Mutational Processes Molding the Genomes of 21 Breast Cancers
Open accessAbstract
All cancers carry somatic mutations. The patterns of mutation in cancer genomes reflect the DNA damage and repair processes to which cancer cells and their precursors have been exposed. To explore these mechanisms further, we generated catalogs of somatic mutation from 21 breast cancers and applied mathematical methods to extract mutational signatures of the underlying processes. Multiple distinct single- and double-nucleotide substitution signatures were discernible. Cancers with BRCA1 or BRCA2 mutations exhibited a characteristic combination of substitution mutation signatures and a distinctive profile of deletions. Complex relationships between somatic mutation prevalence and transcription were detected. A remarkable phenomenon of localized hypermutation, termed "kataegis," was observed. Regions of kataegis differed between cancers but usually colocalized with somatic rearrangements. Base substitutions in these regions were almost exclusively of cytosine at TpC dinucleotides. The mechanisms underlying most of these mutational signatures are unknown. However, a role for the APOBEC family of cytidine deaminases is proposed.
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Cancer whole-genome sequencing is feasible, and thousands of matched tumor-normal pairs have been sequenced, revealing novel biological insights.
“Cancer whole genome sequencing (WGS) is now feasible, with thousands of matched tumor-normal pairs successfully sequenced to date, revealing novel biological insights2–4.”
From Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study (2019) · cites this paper as [2]
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- Authors
- Nik-Zainal, S., Alexandrov, L. B., Wedge, D. C., Van Loo, P., Greenman, C. D., Raine, K., Jones, D., Hinton, J., Marshall, J., Stebbings, L. A., Menzies, A., Martin, S., Leung, K., Chen, L., Leroy, C., Ramakrishna, M., Rance, R., Lau, K. W., Mudie, L. J., Varela, I., McBride, D. J., Bignell, G. R., Cooke, S. L., Shlien, A., Gamble, J., Whitmore, I., Maddison, M., Tarpey, P. S., Davies, H. R., Papaemmanuil, E., Stephens, P. J., McLaren, S., Butler, A. P., Teague, J. W., Jönsson, G., Garber, J. E., Silver, D., Miron, P., Fatima, A., Boyault, S., Langerød, A., Tutt, A., Martens, J. W. M., Aparicio, S. A. J. R., Borg, Å., Salomon, A. V., Thomas, G., Børresen-Dale, A.-L., Richardson, A. L., Neuberger, M. S., Futreal, P. A., Campbell, P. J., & Stratton, M. R.
- Affiliations
- Wellcome Sanger Institute (GB)
- University of East Anglia (GB)
- Dana-Farber Cancer Institute (US)
- Centre Léon Bérard (FR)
- Oslo University Hospital (NO)
- King's College London (GB)
- Erasmus MC (NL)
- University of British Columbia (CA)
- Lund University (SE)
- Brigham and Women's Hospital (US)
- MRC Laboratory of Molecular Biology (GB)
- University of Cambridge (GB)
- Corresponding author
- Stratton, Michael R.
- ORCID
- Alexandrov, Ludmil B.
- Wedge, David C.
- Raine, Keiran
- Jones, David
- Hinton, Jonathan
- Marshall, John
- Menzies, Andrew
- Martin, Sancha
- Chen, Lina
- Ramakrishna, Manasa
- Lau, King Wai
- Varela, Ignacio
- McBride, David J.
- Shlien, Adam
- Tarpey, Patrick S.
- Davies, Helen R.
- Papaemmanuil, Elli
- McLaren, Stuart
- Teague, Jon W.
- Garber, Judy E.
- Silver, Daniel
- Miron, Penelope
- Boyault, Sandrine
- Tutt, Andrew
- Martens, John W.M.
- Aparicio, Samuel A.J.R.
- Borg, Åke
- Thomas, Gilles
- Richardson, Andrea L.
- Neuberger, Michael S.
- Futreal, P. Andrew
- Campbell, Peter J.
- Stratton, Michael R.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2012-05
- Volume
- 149
- Issue
- 5
- Pages
- 979-993
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3414841
- OpenAlex
- W2129136620
- Cited by
- 1,909
- References
- 64
- Citations by year
- 2026: 75 · 2025: 81 · 2024: 102 · 2023: 148 · 2022: 125 · 2021: 175 · 2020: 141 · 2019: 145 · 2018: 126 · 2017: 146 · 2016: 164 · 2015: 142 · 2014: 147 · 2013: 141 · 2012: 46
- FWCI
- 50.38
- Type
- journal article
- Language
- en
- Update notices
- erratum (2015-08-13)
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (acceptedVersion)
- UEA Digital Repository (University of East Anglia) (acceptedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion, other-oa)
- RePub (Erasmus University Rotterdam) (submittedVersion, other-oa)
- Research Portal (King's College London) (submittedVersion)
- Lirias (submittedVersion)
- Lund University Publications (Lund University) (submittedVersion)
- Research Explorer (The University of Manchester) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Funders
- Wellcome Trust (088340, WT088340MA, 098051)
- King's College Hospital NHS Foundation Trust
- National Institute for Health and Care Research (ICGC 08/09)
- King's College London
- European Commission (242006)
- Fonds Wetenschappelijk Onderzoek
- Norges Forskningsråd
- Vlaamse regering
- National Research Council Canada
- Biotechnology and Biological Sciences Research Council (BBS/E/T/000PR6193)
- BC Cancer Agency
- National Cancer Institute (CA 089393, P50CA089393)
- 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
- breast cancer, somatic mutations, mutational signatures, DNA damage and repair, BRCA1, BRCA2, kataegis, somatic rearrangements, APOBEC cytidine deaminases
- MeSH terms
- APOBEC-1 Deaminase, Breast Neoplasms, Cytidine Deaminase, DNA Mutational Analysis, Female, Humans, Mutation, Genes, BRCA1, BRCA2 Protein, Genome-Wide Association Study, High-Throughput Nucleotide Sequencing
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