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Landscape of somatic mutations in 560 breast cancer whole-genome sequences
Open accessAbstract
We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer. Whole-genome sequencing of tumours from 560 breast cancer cases provides a comprehensive genome-wide view of recurrent somatic mutations and mutation frequencies across both protein coding and non-coding regions; several mutational signatures in these cancer genomes are associated with BRCA1 or BRCA2 function and defective homologous-recombination-based DNA repair. This study reports whole-genome sequencing of tumours and normal tissue from 560 breast cancer cases, providing a comprehensive genome-wide view of recurrent somatic mutations and mutation frequencies across both protein coding and non-coding regions. The authors analyse mutational signatures in these cancer genomes, including a new investigation of rearrangement mutational processes, and find several that are associated with BRCA1 or BRCA2 function and defective homologous-recombination-based DNA repair. They also find mutational signatures showing distinct DNA replication strand biases.
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“For example, BRCA inactivation is known to promote genomic instability through homologous recombination deficiencies in several solid tumors such as breast and ovarian cancer.47”
From Evolution of Multiple Myeloma from a Genomic Perspective (2026) · cites this paper as [47]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“Indeed, some mutational footprints were found to be associated with BRCA1/2 deficiency, namely deletions with flanking microhomology, as well as several “mutational signatures” including two COSMIC single nucleotide variant (SNV) signatures and two structural variant (SV) signatures8.”
From Pan-cancer landscape of homologous recombination deficiency. (2020) · cites this paper as [8]
In the citing paper
“These genomic features in the SCAN-B TNBC cohort were comparable to a previously reported WGS cohort8”
From Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study (2019) · cites this paper as [8]
In the citing paper
“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 [9]
In the citing paper
“Seventy-nine out of the 93 previously identified BC driver genes [9] were mutated”
From Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers (2019) · cites this paper as [9]
In the citing paper
“Despite the role of TP53, ATM and CHEK2 in DNA-damage signalling and double-strand breaks detection, these tumours do not show evidence of BRCA-deficient signatures, as previously described [9, 13, 19], but instead they harbour highly complex clustered chromosomal rearrangements.”
From Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers (2019) · cites this paper as [9]
In the citing paper
“The variant was not reported in gnomAD or in the 560 BC genomes cohort [9] and is described by ClinVar (Variation ID: 135816) as ‘Class 3 Uncertain significance’”
From Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers (2019) · cites this paper as [9]
In the citing paper
“Loss of function of BRCA1, BRCA2 and PALB2 yield a high mutation burden and specific signatures inferring defective HR [7, 9, 10, 13].”
From Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers (2019) · cites this paper as [9]
In the citing paper
“These clustered events coincided with amplifications of known BC oncogenes (e.g. ZNF217, ERBB2, CCND1, MYC) [9]”
From Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers (2019) · cites this paper as [9]
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Metadata
- Authors
- Nik-Zainal, S., Davies, H., Staaf, J., Ramakrishna, M., Glodzik, D., Zou, X., Martincorena, I., Alexandrov, L. B., Martin, S., Wedge, D. C., Van Loo, P., Ju, Y. S., Smid, M., Brinkman, A. B., Morganella, S., Aure, M. R., Lingjærde, O. C., Langerød, A., Ringnér, M., Ahn, S.-M., Boyault, S., Brock, J. E., Broeks, A., Butler, A., Desmedt, C., Dirix, L., Dronov, S., Fatima, A., Foekens, J. A., Gerstung, M., Hooijer, G. K. J., Jang, S. J., Jones, D. R., Kim, H.-Y., King, T. A., Krishnamurthy, S., Lee, H. J., Lee, J.-Y., Li, Y., McLaren, S., Menzies, A., Mustonen, V., O’Meara, S., Pauporté, I., Pivot, X., Purdie, C. A., Raine, K., Ramakrishnan, K., Rodríguez-González, F. G., Romieu, G., Sieuwerts, A. M., Simpson, P. T., Shepherd, R., Stebbings, L., Stefansson, O. A., Teague, J., Tommasi, S., Treilleux, I., Van den Eynden, G. G., Vermeulen, P., Vincent-Salomon, A., Yates, L., Caldas, C., Veer, L. V., Tutt, A., Knappskog, S., Tan, B. K. T., Jonkers, J., Borg, Å., Ueno, N. T., Sotiriou, C., Viari, A., Futreal, P. A., Campbell, P. J., Span, P. N., Van Laere, S., Lakhani, S. R., Eyfjord, J. E., Thompson, A. M., Birney, E., Stunnenberg, H. G., van de Vijver, M. J., Martens, J. W. M., Børresen-Dale, A.-L., Richardson, A. L., Kong, G., Thomas, G., & Stratton, M. R.
- Affiliations
- Wellcome Sanger Institute (GB)
- Lund University (SE)
- Los Alamos National Laboratory (US)
- Erasmus MC (NL)
- Radboud University Nijmegen (NL)
- European Bioinformatics Institute (GB)
- Oslo University Hospital (NO)
- University of Oslo (NO)
- Gachon University Gil Medical Center (KR)
- Centre Léon Bérard (FR)
- Brigham and Women's Hospital (US)
- The Netherlands Cancer Institute (NL)
- Université Libre de Bruxelles (BE)
- University of Antwerp (BE)
- Dana-Farber Cancer Institute (US)
- Amsterdam UMC Location University of Amsterdam (NL)
- Asan Medical Center (KR)
- Hanyang University (KR)
- Memorial Sloan Kettering Cancer Center (US)
- The University of Texas MD Anderson Cancer Center (US)
- Institut National du Cancer (FR)
- Inserm (FR)
- Ninewells Hospital (GB)
- Institut Regional du Cancer de Montpellier (FR)
- The University of Queensland (AU)
- Istituto Tumori Bari (IT)
- University of Cambridge (GB)
- Institute of Cancer Research (GB)
- Haukeland University Hospital (NO)
- Singapore General Hospital (SG)
- Institut national de recherche en sciences et technologies du numérique (FR)
- Radboud University Medical Center (NL)
- University of Iceland (IS)
- Corresponding author
- Viari, Alain
- Kong, Gu
- Stratton, Michael R.
- ORCID
- Davies, Helen
- Staaf, Johan
- Ramakrishna, Manasa
- Zou, Xueqing
- Alexandrov, Ludmil B.
- Martin, Sancha
- Wedge, David C.
- Ju, Young Seok
- Smid, Marcel
- Brinkman, Arie B.
- Morganella, Sandro
- Aure, Miriam R.
- Lingjærde, Ole Christian
- Ringnér, Markus
- Ahn, Sung-Min
- Boyault, Sandrine
- Brock, Jane E.
- Broeks, Annegien
- Desmedt, Christine
- Dirix, Luc
- Dronov, Serge
- Gerstung, Moritz
- Hooijer, Gerrit K. J.
- Jang, Se Jin
- Jones, David R.
- Krishnamurthy, Savitri
- Lee, Hee Jin
- Lee, Jeong-Yeon
- Li, Yilong
- McLaren, Stuart
- Menzies, Andrew
- Mustonen, Ville
- Pivot, Xavier
- Purdie, Colin A.
- Raine, Keiran
- Ramakrishnan, Kamna
- Rodríguez-González, F. Germán
- Sieuwerts, Anieta M.
- Simpson, Peter T.
- Shepherd, Rebecca
- Teague, Jon
- Tommasi, Stefania
- Treilleux, Isabelle
- Vermeulen, Peter
- Yates, Lucy
- Caldas, Carlos
- Veer, Laura van’t
- Tutt, Andrew
- Knappskog, Stian
- Tan, Benita Kiat Tee
- Jonkers, Jos
- Borg, Åke
- Ueno, Naoto T.
- Sotiriou, Christos
- Viari, Alain
- Futreal, P. Andrew
- Span, Paul N.
- Lakhani, Sunil R.
- Thompson, Alastair M.
- Birney, Ewan
- Stunnenberg, Hendrik G.
- Martens, John W. M.
- Richardson, Andrea L.
- Kong, Gu
- Thomas, Gilles
- Stratton, Michael R.
- Venue
- Nature
- Published
- 2016-05-02
- Volume
- 534
- Issue
- 7605
- Pages
- 47-54
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4910866
- OpenAlex
- W2344657883
- Semantic Scholar
- abb27e35f11dcd60325f42f270b7811a4e852852
- Cited by
- 2,218
- References
- 60
- Citations by year
- 2026: 125 · 2025: 147 · 2024: 178 · 2023: 271 · 2022: 212 · 2021: 293 · 2020: 288 · 2019: 241 · 2018: 200 · 2017: 181 · 2016: 78
- FWCI
- 97.22
- Type
- journal article
- Language
- en
- Update notices
- correction (2019-01-18)
- Open access
- green
- pure.amsterdamumc.nl
- Licence
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
- Pure Amsterdam UMC (acceptedVersion, other-oa)
- PubMed Central (acceptedVersion)
- Dépôt institutionnel de l'Université libre de Bruxelles (Université Libre de Bruxelles) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- RePub (Erasmus University Rotterdam) (submittedVersion, other-oa)
- HAL (submittedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- Discovery Research Portal (University of Dundee) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Research Portal (King's College London) (submittedVersion)
- Lirias (KU Leuven) (submittedVersion)
- Lund University Publications (Lund University) (submittedVersion)
- Radboud Repository (Radboud University) (submittedVersion)
- RePub (Erasmus University Rotterdam) (submittedVersion)
- Apollo
- Funders
- U.S. Department of Energy (DE-AC52-06NA2-5396, AC52-06NA25396)
- Breast Cancer Research Foundation
- Dana-Farber/Harvard Cancer Center (P50 CA168504)
- University of Dundee
- Wellcome Trust (088177, 077012/Z/05/Z, 100183, 077012, WT100183MA, 098051)
- Francis Crick Institute (10202)
- QIMR Berghofer Medical Research Institute
- Cancer Research UK (60098573, 20952, CB4140, 16942)
- National Institute for Health and Care Research (NF-SI-0515-10090, NF-SI-0611-10154)
- Breast Cancer Campaign
- University of Cambridge
- European Commission (242006)
- National Research Foundation
- Icelandic Centre for Research
- Fonds De La Recherche Scientifique - FNRS
- Cancerfonden
- Cambridge University Hospitals (RG51913)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek
- National Research Foundation of Korea (2015R1A2A1A10052578, 2011-0030105)
- Vetenskapsrådet
- Háskóli Íslands
- Institut National Du Cancer
- Rannís
- National Institutes of Health (DE-AC52-06NA25396)
- National Nuclear Security Administration (DEAC52- 06NA25396)
- National Cancer Institute (CA168504, P30CA008748, P50CA168504)
- Los Alamos National Laboratory (AC52-06NA25396, DE-AC52-06NA25396)
- FP7 Ideas: European Research Council (322737)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › BRCA gene mutations in cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- breast cancer, somatic mutations, driver mutations, mutational signatures, tandem duplication, homologous recombination deficiency, BRCA1, BRCA2, non-coding regions, intronic variants
- MeSH terms
- Breast Neoplasms, DNA Mutational Analysis, DNA Replication, DNA, Neoplasm, Female, Humans, Male, Mutation, Oncogenes, Cohort Studies, Genome, Human, Mutagenesis, Genes, BRCA1, Genomics, Genes, BRCA2, Mutation Rate, Recombinational DNA Repair
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