The DOI matches its Crossref record; 60 of the 60 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
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
Cited by
Sorted by citations
Items 401–500 of 1,002
Ansari‐Pour, N., Zheng, Y., Yoshimatsu, T. F., Sanni, A., Ajani, M., Reynier, J.-B., Tapinos, A., Pitt, J. J., Dentro, S. C., Woodard, A., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27079-w · Cited by 66
Self-citationRajendran, B. K., & Deng, C.-X. (2017) · Oncotarget · doi:10.18632/oncotarget.17225 · Cited by 73
Obesity-associated changes in molecular biology of primary breast cancer
Nguyen, H.-L., Geukens, T., Maetens, M., Aparicio, S. A. J. R., Bassez, A., Borg, Å., Brock, J. E., Broeks, A., Caldas, C., Cardoso, F., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39996-z · Cited by 71
Self-citationMichalak, E. M., & Visvader, J. E. (2016) · Molecular Oncology · doi:10.1016/j.molonc.2016.09.003 · Cited by 69
Molecular Events in the Natural History of Pancreatic Cancer
Oldfield, L. E., Connor, A. A., & Gallinger, S. (2017) · Trends in cancer · doi:10.1016/j.trecan.2017.04.005 · Cited by 65
Molecular signatures in breast cancer
Lal, S., Reed, A. E. M., Luca, X. M. D., & Simpson, P. T. (2017) · Methods · doi:10.1016/j.ymeth.2017.06.032 · Cited by 65
Self-citationOlaparib for the treatment of breast cancer
Griguolo, G., Dieci, M. V., Guarneri, V., & Conte, P. (2018) · Expert Review of Anticancer Therapy · doi:10.1080/14737140.2018.1458613 · Cited by 66
Gonçalves, E., Behan, F. M., Louzada, S., Arnol, D., Stronach, E. A., Yang, F., Yusa, K., Stegle, O., Iorio, F., & Garnett, M. J. (2019) · Genome biology · doi:10.1186/s13059-019-1637-z · Cited by 60
BRCA1-associated structural variations are a consequence of polymerase theta-mediated end-joining
Kamp, J. A., van Schendel, R., Dilweg, I. W., & Tijsterman, M. (2020) · Nature Communications · doi:10.1038/s41467-020-17455-3 · Cited by 65
BRCA1 Mutations in Cancer: Coordinating Deficiencies in Homologous Recombination with Tumorigenesis
Krais, J. J., & Johnson, N. (2020) · Cancer Research · doi:10.1158/0008-5472.can-20-1830 · Cited by 66
Stok, C., Kok, Y. P., van den Tempel, N., & van Vugt, M. A. T. M. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab151 · Cited by 67
DiMarco, A. V., Qin, X., McKinney, B. J., Garcia, N. M. G., Alsten, S. C. V., Mendes, E. A., Force, J. M., Hanks, B. A., Troester, M. A., Owzar, K., et al. (2021) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-21-0146 · Cited by 61
Saving the spandrels? Adaptive genomic variation in conservation and fisheries management
Pearse, D. E. (2016) · Journal of Fish Biology · doi:10.1111/jfb.13168 · Cited by 64
Shukla, N. N., Roberts, S. S., Baki, M. O., Mushtaq, Q. D., Goss, P. E., Park, B. H., Gundem, G., Tian, K., Geiger, H. M., Redfield, K., et al. (2017) · JCO Precision Oncology · doi:10.1200/po.17.00034 · Cited by 64
Resistance to PARP Inhibitors: Lessons from Preclinical Models of BRCA-Associated Cancer
Gogola, E., Rottenberg, S., & Jonkers, J. (2018) · Annual Review of Cancer Biology · doi:10.1146/annurev-cancerbio-030617-050232 · Cited by 66
Self-citationThe Spatial and Genomic Hierarchy of Tumor Ecosystems Revealed by Single-Cell Technologies
Smith, E. A., & Hodges, H. C. (2019) · Trends in cancer · doi:10.1016/j.trecan.2019.05.009 · Cited by 61
Discovery of regulatory noncoding variants in individual cancer genomes by using cis-X
Liu, Y., Li, C., Shen, S., Chen, X., Szlachta, K., Edmonson, M. N., Shao, Y., Ma, X., Hyle, J., Wright, S., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0659-5 · Cited by 64
Leveraging premalignant biology for immune-based cancer prevention
Spira, A. E., Disis, M. L., Schiller, J. T., Vilar, E., Rebbeck, T. R., Bejar, R. L., Ideker, T., Arts, J., Yurgelun, M. B. B., Mesirov, J. P., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1608077113 · Cited by 64
Triangular Relationship between p53, Autophagy, and Chemotherapy Resistance
Xu, J., Patel, N. H., & Gewirtz, D. A. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21238991 · Cited by 66
Oh, S., Bournique, E., Bowen, D., Jalili, P. R., Sanchez, A., Ward, I., Dananberg, A., Manjunath, L., Tran, G. P., Semler, B. L., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25203-4 · Cited by 63
Revisiting the BRCA-pathway through the lens of replication gap suppression
Cantor, S. B. (2021) · DNA repair · doi:10.1016/j.dnarep.2021.103209 · Cited by 63
Epigenetics and environment in breast cancer: New paradigms for anti-cancer therapies
Thakur, C., Qiu, Y., Fu, Y. S., Bi, Z., Zhang, W., Ji, H., & Chen, F. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.971288 · Cited by 74
Tumor organoid biobank-new platform for medical research
Xie, X., Li, X., & Song, W. (2023) · Scientific Reports · doi:10.1038/s41598-023-29065-2 · Cited by 70
Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells
Rosano, D., Sofyalı, E., Dhiman, H., Ghirardi, C., Ivanoiu, D., Heide, T., Vingiani, A., Bertolotti, A., Pruneri, G., Canale, E., et al. (2024) · Cancer Discovery · doi:10.1158/2159-8290.cd-23-1161 · Cited by 65
Genomic signatures as predictive biomarkers of homologous recombination deficiency in ovarian cancer
Vanderstichele, A., Busschaert, P., Olbrecht, S., Lambrechts, D., & Vergote, I. B. (2017) · European Journal of Cancer · doi:10.1016/j.ejca.2017.08.029 · Cited by 62
Panda, A., Betigeri, A. M., Subramanian, K., Ross, J. S., Pavlick, D. C., Ali, S. M., Markowski, P. A., Silk, A. W., Kaufman, H. L., Lattime, E. C., et al. (2017) · JCO Precision Oncology · doi:10.1200/po.17.00146 · Cited by 64
Empirical evaluation of variant calling accuracy using ultra-deep whole-genome sequencing data
Kishikawa, T., Momozawa, Y., Ozeki, T., Mushiroda, T., Inohara, H., Kamatani, Y., Kubo, M., & Okada, Y. (2019) · Scientific Reports · doi:10.1038/s41598-018-38346-0 · Cited by 61
Funnell, T., Zhang, A. W., Grewal, D. S., McKinney, S. E., Bashashati, A., Wang, Y. K., & Shah, S. P. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006799 · Cited by 63
Rydén, L., Loman, N., Larsson, C., Hegardt, C., Vallon-Christersson, J., Malmberg, M., Lindman, H., Ehinger, A., Saal, L. H., & Borg, Å. (2018) · British Journal of Surgery · doi:10.1002/bjs.10741 · Cited by 62
Self-citationLncRNAs in Cancer: From garbage to Junk
Aprile, M., Katopodi, V., Leucci, E., & Costa, V. (2020) · Cancers · doi:10.3390/cancers12113220 · Cited by 63
Random Forest Modelling of High-Dimensional Mixed-Type Data for Breast Cancer Classification
Quist, J., Taylor, L., Staaf, J., & Grigoriadis, A. E. (2021) · Cancers · doi:10.3390/cancers13050991 · Cited by 67
Self-citationDo platinum salts fit all triple negative breast cancers?
Gerratana, L., Fanotto, V., Pelizzari, G., Agostinetto, E., & Puglisi, F. (2016) · Cancer Treatment Reviews · doi:10.1016/j.ctrv.2016.06.004 · Cited by 67
An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures
Collord, G., Tarpey, P. S., Kurbatova, N., Martincorena, I., Morán, S., de Moura, M. C., Nagy, T., Bignell, G. R., Maura, F., Young, M. D., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-31659-0 · Cited by 64
Self-citationAlexiadis, M., Rowley, S. M., Chu, S., Leung, D. T. H., Stewart, C. J. R., Amarasinghe, K. C., Campbell, I., & Fuller, P. J. (2018) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-18-0359 · Cited by 63
Humphries, M. P., Hynes, S. O., Bingham, V., Cougot, D., James, J. A., Patell-Socha, F., Parkes, E. E., Blayney, J. K., O’Rorke, M. A., Irwin, G. W., et al. (2018) · Journal of Oncology · doi:10.1155/2018/2937012 · Cited by 63
Solinas, C., Marcoux, D., Garaud, S., Vitória, J. R., den Eynden, G. V., de Wind, A., Silva, P. D., Boisson, A., Craciun, L., Larsimont, D., et al. (2019) · Cancer Letters · doi:10.1016/j.canlet.2019.02.027 · Cited by 64
Annunziato, S., Lutz, C., Henneman, L., Bhin, J., Wong, K., Siteur, B., van Gerwen, B., de Korte‐Grimmerink, R., Zafra, M. P., Schatoff, E. M., et al. (2020) · The EMBO Journal · doi:10.15252/embj.2019102169 · Cited by 62
Self-citationA Practical Guide for Structural Variation Detection in the Human Genome
Yang, L. (2020) · Current Protocols in Human Genetics · doi:10.1002/cphg.103 · Cited by 66
The mutagenic forces shaping the genomes of lung cancer in never smokers
Díaz‐Gay, M., Zhang, T., Hoang, P. H., Leduc, C., Baine, M. K., Travis, W. D., Sholl, L. M., Joubert, P., Khandekar, A., Wei, Z., et al. (2025) · Nature · doi:10.1038/s41586-025-09219-0 · Cited by 85
Self-citationBarua, D., Gupta, A., & Gupta, S. (2020) · Cancer Letters · doi:10.1016/j.canlet.2020.05.020 · Cited by 59
Clonal replacement and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy
Caswell-Jin, J. L., McNamara, K. L., Reiter, J. G., Sun, R., Hu, Z., Ma, Z., Ding, J., Suarez, C. J., Tilk, S., Raghavendra, A. S., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08593-4 · Cited by 59
Self-citationO'Kane, G. M., Connor, A. A., & Gallinger, S. (2017) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2017.10.007 · Cited by 61
Lee, J. Y., Schizas, M., Geyer, F. C., Selenica, P., Piscuoglio, S., Sakr, R. A., Ng, C. K. Y., Carniello, J. V. S., Towers, R., Giri, D. D., et al. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-1103 · Cited by 60
Self-citationLoibl, S., Treue, D., Budczies, J., Weber, K. E., Stenzinger, A., Schmitt, W., Weichert, W., Jank, P., Furlanetto, J., Klauschen, F., et al. (2019) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-3258 · Cited by 59
Shi, M., Meng, X., Fontugne, J., Chen, C.-L., Radvanyi, F., & Bernard‐Pierrot, I. (2020) · Genome Medicine · doi:10.1186/s13073-020-00781-y · Cited by 57
When breaks get hot: inflammatory signaling in BRCA1/2-mutant cancers
van Vugt, M. A. T. M., & Parkes, E. E. (2022) · Trends in cancer · doi:10.1016/j.trecan.2021.12.003 · Cited by 59
Menghi, F., Banda, K., Kumar, P., Straub, R., Dobrolecki, L. E., Rodriguez, I. V., Yost, S. E., Chandok, H., Radke, M. R., Zhu, A. S., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abn1926 · Cited by 58
Mitotic DNA synthesis is caused by transcription-replication conflicts in BRCA2-deficient cells
Groelly, F. J., Dagg, R. A., Petropoulos, M., Rossetti, G. G., Prasad, B., Παναγόπουλος, Α., Paulsen, T., Karamichali, A., Jones, S. E., Ochs, F., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.07.011 · Cited by 58
Homologous Recombination and Replication Fork Protection: BRCA2 and More!Preprint
Feng, W., & Jasin, M. (2017) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2017.82.035006 · Cited by 66
Adjuvant trastuzumab: a 10-year overview of its benefit
Lambertini, M., Ponde, N. F., Solinas, C., & de Azambuja, E. (2016) · Expert Review of Anticancer Therapy · doi:10.1080/14737140.2017.1264876 · Cited by 60
Cha, S., Lee, E., & Won, H. (2021) · npj Breast Cancer · doi:10.1038/s41523-021-00303-y · Cited by 56
The Application of Genome-Wide 5-Hydroxymethylcytosine Studies in Cancer Research
Thomson, J. P., & Meehan, R. R. (2016) · Epigenomics · doi:10.2217/epi-2016-0122 · Cited by 60
Pellacani, D., Tan, S., Lefort, S., & Eaves, C. J. (2019) · The EMBO Journal · doi:10.15252/embj.2018100330 · Cited by 55
Takaku, M., Grimm, S. A., Kumar, B. D., Bennett, B. D., & Wade, P. A. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa179 · Cited by 58
Molecular analyses of triple-negative breast cancer in the young and elderly
Aine, M., Boyacı, C., Hartman, J., Häkkinen, J., Mitra, S., Campos, A. B., Niméus, E., Ehinger, A., Vallon‐Christersson, J., Borg, Å., et al. (2021) · Breast Cancer Research · doi:10.1186/s13058-021-01392-0 · Cited by 59
Self-citationGłodzik, D., Purdie, C., Rye, I. H., Simpson, P. T., Staaf, J., Span, P. N., Russnes, H. G., & Nik-Zainal, S. (2018) · Annals of Oncology · doi:10.1093/annonc/mdy404 · Cited by 45
Self-citationThe NFIB‐ERO1A axis promotes breast cancer metastatic colonization of disseminated tumour cells
Zilli, F., Ramos, P. M., der Maur, P. A., Jehanno, C., Sethi, A., Coissieux, M., Eichlisberger, T., Sauteur, L., Rouchon, A., Bonapace, L., et al. (2021) · EMBO Molecular Medicine · doi:10.15252/emmm.202013162 · Cited by 57
MDICC: novel method for multi-omics data integration and cancer subtype identification
Yang, Y., Tian, S., Qiu, Y., Zhao, P., & Zou, Q. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac132 · Cited by 57
Li, X., Wang, Y., Deng, S., Zhu, G., Wang, C., Johnson, N. A., Zhang, Z., Tirado, C. R., Xu, Y., Metang, L. A., et al. (2023) · Cancer Cell · doi:10.1016/j.ccell.2023.06.010 · Cited by 61
Mair, B., Konopka, T., Kerzendorfer, C., Sleiman, K., Šalic, Š., Serra, V., Muellner, M. K., Theodorou, V., & Nijman, S. M. B. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006279 · Cited by 59
Proteomics and phosphoproteomics in precision medicine: applications and challenges
Giudice, G., & Petsalaki, E. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx141 · Cited by 56
The challenges of modeling hormone receptor-positive breast cancer in mice
Özdemir, B. C., Sflomos, G., & Brisken, C. (2018) · Endocrine Related Cancer · doi:10.1530/erc-18-0063 · Cited by 57
Yellapantula, V. D., Hultcrantz, M. L., Rustad, E. H., Wasserman, E., Londono, D., Cimera, R., Ciardiello, A. K., Landau, H. J., Akhlaghi, T., Mailankody, S., et al. (2019) · Blood Cancer Journal · doi:10.1038/s41408-019-0264-y · Cited by 57
‘Omics Approaches to Explore the Breast Cancer Landscape
Parsons, J., & Francavilla, C. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2019.00395 · Cited by 58
Optical mapping reveals a higher level of genomic architecture of chained fusions in cancerPreprint
Chan, E. K. F., Cameron, D., Petersen, D. C., Lyons, R. J., Baldi, B. F., Papenfuss, A. T., Thomas, D. M., & Hayes, V. M. (2018) · Genome Research · doi:10.1101/gr.227975.117 · Cited by 57
Targeting Loss of Heterozygosity: A Novel Paradigm for Cancer Therapy
Zhang, X., & Sjöblom, T. (2021) · Pharmaceuticals · doi:10.3390/ph14010057 · Cited by 58
Koedoot, E., van Steijn, E., Vermeer, M., González‐Prieto, R., Vertegaal, A. C. O., Martens, J. W. M., Dévédec, S. E. L., & van de Water, B. (2021) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-021-01863-4 · Cited by 56
Self-citationProgesterone activates GPR126 to promote breast cancer development via the Gi pathway
An, W., Lin, H., Ma, L., Zhang, C., Zheng, Y., Cheng, Q., Ma, C., Wu, X. Y., Zhang, Z., Zhong, Y.-N., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2117004119 · Cited by 56
Non-coding genetic variation in cancer
Cuykendall, T. N., Rubin, M. A., & Khurana, E. (2017) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2016.12.017 · Cited by 55
Homologous recombination DNA repair defects in PALB2-associated breast cancers
Li, A., Geyer, F. C., Blecua, P., Lee, J. Y., Selenica, P., Brown, D. N., Pareja, F. G., Lee, S., Kumar, R., Rivera, B., et al. (2019) · npj Breast Cancer · doi:10.1038/s41523-019-0115-9 · Cited by 56
Self-citationNext-Generation Sequencing for Clinical Management of Multiple Myeloma: Ready for Prime Time?
Bolli, N., Genuardi, E., Ziccheddu, B., Martello, M., Oliva, S., & Terragna, C. (2020) · Frontiers in Oncology · doi:10.3389/fonc.2020.00189 · Cited by 57
The whole-genome panorama of cancer driversPreprint
Sabarinathan, R., Pich, O., Martincorena, I., Rubio-Pérez, C., Juul, M., Wala, J. A., Schumacher, S. E., Shapira, O., Sidiropoulos, N., Waszak, S. M., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/190330 · Cited by 55
Self-citationA recurrent novel MGA–NUTM1 fusion identifies a new subtype of high-grade spindle cell sarcomaPreprint
Diolaiti, D., Cruz, F. S. D., Gundem, G., Bouvier, N., Boulad, M., Zhang, Y., Chou, A. J., Dunkel, I. J., Sanghvi, R., Shah, M. J., et al. (2018) · Molecular Case Studies · doi:10.1101/mcs.a003194 · Cited by 57
Creaney, J., Patch, A., Addala, V., Sneddon, S., Nones, K., Dick, I. M., Lee, G., Newell, F., Rouse, E. J., Naeini, M. M., et al. (2022) · Genome Medicine · doi:10.1186/s13073-022-01060-8 · Cited by 57
RAD51 protects human cells from transcription-replication conflicts
Bhowmick, R., Lerdrup, M., Gadi, S. A., Rossetti, G. G., Singh, M. I., Liu, Y., Halazonetis, T. D., & Hickson, I. D. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.07.010 · Cited by 58
Decoding the interplay between genetic and non-genetic drivers of metastasis
Karras, P., Black, J. R., McGranahan, N., & Marine, J. (2024) · Nature · doi:10.1038/s41586-024-07302-6 · Cited by 60
Cyclin E Deregulation and Genomic Instability
Teixeira, L. K., & Reed, S. I. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-981-10-6955-0_22 · Cited by 55
Pathway-Based Drug-Repurposing Schemes in Cancer: The Role of Translational Bioinformatics
Lemus, E. H., & Martínez-García, M. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2020.605680 · Cited by 57
Abbasi, A., & Alexandrov, L. B. (2021) · DNA repair · doi:10.1016/j.dnarep.2021.103200 · Cited by 59
Self-citationPostpartum breast cancer has a distinct molecular profile that predicts poor outcomes
Jindal, S., Pennock, N. D., Sun, D., Horton, W. R., Ozaki, M. K., Narasimhan, J., Bartlett, A. Q., Weinmann, S. A., Goss, P. E., Borges, V. F., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26505-3 · Cited by 55
Sidali, A., Teotia, V., Solaiman, N. S., Bashir, N., Kanagaraj, R., Murphy, J. J., & Surendranath, K. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms23010096 · Cited by 53
Accurate and sensitive mutational signature analysis with MuSiCal
Jin, H., Gulhan, D., Geiger, B., Ben-Isvy, D., Geng, D., Ljungström, V., & Park, P. J. (2024) · Nature Genetics · doi:10.1038/s41588-024-01659-0 · Cited by 54
Deonovic, B., Wang, Y., Weirather, J. L., Wang, X., & Au, K. F. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1076 · Cited by 56
Zagorac, I., Fernandez-Gaitero, S., Penning, R., Post, H., Bueno, M. J., Mouron, S. A., Manso, L., Morente, M. M., Alonso, S. R., Serra, V., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05742-z · Cited by 59
Dorssers, L. C. J., Gillis, A., Stoop, H., van Marion, R., Nieboer, M. M., van Riet, J., van de Werken, H. J. G., Oosterhuis, J. W., de Ridder, J., & Looijenga, L. H. J. (2019) · British Journal of Cancer · doi:10.1038/s41416-019-0381-1 · Cited by 52
The INPP4B Tumor Suppressor Modulates EGFR Trafficking and Promotes Triple-Negative Breast Cancer
Liu, H., Paddock, M. N., Wang, H., Murphy, C. J., Geck, R. C., Navarro, A. J., Wulf, G. M., Elemento, O., Haucke, V., Cantley, L. C., et al. (2020) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-1262 · Cited by 56
Fumagalli, C., Ranghiero, A., Gandini, S., Corso, F., Taormina, S. V., Camilli, E. D., Rappa, A., Vacirca, D., Viale, G., Guerini‐Rocco, E., et al. (2020) · Breast Cancer Research · doi:10.1186/s13058-020-01345-z · Cited by 57
Keenan, T. E., Li, T., Vallius, T., Guerriero, J. L., Tayob, N., Kochupurakkal, B. S., Davis, J. A., Pastorello, R., Tahara, R. K., Anderson, L., et al. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-3089 · Cited by 57
The PARTNER trial of neoadjuvant olaparib with chemotherapy in triple-negative breast cancer
Abraham, J. E., Pinilla, K., Dayimu, A., Grybowicz, L., Demiris, N., Harvey, C., Drewett, L. M., Lucey, R., Fulton, A., Roberts, A. N., et al. (2024) · Nature · doi:10.1038/s41586-024-07384-2 · Cited by 53
Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations
Li, S., Shuch, B. M., & Gerstein, M. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006685 · Cited by 53
Tumor-Infiltrating CD8 T Cells Predict Clinical Breast Cancer Outcomes in Young Women
Jin, Y. W., & Hu, P. (2020) · Cancers · doi:10.3390/cancers12051076 · Cited by 52
PARP Inhibitors in Pancreatic Cancer
Brown, T. J., & Reiss, K. A. (2021) · The Cancer Journal · doi:10.1097/ppo.0000000000000554 · Cited by 55
Beyond genetics: Exploring the role of epigenetic alterations in breast cancer
Prabhu, K. S., Sadida, H. Q., Kuttikrishnan, S., Junejo, K., Bhat, A. A., & Shahab Uddin, M. S. (2024) · Pathology - Research and Practice · doi:10.1016/j.prp.2024.155174 · Cited by 54
TEX264 drives selective autophagy of DNA lesions to promote DNA repair and cell survival
Lascaux, P., Hoslett, G., Tribble, S., Trugenberger, C., Antičević, I., Otten, C., Torrecilla, I., Koukouravas, S., Zhao, Y., Yang, H., et al. (2024) · Cell · doi:10.1016/j.cell.2024.08.020 · Cited by 59
Kim, J., Jung, H. H., Ahn, S., Bae, S., Lee, S. K., Kim, S. W., Lee, J. E., Nam, S. J., Ahn, J. S., Im, Y., et al. (2016) · Scientific Reports · doi:10.1038/srep31804 · Cited by 54
Self-citationParkin, A., Man, J., Timpson, P., & Pajic, M. (2019) · FEBS Journal · doi:10.1111/febs.15011 · Cited by 54
Mutational processes contributing to the development of multiple myeloma
Hoang, P. H., Cornish, A. J., Dobbins, S. E., Kaiser, M., & Houlston, R. S. (2019) · Blood Cancer Journal · doi:10.1038/s41408-019-0221-9 · Cited by 54
Lee, K.-H., Hwang, H., Noh, H. J., Shin, T.-J., & Cho, J. (2019) · Cancers · doi:10.3390/cancers11122006 · Cited by 52
Savage, P., Pacis, A., Kuasne, H., Liu, L., Lai, D., Wan, A., Dankner, M., Martínez, C., Muñoz-Ramos, V., Pilon, V., et al. (2020) · Communications Biology · doi:10.1038/s42003-020-1042-x · Cited by 54
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
Bailey, M. H., Meyerson, W. U., Dursi, L. J., Wang, L.-B., Dong, G., Liang, W.-W., Weerasinghe, A., Li, S., Li, Y., Kelso, S., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18151-y · Cited by 53
Self-citation
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
About these checks
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
