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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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Citations
Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
PD-1 and PD-L1 Immune Checkpoint Blockade to Treat Breast Cancer
Hartkopf, A. D., Taran, F., Wallwiener, M., Walter, C. B., Krämer, B., Grischke, E., & Brucker, S. Y. (2016) · Breast Care · doi:10.1159/000453569 · Cited by 30,989
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
Self-citationNishimura, R., Osako, T., Nishiyama, Y., Tashima, R., Nakano, M., Fujisue, M., Toyozumi, Y., & Arima, N. (2013) · Oncology · doi:10.1159/000353099 · Cited by 13,239
Comprehensive molecular portraits of human breast tumours
The Cancer Genome Atlas Network (2012) · Nature · doi:10.1038/nature11412 · Cited by 12,129
Signatures of mutational processes in human cancer
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., et al. (2013) · Nature · doi:10.1038/nature12477 · Cited by 9,660
Self-citationVelvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,575
Self-citationThe genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
METABRIC Group, Curtis, C., Shah, S. P., Chin, S.-F., Turashvili, G., Rueda, O. M., Dunning, M. J., Speed, D., Lynch, A. G., Samarajiwa, S., et al. (2012) · Nature · doi:10.1038/nature10983 · Cited by 6,097
Self-citationConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking
Wilkerson, M. D., & Hayes, D. N. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq170 · Cited by 5,645
Mutational heterogeneity in cancer and the search for new cancer-associated genes
Lawrence, M. S., Stojanov, P., Polak, P., Kryukov, G. V., Cibulskis, K., Sivachenko, A., Carter, S. L., Stewart, C., Mermel, C. H., Roberts, S. A., et al. (2013) · Nature · doi:10.1038/nature12213 · Cited by 5,461
Inhibition of Poly(ADP-Ribose) Polymerase in Tumors from BRCA Mutation Carriers
Fong, P. C., Boss, D. S., Yap, T. A., Tutt, A., Wu, P., Mergui-Roelvink, M., Mortimer, P., Swaisland, H., Lau, A., O'Connor, M. J., et al. (2009) · New England Journal of Medicine · doi:10.1056/nejmoa0900212 · Cited by 3,634
Self-citationStratton, M. R., Campbell, P. J., & Futreal, P. A. (2009) · Nature · doi:10.1038/nature07943 · Cited by 3,625
Self-citationDiscovery and saturation analysis of cancer genes across 21 tumour types
Lawrence, M. S., Stojanov, P., Mermel, C. H., Robinson, J. T., Garraway, L. A., Golub, T. R., Meyerson, M., Gabriel, S. B., Lander, E. S., & Getz, G. (2014) · Nature · doi:10.1038/nature12912 · Cited by 3,096 · cited 1×
“To identify new cancer genes, we combined somatic substitutions and indels in protein-coding exons with data from other series12–15,26, constituting a total of 1,332 breast cancers, and searched for mutation clustering in each gene beyond that expected by chance.”
Whole genomes redefine the mutational landscape of pancreatic cancer
Initiative, A. P. C. G., Waddell, N., Pajic, M., Patch, A.-M., Chang, D. K., Kassahn, K. S., Bailey, P., Johns, A. L., Miller, D., Nones, K., et al. (2015) · Nature · doi:10.1038/nature14169 · Cited by 2,642
Self-citationYe, K., Schulz, M. H., Long, Q., Apweiler, R., & Ning, Z. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp394 · Cited by 2,017
The clonal and mutational evolution spectrum of primary triple-negative breast cancers
Shah, S. P., Roth, A., Goya, R., Oloumi, A., Ha, G., Zhao, Y., Turashvili, G., Ding, J., Tse, K., Haffari, G., et al. (2012) · Nature · doi:10.1038/nature10933 · Cited by 1,967
Self-citationMutational Processes Molding the Genomes of 21 Breast Cancers
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., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.024 · Cited by 1,909
Self-citationHighly Recurrent TERT Promoter Mutations in Human Melanoma
Huang, F. W., Hodis, E., Xu, M. J., Kryukov, G. V., Chin, L., & Garraway, L. A. (2013) · Science · doi:10.1126/science.1229259 · Cited by 1,816
The landscape of cancer genes and mutational processes in breast cancer
Stephens, P. J., Tarpey, P. S., Davies, H. R., Loo, P. V., Greenman, C., Wedge, D. C., Nik‐Zainal, S., Martin, S., Varela, I., Bignell, G. R., et al. (2012) · Nature · doi:10.1038/nature11017 · Cited by 1,731
Self-citationA comprehensive catalogue of somatic mutations from a human cancer genome
Pleasance, E. D., Cheetham, R. K., Stephens, P. J., McBride, D. J., Humphray, S. J., Greenman, C. D., Varela, I., Lin, M.-L., Ordóñez, G. R., Bignell, G. R., et al. (2010) · Nature · doi:10.1038/nature08658 · Cited by 1,696
Self-citationWhole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia
Puente, X. S., Pinyol, M., Quesada, V., Conde, L., Ordóñez, G. R., Villamor, N., Escaramís, G., Jares, P., Beà, S., González, M., et al. (2011) · Nature · doi:10.1038/nature10113 · Cited by 1,529
Self-citationThe Life History of 21 Breast Cancers
Nik-Zainal, S., Van Loo, P., Wedge, D. C., Alexandrov, L. B., Greenman, C. D., Lau, K. W., Raine, K., Jones, D., Marshall, J., Ramakrishna, M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.023 · Cited by 1,443
Self-citationDeciphering Signatures of Mutational Processes Operative in Human Cancer
Alexandrov, L. B., Nik‐Zainal, S., Wedge, D. C., Campbell, P. J., & Stratton, M. R. (2013) · Cell Reports · doi:10.1016/j.celrep.2012.12.008 · Cited by 1,277
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Loo, P. V., Nord, S., Lingjærde, O. C., Russnes, H. G., Rye, I. H., Sun, W., Weigman, V., Marynen, P., Zetterberg, A., Naume, B., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1009843107 · Cited by 1,192
Self-citationSequence analysis of mutations and translocations across breast cancer subtypes
Banerji, S. O., Cibulskis, K., Rangel‐Escareño, C., Brown, K., Carter, S. L., Frederick, A. M., Lawrence, M. S., Sivachenko, A., Sougnez, C. L., Zou, L., et al. (2012) · Nature · doi:10.1038/nature11154 · Cited by 1,181
Self-citationA small-cell lung cancer genome with complex signatures of tobacco exposure
Pleasance, E., Stephens, P. J., O’Meara, S., McBride, D. J., Meynert, A. M., Jones, D., Lin, M., Beare, D. M., Lau, K. W., Greenman, C., et al. (2009) · Nature · doi:10.1038/nature08629 · Cited by 1,076
Self-citationWhole-genome analysis informs breast cancer response to aromatase inhibition
Ellis, M. J., Ding, L., Shen, D., Luo, J. R., Suman, V. J., Wallis, J. W., Tine, B. A. V., Hoog, J., Goiffon, R., Goldstein, T. C., et al. (2012) · Nature · doi:10.1038/nature11143 · Cited by 1,040
RCircos: an R package for Circos 2D track plots
Zhang, H., Meltzer, P. S., & Davis, S. R. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-244 · Cited by 995
Frequency of TERT promoter mutations in human cancers
Vinagre, J., Almeida, A., Pópulo, H., Batista, R., Lyra, J., Pinto, V., Coelho, R., Celestino, R., Prazeres, H., Lima, L., et al. (2013) · Nature Communications · doi:10.1038/ncomms3185 · Cited by 898
Mechanisms underlying mutational signatures in human cancers
Helleday, T., Eshtad, S., & Nik‐Zainal, S. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3729 · Cited by 861
Self-citationAbkevich, V., Timms, K. M., Hennessy, B. T., Potter, J., Carey, M. S., Meyer, L. A., Smith‐McCune, K., Broaddus, R. R., Lu, K. H., Chen, J., et al. (2012) · British Journal of Cancer · doi:10.1038/bjc.2012.451 · Cited by 817
Interpreting cDNA sequences: Some insights from studies on translation
Kozak, M. (1996) · Mammalian Genome · doi:10.1007/s003359900171 · Cited by 774
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Wu, Y.-M., Su, F., Sundaram, S. K., Khazanov, N. A., Ateeq, B., Cao, X., Lonigro, R. J., Vats, P., Wang, R., Lin, S., et al. (2013) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0050 · Cited by 759
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West, J. A., Davis, C. P., Sunwoo, H., Simon, M. D., Sadreyev, R. I., Wang, P. I., Tolstorukov, M. Y., & Kingston, R. E. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.07.012 · Cited by 727
Popova, T. G., Manié, É., Rieunier, G., Caux‐Moncoutier, V., Tirapo, C., Dubois, T., Delattre, O., Sigal‐Zafrani, B., Bollet, M. A., Longy, M., et al. (2012) · Cancer Research · doi:10.1158/0008-5472.can-12-1470 · Cited by 683
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Birkbak, N. J., Wang, Z. C., Kim, J.-Y., Eklund, A. C., Li, Q., Tian, R., Bowman-Colin, C., Li, Y., Greene-Colozzi, A., Iglehart, J. D., et al. (2012) · Cancer Discovery · doi:10.1158/2159-8290.cd-11-0206 · Cited by 656
Self-citationKozarewa, I., Ning, Z., Quail, M. A., Sanders, M. J., Berriman, M., & Turner, D. J. (2009) · Nature Methods · doi:10.1038/nmeth.1311 · Cited by 575
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Weinhold, N., Jacobsen, A., Schultz, N., Sander, C., & Lee, W. (2014) · Nature Genetics · doi:10.1038/ng.3101 · Cited by 484
Extracellular matrix signature identifies breast cancer subgroups with different clinical outcome
Bergamaschi, A., Tagliabue, E., Sørlie, T., Naume, B., Triulzi, T., Orlandi, R., Russnes, H., Nesland, J. M., Tammi, R., Auvinen, P., et al. (2007) · The Journal of Pathology · doi:10.1002/path.2278 · Cited by 387
Self-citationIntegrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics
Khurana, E., Fu, Y., Colonna, V., Mu, X. J., Kang, H. M., Lappalainen, T., Sboner, A., Lochovsky, L., Chen, J., Harmanci, A. O., et al. (2013) · Science · doi:10.1126/science.1235587 · Cited by 368
Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer
Robinson, D. R., Sundaram, S. K., Wu, Y.-M., Shankar, S., Cao, X., Ateeq, B., Asangani, I. A., Iyer, M. K., Maher, C. A., Grasso, C. S., et al. (2011) · Nature Medicine · doi:10.1038/nm.2580 · Cited by 343
Novel patterns of genome rearrangement and their association with survival in breast cancerPreprint
Hicks, J. B., Krasnitz, A., Lakshmi, B. V., Navin, N. E., Riggs, M. G., Leibu, E., Esposito, D., Alexander, J., Troge, J. E., Grubor, V. D., et al. (2006) · Genome Research · doi:10.1101/gr.5460106 · Cited by 321
Self-citationVoineagu, I., Narayanan, V., Lobachev, K. S., & Mirkin, S. M. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804510105 · Cited by 269
The topography of mutational processes in breast cancer genomes
Morganella, S., Alexandrov, L. B., Głodzik, D., Zou, X., Davies, H. R., Staaf, J., Sieuwerts, A. M., Brinkman, A. B., Martin, S., Ramakrishna, M., et al. (2016) · Nature Communications · doi:10.1038/ncomms11383 · Cited by 252
Self-citationInverted repeats, stem‐loops, and cruciforms: Significance for initiation of DNA replication
Pearson, C. E., Zorbas, H., Price, G. B., & Zannis-Hadjopoulos, M. (1996) · Journal of Cellular Biochemistry · doi:10.1002/(sici)1097-4644(199610)63:1 · Cited by 171
Targeting the DNA repair defect of BRCA tumours
Turner, N. C., Tutt, A. N. J., & Ashworth, A. (2005) · Current Opinion in Pharmacology · doi:10.1016/j.coph.2005.03.006 · Cited by 164
Self-citationStatistical Analysis of Pathogenicity of Somatic Mutations in Cancer
Greenman, C., Wooster, R., Futreal, P. A., Stratton, M. R., & Easton, D. F. (2006) · Genetics · doi:10.1534/genetics.105.044677 · Cited by 163
Self-citationSun, L., Craiu, R. V., Paterson, A. D., & Bull, S. B. (2006) · Genetic Epidemiology · doi:10.1002/gepi.20164 · Cited by 149
Treatment with olaparib in a patient with PTEN-deficient endometrioid endometrial cancer
Forster, M. D., Dedes, K. J., Sandhu, S. K., Frentzas, S., Kristeleit, R. S., Ashworth, A., Poole, C. J., Weigelt, B., Kaye, S. B., & Molife, L. R. (2011) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2011.42 · Cited by 125
Short Inverted Repeats Are Hot Spots For Genetic Instability: Relevance to Cancer Genomes
Lu, S., Wang, G., Bacolla, A., Zhao, J., Spitser, S. A., & Vasquez, K. M. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.02.039 · Cited by 117
Giacomini, C. P., Sun, S., Varma, S., Shain, A. H., Giacomini, M. M., Balagtas, J. M. S., Sweeney, R. T., Lai, E., Fitz, C. D. V., Forster, A. D., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003464 · Cited by 117
Natrajan, R., Wilkerson, P. M., Marchiò, C., Piscuoglio, S., Ng, C. K. Y., Wai, P. T., Lambros, M. B. K., Samartzis, E. P., Dedes, K. J., Frankum, J. R., et al. (2014) · The Journal of Pathology · doi:10.1002/path.4325 · Cited by 110
Sundaram, S. K., Shankar, S., DeRoo, S. C., Iyer, M. K., Palanisamy, N., Chinnaiyan, A. M., & Kumar‐Sinha, C. (2012) · Neoplasia · doi:10.1593/neo.12914 · Cited by 73
Transcription regulatory region analysis using signal detection and fuzzy clustering.
Pickert, L., Reuter, I., Klawonn, F., & Wingender, E. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.3.244 · Cited by 63
Karlsson, J., Lilljebjörn, H., Mengelbier, L. H., Valind, A., Rissler, M., Øra, I., Fioretos, T., & Gisselsson, D. (2014) · Cancer Letters · doi:10.1016/j.canlet.2014.11.057 · Cited by 46
Genome Update: DNA repeats in bacterial genomes
Ussery, D. W., Binnewies, T. T., Gouveia‐Oliveira, R., Jarmer, H. Ø., & Hallin, P. F. (2004) · Microbiology · doi:10.1099/mic.0.27628-0 · Cited by 38
Fang, M., Toher, J. L., Morgan, M. T., Davison, J., Tannenbaum, S. H., & Claffey, K. P. (2010) · Cancer · doi:10.1002/cncr.25770 · Cited by 34
Wójcik, E. A., Brzostek, A. M., Bacolla, A., Mackiewicz, P., Vásquez, K. M., Korycka‐Machała, M., Jaworski, A., & Dziadek, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0051064 · Cited by 34
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Tubío, J. M. C. (2015) · Briefings in Functional Genomics · doi:10.1093/bfgp/elv016 · Cited by 26
Naidu, R. (2011) · International Journal of Oncology · doi:10.3892/ijo.2011.1081 · Cited by 16
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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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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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