated cytidine deamination57.”
From Co-occurring genomic alterations in non-small-cell lung cancer biology and therapy (2019) · cites this paper as [57]
Melanoma somatic mutations consist almost entirely of C to T transitions, 28% of which are TCC to T mutations.
“Melanoma somatic mutations consist almost entirely of C → T transitions, 28% of which are TCC → T mutations (19,31).”
From Evidence for recent, population-specific evolution of the human mutation rate (2015) · cites this paper as [19]
Excess C to T transitions are characteristic of several mutagenic processes including UV damage and cytosine deamination.
“Excess C → T transitions are characteristic of several different mutagenic processes including UV damage and cytosine deamination (19).”
From Evidence for recent, population-specific evolution of the human mutation rate (2015) · cites this paper as [19]
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The future of cancer treatment: immunomodulation, CARs and combination immunotherapy
Khalil, D. N., Smith, E. L., Brentjens, R. J., & Wolchok, J. D. (2016) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2016.25 · Cited by 1,151 · see citing works
Consensus guidelines for the definition, detection and interpretation of immunogenic cell death
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Self-citationGenomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
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Somatic mutant clones colonize the human esophagus with age
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Self-citation
- Authors
- Initiative, A. P. C. G., Alexandrov, L. B., ICGC Breast Cancer Consortium, ICGC MMML-Seq Consortium, PedBrain, I., Nik-Zainal, S., Wedge, D. C., Aparicio, S. A. J. R., Behjati, S., Biankin, A. V., Bignell, G. R., Bolli, N., Borg, A., Børresen-Dale, A.-L., Boyault, S., Burkhardt, B., Butler, A. P., Caldas, C., Davies, H. R., Desmedt, C., Eils, R., Eyfjörd, J. E., Foekens, J. A., Greaves, M., Hosoda, F., Hutter, B., Ilicic, T., Imbeaud, S., Imielinski, M., Jäger, N., Jones, D. T. W., Jones, D., Knappskog, S., Kool, M., Lakhani, S. R., López-Otín, C., Martin, S., Munshi, N. C., Nakamura, H., Northcott, P. A., Pajic, M., Papaemmanuil, E., Paradiso, A., Pearson, J. V., Puente, X. S., Raine, K., Ramakrishna, M., Richardson, A. L., Richter, J., Rosenstiel, P., Schlesner, M., Schumacher, T. N., Span, P. N., Teague, J. W., Totoki, Y., Tutt, A. N. J., Valdés-Mas, R., van Buuren, M. M., van ’t Veer, L., Vincent-Salomon, A., Waddell, N., Yates, L. R., Zucman-Rossi, J., Andrew Futreal, P., McDermott, U., Lichter, P., Meyerson, M., Grimmond, S. M., Siebert, R., Campo, E., Shibata, T., Pfister, S. M., Campbell, P. J., & Stratton, M. R.
- Affiliations
- Wellcome Sanger Institute (GB)
- BC Cancer Agency (CA)
- University of Cambridge (GB)
- Garvan Institute of Medical Research (AU)
- Lund University (SE)
- Oslo University Hospital (NO)
- Justus-Liebig-Universität Gießen (DE)
- Université Libre de Bruxelles (BE)
- German Cancer Research Center (DE)
- Erasmus MC Cancer Institute (NL)
- Inserm (FR)
- Broad Institute (US)
- The University of Queensland (AU)
- Universidad de Oviedo (ES)
- Harvard University (US)
- National Cancer Center Research Institute (JP)
- University of Glasgow (GB)
- Brigham and Women's Hospital (US)
- The Netherlands Cancer Institute (NL)
- Radboud University Medical Center (NL)
- King's College London (GB)
- Christian-Albrechts-Universität zu Kiel (DE)
- Corresponding author
- Stratton, Michael R.
- ORCID
- Alexandrov, Ludmil B.
- Wedge, David C.
- Aparicio, Samuel A. J. R.
- Behjati, Sam
- Biankin, Andrew V.
- Bolli, Niccolò
- Boyault, Sandrine
- Burkhardt, Birgit
- Caldas, Carlos
- Davies, Helen R.
- Desmedt, Christine
- Eils, Roland
- Hutter, Barbara
- Imbeaud, Sandrine
- Imielinski, Marcin
- Jäger, Natalie
- Knappskog, Stian
- Kool, Marcel
- Lakhani, Sunil R.
- Martin, Sancha
- Munshi, Nikhil C.
- Nakamura, Hiromi
- Northcott, Paul A.
- Pajic, Marina
- Papaemmanuil, Elli
- Paradiso, Angelo
- Pearson, John V.
- Raine, Keiran
- Ramakrishna, Manasa
- Richardson, Andrea L.
- Richter, Julia
- Rosenstiel, Philip
- Schlesner, Matthias
- Schumacher, Ton N.
- Span, Paul N.
- Teague, Jon W.
- Totoki, Yasushi
- Tutt, Andrew N. J.
- Waddell, Nicola
- Yates, Lucy R.
- McDermott, Ultan
- Meyerson, Matthew
- Grimmond, Sean M.
- Siebert, Reiner
- Shibata, Tatsuhiro
- Pfister, Stefan M.
- Campbell, Peter J.
- Stratton, Michael R.
- Venue
- Nature
- Published
- 2013-08-14
- Volume
- 500
- Issue
- 7463
- Pages
- 415-421
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3776390
- OpenAlex
- W2152061559
- Cited by
- 9,660
- References
- 67
- Citations by year
- 2026: 384 · 2025: 552 · 2024: 643 · 2023: 854 · 2022: 921 · 2021: 1119 · 2020: 1130 · 2019: 939 · 2018: 873 · 2017: 815 · 2016: 660 · 2015: 421 · 2014: 286 · 2013: 45 · 2012: 2
- FWCI
- 165.61
- Type
- journal article
- Language
- en
- Update notices
- erratum (2013-10-09)
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Pure Amsterdam UMC (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- HAL (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Consultation of the Doctoral Thesis Database (TESEO) (Ministerio de Educación, Cultura y Deporte) (submittedVersion, cc-by-nc-nd)
- Dépôt institutionnel de l'Université libre de Bruxelles (Université Libre de Bruxelles) (submittedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Minerva Access (University of Melbourne) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- Lund University Publications (Lund University) (submittedVersion)
- Radboud Repository (Radboud University) (submittedVersion)
- OPUS (Augsburg University) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion)
- Apollo
- Funders
- Deutsches Krebsforschungszentrum (69120)
- Wellcome Trust (088340, 093867, 098051)
- Broad Institute
- Canada's Michael Smith Genome Sciences Centre
- Cancer Research UK
- University of Glasgow
- Agence Nationale de la Recherche (ANR-10-LABX-0015)
- Institut National de la Santé et de la Recherche Médicale
- University of New South Wales
- Lunds Universitet
- Universitetet i Oslo
- Háskóli Íslands
- Universitat de Barcelona
- BC Cancer Agency
- Labex Immuno-Oncology
- Medisinske fakultet, Universitetet i Oslo
- Cancer Research UK Cambridge Institute, University of Cambridge
- National Cancer Institute (T32CA009216)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Keywords
- mutational signatures, somatic mutations, cancer genome, APOBEC cytidine deaminases, kataegis, hypermutation, patient age, cancer etiology, cancer types
- MeSH terms
- Aging, Algorithms, Cell Transformation, Neoplastic, Cytidine Deaminase, DNA, DNA Mutational Analysis, Humans, Models, Genetic, Mutagens, Mutation, Neoplasms, Organ Specificity, Transcription, Genetic, Reproducibility of Results, Mutagenesis, Insertional, Mutagenesis, Sequence Deletion
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