The DOI matches its Crossref record; 24 of the 24 references it cites were found in a registry or an index.
The clonal and mutational evolution spectrum of primary triple-negative breast cancers
Open accessAbstract
Primary triple-negative breast cancers (TNBCs), a tumour type defined by lack of oestrogen receptor, progesterone receptor and ERBB2 gene amplification, represent approximately 16% of all breast cancers. Here we show in 104 TNBC cases that at the time of diagnosis these cancers exhibit a wide and continuous spectrum of genomic evolution, with some having only a handful of coding somatic aberrations in a few pathways, whereas others contain hundreds of coding somatic mutations. High-throughput RNA sequencing (RNA-seq) revealed that only approximately 36% of mutations are expressed. Using deep re-sequencing measurements of allelic abundance for 2,414 somatic mutations, we determine for the first time-to our knowledge-in an epithelial tumour subtype, the relative abundance of clonal frequencies among cases representative of the population. We show that TNBCs vary widely in their clonal frequencies at the time of diagnosis, with the basal subtype of TNBC showing more variation than non-basal TNBC. Although p53 (also known as TP53), PIK3CA and PTEN somatic mutations seem to be clonally dominant compared to other genes, in some tumours their clonal frequencies are incompatible with founder status. Mutations in cytoskeletal, cell shape and motility proteins occurred at lower clonal frequencies, suggesting that they occurred later during tumour progression. Taken together, our results show that understanding the biology and therapeutic responses of patients with TNBC will require the determination of individual tumour clonal genotypes.
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?
In the citing paper
“It is estimated that p53 is mutated in approximately 50% of all cancers with 60% of TNBCs bearing mutations in p53 (14, 15);”
From Potentiation of carboplatin-mediated DNA damage by the Mdm2 modulator Nutlin-3a in a humanized orthotopic breast-to-lung metastatic model (2015) · cites this paper as [15]
In the citing paper
“It is estimated that p53 is mutated in approximately 50% of all cancers with 60% of TNBCs bearing mutations in p53 (14, 15);”
From Potentiation of carboplatin-mediated DNA damage by the Mdm2 modulator Nutlin-3a in a humanized orthotopic breast-to-lung metastatic model (2015) · cites this paper as [15]
In the citing paper
“Approximately 60% of basal TNBCs bear mutations in p53 (15) and ~90% of mutations in p53 occur in the DNA binding domain.”
From Potentiation of carboplatin-mediated DNA damage by the Mdm2 modulator Nutlin-3a in a humanized orthotopic breast-to-lung metastatic model (2015) · cites this paper as [15]
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
Molecular portraits of human breast tumours
Perou, C., Sørlie, T., Eisen, M., van de Rijn, M., Jeffrey, S., Rees, C. A., Pollack, J., Ross, D., Johnsen, H., Akslen, L., et al. (2000) · Nature · doi:10.1038/35021093 · Cited by 16,551
Sørlie, T., Perou, C. M., Tibshirani, R. J., Aas, T., Geisler, S. B., Johnsen, H., Hastie, T. J., Eisen, M. B., van de Rijn, M., Jeffrey, S. S., et al. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.191367098 · Cited by 11,506
Integrated genomic analyses of ovarian carcinoma
Perou, C. M. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/hvp3-wg08 · Cited by 7,927
The 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-citationSupervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes
Parker, J. S., Mullins, M., Cheang, M. C. U., Leung, S. C. Y., Voduc, D. K., Vickery, T. L., Davies, S. R., Fauron, C. M. ‐., He, X., Hu, Z., et al. (2009) · Journal of Clinical Oncology · doi:10.1200/jco.2008.18.1370 · Cited by 4,818
Somatic mutations affect key pathways in lung adenocarcinoma
Ding, L., Getz, G., Wheeler, D. A., Mardis, E. R., McLellan, M. D., Cibulskis, K., Sougnez, C., Greulich, H., Muzny, D. M., Morgan, M. B., et al. (2008) · Nature · doi:10.1038/nature07423 · Cited by 2,681
The Mutational Landscape of Head and Neck Squamous Cell Carcinoma
Stransky, N., Egloff, A. M., Tward, A. D., Kostic, A. D., Cibulskis, K., Sivachenko, A., Kryukov, G. V., Lawrence, M. S., Sougnez, C. L., McKenna, A., et al. (2011) · Science · doi:10.1126/science.1208130 · Cited by 2,541
Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1
Agrawal, N., Frederick, M. J., Pickering, C. R., Bettegowda, C., Chang, K., Li, R. J., Fakhry, C., Xie, T., Zhang, J., Wang, J., et al. (2011) · Science · doi:10.1126/science.1206923 · Cited by 1,697
Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma
Morin, R. D., Mendez-Lago, M., Mungall, A. J., Goya, R., Mungall, K. L., Corbett, R. D., Johnson, N. A., Severson, T. M., Chiu, R., Field, M., et al. (2011) · Nature · doi:10.1038/nature10351 · Cited by 1,614
Self-citationGenome remodelling in a basal-like breast cancer metastasis and xenograft
Ding, L., Ellis, M. J., Li, S., Larson, D. E., Chen, K., Wallis, J. W., Harris, C. C., McLellan, M. D., Fulton, R. S., Fulton, L., et al. (2010) · Nature · doi:10.1038/nature08989 · Cited by 1,144
Flagged first, then by citations
Cited by
Sorted by citations
Items 401–500 of 1,003
Ghosh, S., Javia, A., Shetty, S. R., Bardoliwala, D., Maiti, K., Banerjee, S., Khopade, A. J., Misra, A. R., Sawant, K. K., & Bhowmick, S. (2021) · Journal of Controlled Release · doi:10.1016/j.jconrel.2021.07.014 · Cited by 95
Montero, J. C., Esparı́s-Ogando, A., Re-Louhau, M. F., Seoane, S., Abad, M., Calero, R., Ocaña, A., & Pandiella, A. (2012) · Oncogene · doi:10.1038/onc.2012.572 · Cited by 93
Breast Cancer Genomics From Microarrays to Massively Parallel Sequencing: Paradigms and New Insights
Ng, C. K. Y., Schultheis, A. M., Bidard, F., Weigelt, B., & Reis-Filho, J. S. (2015) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djv015 · Cited by 96
Age influences on the molecular presentation of tumours
Li, C. H., Haider, S. A., & Boutros, P. C. (2022) · Nature Communications · doi:10.1038/s41467-021-27889-y · Cited by 98
Genomic Determinants of PI3K Pathway Inhibitor Response in Cancer
Weigelt, B., & Downward, J. (2012) · Frontiers in Oncology · doi:10.3389/fonc.2012.00109 · Cited by 94
Avery‐Kiejda, K. A., Braye, S. G., Mathe, A., Forbes, J., & Scott, R. J. (2014) · BMC Cancer · doi:10.1186/1471-2407-14-51 · Cited by 91
Baenke, F., Dubuis, S., Brault, C., Weigelt, B., Dankworth, B., Griffiths, B. L., Jiang, M., Mackay, A. G., Saunders, B., Spencer‐Dene, B., et al. (2015) · The Journal of Pathology · doi:10.1002/path.4562 · Cited by 93
Robinson, T., Liu, J. C., Vizeacoumar, F. S., Sun, T., MacLean, N., Egan, S. E., Schimmer, A. D., Datti, A., & Zacksenhaus, E. (2013) · PLoS ONE · doi:10.1371/journal.pone.0078641 · Cited by 95
Transcriptome Analysis of Wnt3a-Treated Triple-Negative Breast Cancer Cells
Maubant, S., Tesson, B. M., Maire, V., Ye, M., Rigaill, G. J., Gentien, D., Cruzalegui, F. H., Tucker, G. C., Roman‐Roman, S., & Dubois, T. (2015) · PLoS ONE · doi:10.1371/journal.pone.0122333 · Cited by 85
Liu, C., Srihari, S., Cao, K. L., Chenevix‐Trench, G., Simpson, P. T., Ragan, M. A., & Khanna, K. K. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku284 · Cited by 91
Personalized medicine in breast cancer: pharmacogenomics approaches
Jeibouei, S., Akbari, M. E., Kalbasi, A., Aref, A. R., Ajoudanian, M., Rezvani, A., & Zali, H. (2019) · Pharmacogenomics and Personalized Medicine · doi:10.2147/pgpm.s167886 · Cited by 108
Genetic and Non-Genetic Mechanisms Underlying Cancer Evolution
Shlyakhtina, Y., Moran, K. L., & Portal, M. M. (2021) · Cancers · doi:10.3390/cancers13061380 · Cited by 91
Parallel evolution of tumour subclones mimics diversity between tumours
Martinez, P., Birkbak, N. J., Gerlinger, M., McGranahan, N., Burrell, R. A., Rowan, A., Joshi, T., Fisher, R. A., Larkin, J., Szállási, Z., et al. (2013) · The Journal of Pathology · doi:10.1002/path.4214 · Cited by 88
The AURORA initiative for metastatic breast cancer
Zardavas, D., Maetens, M., Irrthum, A., Goulioti, T., Engelen, K., Fumagalli, D., Salgado, R., Aftimos, P. G., Saini, K. S., Sotiriou, C. P., et al. (2014) · British Journal of Cancer · doi:10.1038/bjc.2014.341 · Cited by 88
Patterns of Genomic Instability in Breast Cancer
Kalimutho, M., Nones, K., Srihari, S., Duijf, P. H. G., Waddell, N., & Khanna, K. K. (2019) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2019.01.005 · Cited by 87
Expression and clinical significance of MAPK and EGFR in triple‑negative breast cancer
Jiang, W., Wang, X., Zhang, C., Xue, L., & Yang, L. (2020) · Oncology Letters · doi:10.3892/ol.2020.11274 · Cited by 88
Ferrari‐Amorotti, G., Chiodoni, C., Shen, F., Cattelani, S., Soliera, A. R., Manzotti, G., Grisendi, G., Dominici, M., Rivasi, F., Colombo, M. P., et al. (2014) · Neoplasia · doi:10.1016/j.neo.2014.10.006 · Cited by 88
Boisserie-Lacroix, M., MacGrogan, G. M., Debled, M., Ferron, S., Asad-Syed, M., McKelvie‐Sebileau, P., Mathoulin‐Pélissier, S., Brouste, V., & Hurtevent-Labrot, G. (2013) · The Oncologist · doi:10.1634/theoncologist.2013-0380 · Cited by 88
Krings, G., Joseph, N. M., Bean, G. R., Solomon, D. A., Onodera, C. S., Talevich, E., Yeh, I., Grenert, J. P., Hosfield, E. M., Crawford, E. D., et al. (2017) · Modern Pathology · doi:10.1038/modpathol.2017.32 · Cited by 88
Tang, Q., Moore, J. C., Ignatius, M. S., Tenente, I. M., Hayes, M. N., Garcia, E. G., Yordán, N. T., Bourque, C., He, S., Blackburn, J. S., et al. (2016) · Nature Communications · doi:10.1038/ncomms10358 · Cited by 91
Wang, Z., Chen, Z., Jiang, G., Wu, Y., Liu, T., Yi, Y., Zeng, J., Du, J., & Wang, H. (2016) · Cellular Signalling · doi:10.1016/j.cellsig.2016.02.006 · Cited by 87
Willard, S. S., & Koochekpour, S. (2013) · International Journal of Biological Sciences · doi:10.7150/ijbs.6475 · Cited by 86
Intratumor heterogeneity predicts metastasis of triple-negative breast cancer
Yang, F., Wang, Y., Li, Q., Cao, L., Sun, Z., Jin, J., Fang, H., Zhu, A., Li, Y., Zhang, W., et al. (2017) · Carcinogenesis · doi:10.1093/carcin/bgx071 · Cited by 86
The emerging roles of CDK12 in tumorigenesis
Paculová, H., & Kohoutek, J. (2017) · Cell Division · doi:10.1186/s13008-017-0033-x · Cited by 89
Nuclear TAZ expression associates with the triple-negative phenotype in breast cancer
Díaz‐Martín, J., López‐García, M. Á., Romero‐Pérez, L., Atienza-Amores, M. R., Pecero, M. L., Castilla, M. Á., Biscuola, M., Santón, A., & Palacios, J. (2015) · Endocrine Related Cancer · doi:10.1530/erc-14-0456 · Cited by 86
Epigenetic Alterations in Triple-Negative Breast Cancer—The Critical Role of Extracellular Matrix
Zolota, V., Tzelepi, V., Piperigkou, Z., Kourea, H. P., Papakonstantinou, Ε., Argentou, M., & Karamanos, N. K. (2021) · Cancers · doi:10.3390/cancers13040713 · Cited by 85
The challenge of intratumour heterogeneity in precision medicine
Seoane, J., & Mattos‐Arruda, L. D. (2014) · Journal of Internal Medicine · doi:10.1111/joim.12240 · Cited by 85
Knutson, T. P., Truong, T. H., Ma, S., Brady, N. J., Sullivan, M. E., Raj, G. V., Schwertfeger, K. L., & Lange, C. A. (2017) · Journal of Hematology & Oncology · doi:10.1186/s13045-017-0462-7 · Cited by 86
A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression
Liu, Y., Gu, Q., Hou, J. P., Han, J., & Ma, J. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-37 · Cited by 84
Genome evolution in ductal carcinoma in situ: invasion of the clones
Casasent, T. D., Edgerton, M. E., & Navin, N. E. (2016) · The Journal of Pathology · doi:10.1002/path.4840 · Cited by 84
Practical Approach to Triple-Negative Breast Cancer
Gadi, V. K., & Davidson, N. E. (2017) · Journal of Oncology Practice · doi:10.1200/jop.2017.022632 · Cited by 82
Breast Cancer Neoantigens Can Induce CD8+ T-Cell Responses and Antitumor Immunity
Zhang, X., Kim, S., Hundal, J., Herndon, J. M., Li, S., Petti, A. A., Soysal, S. D., Li, L., McLellan, M. D., Hoog, J., et al. (2017) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-16-0264 · Cited by 86
Marotti, J. D., Abreu, F. B. D., Wells, W. A., & Tsongalis, G. J. (2017) · American Journal Of Pathology · doi:10.1016/j.ajpath.2017.05.018 · Cited by 88
Mitochondrial quality control: The role of mitophagy in aging
Shi, R., Guberman, M., & Kirshenbaum, L. A. (2017) · Trends in Cardiovascular Medicine · doi:10.1016/j.tcm.2017.11.008 · Cited by 87
HER2 missense mutations have distinct effects on oncogenic signaling and migration
Zabransky, D. J., Yankaskas, C. L., Cochran, R. L., Wong, H. Y., Croessmann, S., Chu, D. T. W., Kavuri, S. M., Brewer, M. R., Rosen, D. M., Dalton, W. B., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1516853112 · Cited by 83
The Dual Roles of the Atypical Protein Kinase Cs in Cancer
Reina‐Campos, M., Díaz-Meco, M. T., & Moscat, J. (2019) · Cancer Cell · doi:10.1016/j.ccell.2019.07.010 · Cited by 86
Kim, S. Y., Jung, S., Kim, M. S., Baek, I.-P., Lee, S. H., Kim, T., Chung, Y., & Lee, S. H. (2015) · Oncotarget · doi:10.18632/oncotarget.3162 · Cited by 81
Fusco, N., Geyer, F. C., Filippo, M. R. D., Martelotto, L. G., Ng, C. K. Y., Piscuoglio, S., Guerini‐Rocco, E., Schultheis, A. M., Fuhrmann, L., Wang, L., et al. (2016) · Modern Pathology · doi:10.1038/modpathol.2016.134 · Cited by 85
Nesprins in health and disease
Cartwright, S., & Karakesisoglou, I. (2013) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2013.12.010 · Cited by 79
A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data
Li, B., & Li, J. Z. (2014) · Genome biology · doi:10.1186/s13059-014-0473-4 · Cited by 76
Vitali, F., Cohen, L. D., Demartini, A., Amato, A. M., Eterno, V., Zambelli, A., & Bellazzi, R. (2016) · PLoS ONE · doi:10.1371/journal.pone.0162407 · Cited by 81
COTI-2 reactivates mutant p53 and inhibits growth of triple-negative breast cancer cells
Synnott, N. C., O’Connell, D. J., Crown, J. P., & Duffy, M. J. (2019) · Breast Cancer Research and Treatment · doi:10.1007/s10549-019-05435-1 · Cited by 82
A novel min-cost flow method for estimating transcript expression with RNA-Seq
Tomescu, A. I., Kuosmanen, A., Rizzi, R., & Mäkinen, V. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-s5-s15 · Cited by 82
Tumor Sequencing and Patient-Derived Xenografts in the Neoadjuvant Treatment of Breast Cancer
Goetz, M. P., Kalari, K. R., Suman, V. J., Moyer, A. M., Yu, J., Visscher, D. W., Dockter, T., Vedell, P. T., Sinnwell, J. P., Tang, X., et al. (2016) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djw306 · Cited by 78
Androgen receptor function and targeted therapeutics across breast cancer subtypes
Kolyvas, E. A., Caldas, C., Kelly, K., & Ahmad, S. S. (2022) · Breast Cancer Research · doi:10.1186/s13058-022-01574-4 · Cited by 80
Self-citationGuernet, A. A., Mungamuri, S. K., Cartier, D., Sachidanandam, R., Jayaprakash, A. D., Adriouch, S., Vézain, M., Charbonnier, F., Rohkin, G., Coutant, S., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.06.017 · Cited by 85
Germline Mutations in Triple-Negative Breast Cancer
Hahnen, E., Hauke, J., Engel, C., Neidhardt, G., Rhiem, K., & Schmutzler, R. K. (2017) · Breast Care · doi:10.1159/000455999 · Cited by 79
Molecular Oncology of Breast Cancer
Joshi, H. N., & Press, M. F. (2017) · Elsevier eBooks · doi:10.1016/b978-0-323-35955-9.00022-2 · Cited by 85
The Omics of Triple-Negative Breast Cancers
Xu, H., Eirew, P. D., Mullaly, S. C., & Aparicio, S. A. J. R. (2013) · Clinical Chemistry · doi:10.1373/clinchem.2013.207167 · Cited by 80
Self-citationBreast cancer intratumour heterogeneity: current status and clinical implications
Joseph, C., Papadaki, A., Althobiti, M. M., Alsaleem, M. A., Aleskandarany, M. A., & Rakha, E. A. (2018) · Histopathology · doi:10.1111/his.13642 · Cited by 79
Li, J.-P., Zhang, X.-M., Zhang, Z., Zheng, L.-H., Jindal, S., & Liu, Y. (2019) · Medicine · doi:10.1097/md.0000000000015449 · Cited by 85
Wang, J., Zhang, C., Chen, K., Tang, H., Tang, J., Song, C., & Xie, X. (2015) · Breast Cancer Research and Treatment · doi:10.1007/s10549-015-3467-3 · Cited by 80
Estrogen receptor mutations and functional consequences for breast cancer
Thomas, C. G., & Gustafsson, J.-Α. (2015) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2015.06.007 · Cited by 77
Hirshfield, K. M., Tolkunov, D., Zhong, J., Ali, S. M., Stein, M. N., Murphy, S., Vig, H. S., Vázquez, A., Glod, J. W., Moss, R. A., et al. (2016) · The Oncologist · doi:10.1634/theoncologist.2016-0049 · Cited by 80
Clonality and Evolutionary History of Rhabdomyosarcoma
Chen, L., Shern, J. F., Wei, J. S., Yohe, M. E., Song, Y., Hurd, L., Liao, H., Catchpoole, D. R., Skapek, S. X., Barr, F. G., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005075 · Cited by 77
Bochtler, T., Stölzel, F., Heilig, C. E., Kunz, C., Mohr, B., Jauch, A. S., Janssen, J. W. G., Krämer, M., Benner, A., Bornhäuser, M., et al. (2013) · Journal of Clinical Oncology · doi:10.1200/jco.2013.50.7921 · Cited by 76
Rajput, S., Khera, N., Guo, Z., Hoog, J., Li, S., & Ma, C. X. (2016) · Oncotarget · doi:10.18632/oncotarget.10870 · Cited by 78
Alexa‐Stratulat, T., Pešić, M., Gašparović, A. Č., Trougakos, I. P., & Riganti, C. (2019) · Drug Resistance Updates · doi:10.1016/j.drup.2019.100643 · Cited by 77
Lips, E. H., Michaut, M., Hoogstraat, M., Mulder, L., Besselink, N. J. M., Koudijs, M. J., Cuppen, E. P. J. G., Voest, E. E., Bernards, R., Nederlof, P. M., et al. (2015) · Breast Cancer Research · doi:10.1186/s13058-015-0642-8 · Cited by 76
Mutations in the Kinase Domain of the HER2/ERBB2 Gene Identified in a Wide Variety of Human Cancers
Wen, W., Chen, W., Xiao, N., Bender, R. P., Ghazalpour, A., Tan, Z., Swensen, J. J., Millis, S. Z., Basu, G. D., Gatalica, Z., et al. (2015) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2015.04.003 · Cited by 76
The genetic landscape of breast carcinomas with neuroendocrine differentiation
Marchiò, C., Geyer, F. C., Ng, C. K. Y., Piscuoglio, S., Filippo, M. R. D., Cupo, M., Schultheis, A. M., Lim, R. S., Burke, K. A., Guerini‐Rocco, E., et al. (2016) · The Journal of Pathology · doi:10.1002/path.4837 · Cited by 78
p53 Maintains Baseline Expression of Multiple Tumor Suppressor Genes
Pappas, K., Xu, J., Zairis, S., Resnick‐Silverman, L., Abate, F., Steinbach, N., Ozturk, S., Saal, L. H., Su, T., Cheung, P., et al. (2017) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-17-0089 · Cited by 77
Goswami, R. S., Patel, K. P., Singh, R. R., Meric‐Bernstam, F., Kopetz, S., Subbiah, V., Álvarez, R. H., Davies, M. A., Jabbar, K. J., Roy‐Chowdhuri, S., et al. (2015) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-14-2391 · Cited by 75
Miragaya, J. G., Palafox, M., Paré, L., Yoldi, G., Ferrer, I., Vila, S., Galván, P., Pellegrini, P., Perez‐Montoyo, H., Igea, A., et al. (2017) · Stem Cell Reports · doi:10.1016/j.stemcr.2017.03.026 · Cited by 79
Barrett, M. T., Lenkiewicz, E., Malasi, S., Basu, A., Yearley, J. H., Annamalai, L., McCullough, A. E., Kosiorek, H., Narang, P., Sayres, M. A. W., et al. (2018) · Breast Cancer Research · doi:10.1186/s13058-018-1004-0 · Cited by 77
Liu, H., Murphy, C. J., Karreth, F. A., Emdal, K. B., White, F. M., Elemento, O., Toker, A., Wulf, G. M., & Cantley, L. C. (2017) · Cancer Discovery · doi:10.1158/2159-8290.cd-17-0679 · Cited by 73
Breast cancer classification: linking molecular mechanisms to disease prognosis
Fard, A. T., Srihari, S., & Ragan, M. A. (2014) · Briefings in Bioinformatics · doi:10.1093/bib/bbu020 · Cited by 75
Death-associated protein kinase 1 promotes growth of p53-mutant cancers
Zhao, J., Zhao, D., Poage, G. M., Mazumdar, A., Zhang, Y., Hill, J. L., Hartman, Z. C., Savage, M. I., Mills, G. B., & Brown, P. H. (2015) · Journal of Clinical Investigation · doi:10.1172/jci70805 · Cited by 74
The mutational landscape of the SCAN‐B real‐world primary breast cancer transcriptome
Brueffer, C., Gladchuk, S., Winter, C., Vallon‐Christersson, J., Hegardt, C., Häkkinen, J., George, A. M., Chen, Y., Ehinger, A., Larsson, C., et al. (2020) · EMBO Molecular Medicine · doi:10.15252/emmm.202012118 · Cited by 72
Clinical utility of whole-genome sequencing in precision oncology
Rosenquist, R., Cuppen, E. P. J. G., Buettner, R., Caldas, C., Dreau, H. M.-P., Elemento, O., Frederix, G., Grimmond, S. M., Haferlach, T., Jobanputra, V., et al. (2021) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2021.06.018 · Cited by 73
Self-citationMapping Phenotypic Plasticity upon the Cancer Cell State Landscape Using Manifold Learning
Burkhardt, D. B., Juan, B. P. S., Lock, J. G., Krishnaswamy, S., & Chaffer, C. L. (2022) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-0282 · Cited by 74
Huang, P., Zhou, X., Zheng, M., Yu, Y., Jin, G., & Zhang, S. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1263537 · Cited by 74
GATA3 mutations define a unique subtype of luminal‐like breast cancer with improved survival
Jiang, Y., Yu, K., Zuo, W., Peng, W., & Shao, Z. (2014) · Cancer · doi:10.1002/cncr.28566 · Cited by 74
Breast cancer intratumor genetic heterogeneity: causes and implications
Ng, C. K. Y., Pemberton, H. N., & Reis-Filho, J. S. (2012) · Expert Review of Anticancer Therapy · doi:10.1586/era.12.85 · Cited by 77
Kummar, S., Wade, J. L., Oza, A. M., Sullivan, D. M., Chen, A. P., Gandara, D. R., Ji, J. J., Kinders, R. J., Wang, L., Allen, D. E., et al. (2016) · Investigational New Drugs · doi:10.1007/s10637-016-0335-x · Cited by 74
Co-targeting EGFR and mTOR with gefitinib and everolimus in triple-negative breast cancer cells
Guerrab, A. E., Bamdad, M., Bignon, Y., Penault-Llorca, F. M., & Aubel, C. (2020) · Scientific Reports · doi:10.1038/s41598-020-63310-2 · Cited by 75
Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing
Demeulemeester, J., Kumar, P., Møller, E. K., Nord, S., Wedge, D. C., Peterson, A., Mathiesen, R. R., Fjelldal, R., Esteki, M. Z., Theunis, K., et al. (2016) · Genome biology · doi:10.1016/s0959-8049(16)61063-8 · Cited by 77
Rajendran, B. K., & Deng, C.-X. (2017) · Oncotarget · doi:10.18632/oncotarget.17225 · Cited by 73
The current landscape of the antimicrobial peptide melittin and its therapeutic potential
Zhang, H.-Q., Sun, C., Xu, N., & Liu, W. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1326033 · Cited by 73
Somatic Cell Fusions Reveal Extensive Heterogeneity in Basal-like Breast Cancer
Su, Y., Subedee, A., Bloushtain-Qimron, N., Savova, V., Krzystanek, M., Li, L., Marusyk, A., Tabassum, D. P., Zak, A., Flacker, M. J., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.05.011 · Cited by 72
Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations
Yang, F., Petsalaki, E., Rolland, T., HILL, D. E., Vidal, M., & Roth, F. P. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004147 · Cited by 71
A Targetable EGFR-Dependent Tumor-Initiating Program in Breast Cancer
Savage, P., Blanchet-Cohen, A., Revil, T., Badescu, D., Saleh, S. M. I., Wang, Y.-C., Zuo, D., Liu, L., Bertos, N., Muñoz-Ramos, V., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.10.015 · Cited by 74
Cell Fusion Connects Oncogenesis with Tumor Evolution
Zhou, X., Merchak, K., Lee, W., Grande, J. P., Cascalho, M., & Platt, J. L. (2015) · American Journal Of Pathology · doi:10.1016/j.ajpath.2015.03.014 · Cited by 72
Zhang, H., Cohen, A. L., Krishnakumar, S., Wapnir, I., Veeriah, S., Deng, G. Y., Coram, M., Piskun, C. M., Longacre, T. A., Herrler, M., et al. (2014) · Breast Cancer Research · doi:10.1186/bcr3640 · Cited by 73
Targeting the duality of cancer
Arbiser, J. L., Bonner, M. Y., & Gilbert, L. C. (2017) · npj Precision Oncology · doi:10.1038/s41698-017-0026-x · Cited by 72
Colen, R. R., Foster, I. T., Gatenby, R. A., Giger, M. L., Gillies, R. J., Gutman, D. A., Heller, M. T., Jain, R., Madabhushi, A., Madhavan, S., et al. (2014) · Translational Oncology · doi:10.1016/j.tranon.2014.07.007 · Cited by 72
Mutlu, M., Saatci, Ö., Ansari, S. A., Yurdusev, E., Shehwana, H., Konu, Ö., Raza, U., & Şahin, Ö. (2016) · Scientific Reports · doi:10.1038/srep32541 · Cited by 73
nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencingPreprint
McPherson, A., Wu, C., Wyatt, A. W., Shah, S. P., Collins, C. C., & Şahinalp, S. C. (2012) · Genome Research · doi:10.1101/gr.136572.111 · Cited by 69
Self-citationAromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers
Miller, C. A., Gindin, Y., Lu, C., Griffith, O. L., Griffith, M., Shen, D., Hoog, J., Li, T., Larson, D. E., Watson, M. A., et al. (2016) · Nature Communications · doi:10.1038/ncomms12498 · Cited by 69
Self-citationUpdate on the Treatment of Early-Stage Triple-Negative Breast Cancer
Sharma, P. (2018) · Current Treatment Options in Oncology · doi:10.1007/s11864-018-0539-8 · Cited by 69
Computer-Aided Ligand Discovery for Estrogen Receptor Alpha
Bafna, D., Ban, F., Rennie, P. S., Singh, K., & Cherkasov, A. R. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21124193 · Cited by 73
Holland, J. D., Győrffy, B., Vogel, R., Eckert, K., Valenti, G., Fang, L., Lohneis, P., Elezkurtaj, S., Ziebold, U., & Birchmeier, W. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.11.001 · Cited by 74
Guerini‐Rocco, E., Hodi, Z., Piscuoglio, S., Ng, C. K. Y., Rakha, E. A., Schultheis, A. M., Marchiò, C., Paula, A. D. C., Filippo, M. R. D., Martelotto, L. G., et al. (2015) · The Journal of Pathology · doi:10.1002/path.4566 · Cited by 71
The Transcriptional Landscape of p53 Signalling Pathway
Tanikawa, C., Zhang, Y., Yamamoto, R., Tsuda, Y., Tanaka, M., Funauchi, Y., Mori, J., Imoto, S., Yamaguchi, R., Nakamura, Y., et al. (2017) · EBioMedicine · doi:10.1016/j.ebiom.2017.05.017 · Cited by 72
Synnott, N. C., Bauer, M. R., Madden, S. F., Murray, A. M., Klinger, R. W., O’Donovan, N., O’Connor, D. P., Gallagher, W. M., Crown, J. P., Fersht, A. R., et al. (2017) · Cancer Letters · doi:10.1016/j.canlet.2017.09.053 · Cited by 72
Targeting MYCN-expressing triple-negative breast cancer with BET and MEK inhibitors
Schafer, J. M., Lehmann, B. D., Ericsson, P. I. G., Marshall, C. B., Beeler, J. S., Redman, L. N., Jin, H., Sanchez, V. M., Stubbs, M. C., Scherle, P., et al. (2020) · Science Translational Medicine · doi:10.1126/scitranslmed.aaw8275 · Cited by 69
Kriegsmann, M., Endris, V., Wolf, T. A., Pfarr, N., Stenzinger, A., Loibl, S., Denkert, C., Schneeweiß, A., Budczies, J., Sinn, H., et al. (2014) · Oncotarget · doi:10.18632/oncotarget.2481 · Cited by 69
Silva, J. L., Rangel, L. P., da Costa, D. C. F., Cordeiro, Y., & Gallo, C. V. D. M. (2013) · Bioscience Reports · doi:10.1042/bsr20130065 · Cited by 72
Genetic Mutations and Epigenetic Modifications: Driving Cancer and Informing Precision Medicine
Coyle, K. M., Boudreau, J. E., & Marcato, P. (2017) · BioMed Research International · doi:10.1155/2017/9620870 · Cited by 72
Cornen, S., Guillé, A., Adélaı̈de, J., Addou-Klouche, L., Finetti, P., Saade, M.-R., Manai, M., Carbuccia, N., Bekhouche, I., Letessier, A., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0081843 · Cited by 69
Metadata
- Authors
- Shah, S. P., Roth, A., Goya, R., Oloumi, A., Ha, G., Zhao, Y., Turashvili, G., Ding, J., Tse, K., Haffari, G., Bashashati, A., Prentice, L. M., Khattra, J., Burleigh, A., Yap, D., Bernard, V., McPherson, A., Shumansky, K., Crisan, A., Giuliany, R., Heravi-Moussavi, A., Rosner, J., Lai, D., Birol, I., Varhol, R., Tam, A., Dhalla, N., Zeng, T., Ma, K., Chan, S. K., Griffith, M., Moradian, A., Cheng, S.-W. G., Morin, G. B., Watson, P., Gelmon, K., Chia, S., Chin, S.-F., Curtis, C., Rueda, O. M., Pharoah, P. D., Damaraju, S., Mackey, J., Hoon, K., Harkins, T., Tadigotla, V., Sigaroudinia, M., Gascard, P., Tlsty, T., Costello, J. F., Meyer, I. M., Eaves, C. J., Wasserman, W. W., Jones, S., Huntsman, D., Hirst, M., Caldas, C., Marra, M. A., & Aparicio, S.
- Affiliations
- University of British Columbia (CA)
- Canada's Michael Smith Genome Sciences Centre (CA)
- BC Cancer Agency (CA)
- University of Cambridge (GB)
- University of Southern California (US)
- Cancer Research UK (GB)
- University of Alberta (CA)
- University of California, San Francisco (US)
- Corresponding author
- Shah, Sohrab P.
- Caldas, Carlos
- Marra, Marco A.
- Aparicio, Samuel
- ORCID
- Shah, Sohrab P.
- Roth, Andrew
- Ha, Gavin
- Zhao, Yongjun
- Turashvili, Gulisa
- Ding, Jiarui
- Haffari, Gholamreza
- Bashashati, Ali
- Prentice, Leah M.
- Burleigh, Angela
- Yap, Damian
- McPherson, Andrew
- Crisan, Anamaria
- Rosner, Jamie
- Lai, Daniel
- Varhol, Richard
- Tam, Angela
- Griffith, Malachi
- Moradian, Annie
- Cheng, S.-W. Grace
- Morin, Gregg B.
- Watson, Peter
- Gelmon, Karen
- Chia, Stephen
- Chin, Suet-Feung
- Curtis, Christina
- Rueda, Oscar M.
- Pharoah, Paul D.
- Damaraju, Sambasivarao
- Mackey, John
- Harkins, Timothy
- Gascard, Philippe
- Tlsty, Thea
- Costello, Joseph F.
- Meyer, Irmtraud M.
- Eaves, Connie J.
- Wasserman, Wyeth W.
- Jones, Steven
- Huntsman, David
- Hirst, Martin
- Caldas, Carlos
- Marra, Marco A.
- Aparicio, Samuel
- Venue
- Nature
- Published
- 2012-04-04
- Volume
- 486
- Issue
- 7403
- Pages
- 395-399
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3863681
- OpenAlex
- W2063382533
- Cited by
- 1,967
- References
- 23
- Citations by year
- 2026: 40 · 2025: 61 · 2024: 71 · 2023: 131 · 2022: 132 · 2021: 119 · 2020: 131 · 2019: 120 · 2018: 135 · 2017: 173 · 2016: 179 · 2015: 198 · 2014: 199 · 2013: 201 · 2012: 76
- FWCI
- 71.57
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (submittedVersion)
- eSpace (Curtin University) (submittedVersion)
- Funders
- U.S. Department of Defense
- Memorial Sloan-Kettering Cancer Center
- Canada's Michael Smith Genome Sciences Centre
- Canadian Breast Cancer Research Alliance
- Michael Smith Health Research BC
- Cancer Research UK
- National Institute for Health and Care Research (NF-SI-0611-10154)
- Cure Brain Cancer Foundation
- BC Cancer Foundation
- National Institutes of Health
- Imperial Experimental Cancer Medicine Centre
- BC Cancer Agency
- National Institute of General Medical Sciences (R01GM084875)
- National Institute of Environmental Health Sciences (U01ES017154)
- Congressionally Directed Medical Research Programs
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Breast Cancer Treatment Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › BRCA gene mutations in cancer
- Keywords
- triple-negative breast cancer, clonal evolution, somatic mutations, copy number variation, cancer genomics, TP53 mutation, PIK3CA mutation, PTEN mutation, basal subtype, tumor progression, founder mutation, clonal heterogeneity
- MeSH terms
- Alleles, Breast Neoplasms, Clone Cells, DNA Mutational Analysis, Female, Genotype, Humans, Mutation, Reproducibility of Results, Gene Expression Regulation, Neoplastic, Point Mutation, Sequence Analysis, RNA, Disease Progression, Evolution, Molecular, Gene Expression Profiling, INDEL Mutation, DNA Copy Number Variations, Precision Medicine, High-Throughput Nucleotide Sequencing
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
