Cited by 1,967Cancer Genomics and DiagnosticsBreast Cancer Treatment StudiesBRCA gene mutations in cancer

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 access

Shah, Sohrab P., Roth, Andrew, Goya, Rodrigo, Oloumi, Arusha, Ha, Gavin, Zhao, Yongjun, Turashvili, Gulisa, Ding, Jiarui, Tse, Kane, Haffari, Gholamreza, Bashashati, Ali, Prentice, Leah M., Khattra, Jaswinder, Burleigh, Angela, Yap, Damian, Bernard, Virginie, McPherson, Andrew, Shumansky, Karey, Crisan, Anamaria, Giuliany, Ryan, Heravi-Moussavi, Alireza, Rosner, Jamie, Lai, Daniel, Birol, Inanc, Varhol, Richard, Tam, Angela, Dhalla, Noreen, Zeng, Thomas, Ma, Kevin, Chan, Simon K., 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, Hoon, Kelly, Harkins, Timothy, Tadigotla, Vasisht, Sigaroudinia, Mahvash, 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·2012·Nature

DOI 10.1038/nature10933PMC PMC3863681

Open this paper in CoChat — free account

Abstract

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.

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

Crossref · 10.1038/nature10933

Cites

24 of 24 references verified0 citation errors · 0 not checkable

Statistics

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

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
Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications
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-citation
Supervised 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-citation
Genome 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

Show all 23 references

Sorted by citations

Items 701–800 of 1,003

Viral-Cellular DNA Junctions as Molecular Markers for Assessing Intra-Tumor Heterogeneity in Cervical Cancer and for the Detection of Circulating Tumor DNA
Carow, K., Gölitz, M., Wolf, M., Häfner, N., Jansen, L., Hoyer, H., Schwarz, E., Runnebaum, I. B., & Dürst, M. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18102032 · Cited by 43
Prevalence of MDM2 amplification and coalterations in 523 advanced cancer patients in the MD Anderson phase 1 clinic
Dembla, V., Somaiah, N., Barata, P. C., Hess, K. R., Fu, S., Jankú, F., Karp, D. D., Naing, A., Piha-Paul, S. A., Subbiah, V., et al. (2018) · Oncotarget · doi:10.18632/oncotarget.26075 · Cited by 41
A subgroup of microRNAs defines PTEN-deficient, triple-negative breast cancer patients with poorest prognosis and alterations in RB1, MYC, and Wnt signaling
Wang, D., Gendoo, D. M. A., Ben‐David, Y., Woodgett, J. R., & Zacksenhaus, E. (2019) · Breast Cancer Research · doi:10.1186/s13058-019-1098-z · Cited by 42
Personalized treatment in metastatic triple‐negative breast cancer: The outlook in 2020
Azim, H. A., Ghosn, M. G., Oualla, K., & Kassem, L. M. H. (2019) · The Breast Journal · doi:10.1111/tbj.13713 · Cited by 43
Potentiation of carboplatin-mediated DNA damage by the Mdm2 modulator Nutlin-3a in a humanized orthotopic breast-to-lung metastatic model
Tonsing-Carter, E., Bailey, B. J., Saadatzadeh, M. R., Ding, J., Wang, H., Sinn, A. L., Peterman, K. M., Spragins, T. K., Silver, J. M., Sprouse, A. A., et al. (2015) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-15-0237 · Cited by 42
Self-citation
Anti-androgen therapy in triple-negative breast cancer
Barton, V. N., Gordon, M. A., Richer, J. K., & ELIAS, A. D. (2016) · Therapeutic Advances in Medical Oncology · doi:10.1177/1758834016646735 · Cited by 42
Machine learning-based prediction model for distant metastasis of breast cancer
Duan, H., Zhang, Y., Qiu, H., Fu, X., Liu, C., Zang, X., Wu, Z., Wu, Z., Li, X., Zhang, Q., et al. (2024) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2024.107943 · Cited by 42
Intra-tumor heterogeneity: lessons from microbial evolution and clinical implications
de Bruin, E. C., Taylor, T., & Swanton, C. (2013) · Genome Medicine · doi:10.1186/gm505 · Cited by 44
Reversion to an embryonic alternative splicing program enhances leukemia stem cell self-renewal
Holm, F., Hellqvist, E., Mason, C. N., Ali, S. A., Santos, N. P. D., Barrett, C. L., Chun, H.-J. E., Minden, M. D., Moore, R. A., Marra, M. A., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1506943112 · Cited by 42
Self-citation
Prolonged Response to Trastuzumab in a Patient With HER2-Nonamplified Breast Cancer With Elevated HER2 Dimerization Harboring anERBB2S310F Mutation
Chumsri, S., Weidler, J. M., Ali, S. M., Balasubramanian, S., Wallweber, G. J., Eli, L. D., Chenna, A., Huang, W., DeRidder, A. M., Goicocheal, L., et al. (2015) · Journal of the National Comprehensive Cancer Network · doi:10.6004/jnccn.2015.0132 · Cited by 42
Identification of frequent somatic mutations in inflammatory breast cancer
Matsuda, N., Lim, B., Wang, Y., Krishnamurthy, S., Woodward, W. A., Álvarez, R. H., Lucci, A., Valero, V., Reuben, J. M., Meric‐Bernstam, F., et al. (2017) · Breast Cancer Research and Treatment · doi:10.1007/s10549-017-4165-0 · Cited by 42
Mitochondrial dysfunction activates lysosomal-dependent mitophagy selectively in cancer cells
Biel, T. G., & Rao, V. A. (2017) · Oncotarget · doi:10.18632/oncotarget.23171 · Cited by 44
Genetic and clinical landscape of breast cancers with germline BRCA1/2 variants
Inagaki‐Kawata, Y., Yoshida, K., Kawaguchi‐Sakita, N., Kawashima, M., Nishimura, T., Senda, N., Shiozawa, Y., Takeuchi, Y., Inoue, Y., Sato‐Otsubo, A., et al. (2020) · Communications Biology · doi:10.1038/s42003-020-01301-9 · Cited by 44
Breast Cancer Heterogeneity in Primary and Metastatic Disease
Kalinowski, L., Saunus, J. M., Reed, A. E. M., & Lakhani, S. R. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-20301-6_6 · Cited by 47
Disentangling the aneuploidy and senescence paradoxes: a study of triploid breast cancers non-responsive to neoadjuvant therapy
Gerashchenko, B. I., Salmiņa, K., Eglītis, J., Huna, A., Grjunberga, V., & Erenpreisa, J. A. (2016) · Histochemistry and Cell Biology · doi:10.1007/s00418-016-1415-x · Cited by 42
Mapping genomic and transcriptomic alterations spatially in epithelial cells adjacent to human breast carcinoma
Abdalla, M., Tran‐Thanh, D., Moreno, J. C. A., Iakovlev, V. V., Nair, R., Kanwar, N., Abdalla, M., Lee, J. P. Y., Kwan, J. Y. Y., Cawthorn, T. R., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01357-y · Cited by 41
Brain metastasis: New opportunities to tackle therapeutic resistance
Seoane, J., & Mattos‐Arruda, L. D. (2014) · Molecular Oncology · doi:10.1016/j.molonc.2014.05.009 · Cited by 41
New concepts in breast cancer genomics and genetics
Gonçalves, R., Warner, W. A., Luo, J. R., & Ellis, M. J. (2014) · Breast Cancer Research · doi:10.1186/s13058-014-0460-4 · Cited by 43
Genetic heterogeneity and actionable mutations in HER2-positive primary breast cancers and their brain metastases
Mattos‐Arruda, L. D., Ng, C. K. Y., Piscuoglio, S., González‐Cao, M., Lim, R. S., Filippo, M. R. D., Fusco, N., Schultheis, A. M., Ortiz, C., Viteri, S., et al. (2018) · Oncotarget · doi:10.18632/oncotarget.25041 · Cited by 41
Molecular characterization of metaplastic breast carcinoma via next-generation sequencing
Zhai, J., Giannini, G., Ewalt, M. D., Zhang, E. Y., Invernizzi, M., Niland, J. C., & Lai, L. L. (2018) · Human Pathology · doi:10.1016/j.humpath.2018.11.023 · Cited by 41
MicroRNA-based potential diagnostic, prognostic and therapeutic applications in triple-negative breast cancer
Tang, Q., Ouyang, H., He, D., Yu, C., & Tang, G. (2019) · Artificial Cells Nanomedicine and Biotechnology · doi:10.1080/21691401.2019.1638791 · Cited by 41
The advance of adjuvant treatment for triple-negative breast cancer
Ge, J., Zuo, W., Chen, Y., Shao, Z., & Yu, K. (2021) · Cancer Biology and Medicine · doi:10.20892/j.issn.2095-3941.2020.0752 · Cited by 45
Identification of a five genes prognosis signature for triple-negative breast cancer using multi-omics methods and bioinformatics analysis
Ma, J., Chen, C., Liu, S., Ji, J., Wu, D., Huang, P. F., Wei, D., Fan, Z., & Ren, L. (2022) · Cancer Gene Therapy · doi:10.1038/s41417-022-00473-2 · Cited by 40
Precision Medicine in Breast Cancer: Genes, Genomes, and the Future of Genomically Driven Treatments
Stover, D. G., & Wagle, N. (2015) · Current Oncology Reports · doi:10.1007/s11912-015-0438-0 · Cited by 39
Triple negative breast carcinoma EGFR amplification is not associated with EGFR, Kras or ALK mutations
Secq, V., Villeret, J., Fina, F., Carmassi, M., Carcopino, X., Garcia, S., Metellus, I., Boubli, L., Iovanna, J., & Charpin, C. (2014) · British Journal of Cancer · doi:10.1038/bjc.2013.794 · Cited by 40
Enriched variations in TEKT4 and breast cancer resistance to paclitaxel
Jiang, Y., Yu, K., Peng, W.-T., Di, G., Wu, J., Liu, G., & Shao, Z.-M. (2014) · Nature Communications · doi:10.1038/ncomms4802 · Cited by 40
Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing
Jiao, X., Hooper, S. D., Djureinovic, T., Larsson, C., Wärnberg, F., Tellgren‐Roth, C., Botling, J., & Sjöblom, T. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-165 · Cited by 40
Triple-negative breast cancer: bridging the gap from cancer genomics to predictive biomarkers
Davis, S. L., Eckhardt, S., Tentler, J. J., & Diamond, J. R. (2014) · Therapeutic Advances in Medical Oncology · doi:10.1177/1758834013519843 · Cited by 40
A simple consensus approach improves somatic mutation prediction accuracy
Goode, D. L., Hunter, S. M., Doyle, M., Ma, T., Rowley, S. M., Choong, D., Ryland, G. L., & Campbell, I. (2013) · Genome Medicine · doi:10.1186/gm494 · Cited by 40
Triple-negative breast cancer
Hirshfield, K. M., & Ganesan, S. (2013) · Current Opinion in Obstetrics & Gynecology · doi:10.1097/gco.0000000000000038 · Cited by 40
Favorable Prognostic Impact in Loss of TP53 and PIK3CA Mutations after Neoadjuvant Chemotherapy in Breast Cancer
Jiang, Y., Yu, K., Bao, J., Peng, W.-T., & Shao, Z. (2014) · Cancer Research · doi:10.1158/0008-5472.can-14-0092 · Cited by 40
Sensitizing Triple-Negative Breast Cancer to PI3K Inhibition by Cotargeting IGF1R
de Lint, K., Poell, J. B., Soueidan, H., Jastrzebski, K., Rodriguez, J. V., Lieftink, C., Wessels, L. F. A., & Beijersbergen, R. L. (2016) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-15-0865 · Cited by 42
The path to routine use of genomic biomarkers in the cancer clinicPreprint
Boutros, P. C. (2015) · Genome Research · doi:10.1101/gr.191114.115 · Cited by 41
The 41st David A. Karnofsky Memorial Award Lecture: Academic Research Worldwide—Quo Vadis?
Piccart, M. J. (2013) · Journal of Clinical Oncology · doi:10.1200/jco.2013.53.2549 · Cited by 39
Specific cell differentiation in breast cancer: a basis for histological classification
Rakha, E. A., Toss, M. S., & Quinn, C. (2021) · Journal of Clinical Pathology · doi:10.1136/jclinpath-2021-207487 · Cited by 39
Predictive biomarkers of response and survival following immunotherapy with a PD-L1 inhibitor benmelstobart (TQB2450) and antiangiogenic therapy with a VEGFR inhibitor anlotinib for pretreated advanced triple negative breast cancer
Han, Y., Wang, J., Sun, T., Ouyang, Q., Li, J., Yuan, J., & Xu, B. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01672-5 · Cited by 43
PKCζ Promotes Breast Cancer Invasion by Regulating Expression of E-cadherin and Zonula Occludens-1 (ZO-1) via NFκB-p65
Paul, A., Danley, M., Saha, B., Tawfik, O. W., & Paul, S. (2015) · Scientific Reports · doi:10.1038/srep12520 · Cited by 45
Endoplasmic Reticulum-resident Heat Shock Protein 90 (HSP90) Isoform Glucose-regulated Protein 94 (GRP94) Regulates Cell Polarity and Cancer Cell Migration by Affecting Intracellular Transport
Ghosh, S., Shinogle, H. E., Galeva, N. A., Dobrowsky, R. T., & Blagg, B. S. J. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.688374 · Cited by 39
TP53 mutations and protein immunopositivity may predict for poor outcome but also for trastuzumab benefit in patients with early breast cancer treated in the adjuvant setting
Fountzilas, G., Giannoulatou, E., Alexopoulou, Z., Zagouri, F., Timotheadou, E. T., Papadopoulou, K., Lakis, S., Bobos, M., Poulios, C., Sotiropoulou, M. G., et al. (2016) · Oncotarget · doi:10.18632/oncotarget.9022 · Cited by 39
Simul-seq: combined DNA and RNA sequencing for whole-genome and transcriptome profiling
Reuter, J., Spacek, D. V., Pai, R. K., & Snyder, M. P. (2016) · Nature Methods · doi:10.1038/nmeth.4028 · Cited by 37
MDM4 is a rational target for treating breast cancers with mutant p53
Miranda, P. J., Buckley, D., Raghu, D., Pang, J., Takano, E. A., Vijayakumaran, R., Teunisse, A. F. A. S., Posner, A., Procter, T., Herold, M. J., et al. (2017) · The Journal of Pathology · doi:10.1002/path.4877 · Cited by 39
Male breast cancer precursor lesions: analysis of the EORTC 10085/TBCRC/BIG/NABCG International Male Breast Cancer Program
Doebar, S. C., Slaets, L., Cardoso, F., Giordano, S. H., Bartlett, J. M. S., Tryfonidis, K., Dijkstra, N., Schröder, C. P., van Asperen, C. J., Linderholm, B. K., et al. (2017) · Modern Pathology · doi:10.1038/modpathol.2016.229 · Cited by 39
Computational approaches for inferring tumor evolution from single-cell genomic data
Zafar, H., Navin, N. E., Nakhleh, L. K., & Chen, K. (2017) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2017.11.008 · Cited by 35
Tumor‐stroma interactions differentially alter drug sensitivity based on the origin of stromal cells
Landry, B. D., Leete, T., Richards, R., Cruz‐Gordillo, P., Schwartz, H. R., Honeywell, M. E., Ren, G., Schwartz, A. D., Peyton, S. R., & Lee, M. J. (2018) · Molecular Systems Biology · doi:10.15252/msb.20188322 · Cited by 39
Targeting homologous repair deficiency in breast and ovarian cancers: Biological pathways, preclinical and clinical data
Chartron, E., Theillet, C. G., Guiu, S., & Jacot, W. (2018) · Critical Reviews in Oncology/Hematology · doi:10.1016/j.critrevonc.2018.10.012 · Cited by 40
Combined p53- and PTEN-deficiency activates expression of mesenchyme homeobox 1 (MEOX1) required for growth of triple-negative breast cancer
Gasparyan, M., Lo, M., Jiang, H., Lin, C.-C. A., & Sun, D. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.010710 · Cited by 38
The Natural Products and Extracts: Anti‐Triple‐Negative Breast Cancer in Vitro
Chen, H., Yang, J., Yang, Y., Zhang, J., Yao, X., & Lu, X. (2021) · Chemistry & Biodiversity · doi:10.1002/cbdv.202001047 · Cited by 40
CD24 negativity reprograms mitochondrial metabolism to PPARα and NF-κB-driven fatty acid β-oxidation in triple-negative breast cancer
Murthy, D., Dutta, D., Attri, K. S., Samanta, T., Yang, S., Jung, K. H., Latario, S. G., Putluri, V., Huang, S., Putluri, N., et al. (2023) · Cancer Letters · doi:10.1016/j.canlet.2024.216724 · Cited by 37
Liquid Biopsy and its Potential for Management of Hepatocellular Carcinoma
Zhou, J., Huang, A., & Yang, X. (2016) · Journal of Gastrointestinal Cancer · doi:10.1007/s12029-016-9801-0 · Cited by 42
Targeting mTOR pathway inhibits tumor growth in different molecular subtypes of triple-negative breast cancers
Hatem, R., Botty, R. E., Château‐Joubert, S., Servely, J., Labiod, D., de Plater, L., Assayag, F., Coussy, F., Callens, C., Vacher, S., et al. (2016) · Oncotarget · doi:10.18632/oncotarget.10195 · Cited by 40
Mutation patterns in small cell and non-small cell lung cancer patients suggest a different level of heterogeneity between primary and metastatic tumors
Saber, A., Hiltermann, T. J. N., Kok, K., Terpstra, M. M., de Lange, K., Timens, W., Groen, H. J. M., & van den Berg, A. (2016) · Carcinogenesis · doi:10.1093/carcin/bgw128 · Cited by 39
Potential Management of Circulating Tumor DNA as a Biomarker in Triple-Negative Breast Cancer
Shang, M., Chang, C., Pei, Y., Guan, Y., Chang, J., & Li, H. (2018) · Journal of Cancer · doi:10.7150/jca.28458 · Cited by 37
Differential gene expression analysis of HNSCC tumors deciphered tobacco dependent and independent molecular signatures
Shaikh, I., Ansari, A., Ayachit, G., Gandhi, M., Sharma, P., Bhairappanavar, S. B., Joshi, C. G., & Das, J. (2019) · Oncotarget · doi:10.18632/oncotarget.27249 · Cited by 41
Cancer Vaccines for Triple-Negative Breast Cancer: A Systematic Review
Hosseini, M., Seyedpour, S., Khodaei, B., Loghman, A. H., Seyedpour, N., Yazdi, M. H., & Rezaei, N. (2023) · Vaccines · doi:10.3390/vaccines11010146 · Cited by 38
ReMixT: clone-specific genomic structure estimation in cancer
McPherson, A., Roth, A. J. L., Ha, G., Chauve, C., Steif, A., de Souza, C. P. E., Eirew, P. D., Bouchard‐Côté, A., Aparicio, S. A. J. R., Şahinalp, S. C., et al. (2017) · Genome biology · doi:10.1186/s13059-017-1267-2 · Cited by 36
Self-citation
Chromosomal Instability in Genome Evolution: From Cancer to Macroevolution
Comaills, V., & Castellano‐Pozo, M. (2023) · Biology · doi:10.3390/biology12050671 · Cited by 40
Atezolizumab in Combination With Carboplatin and Survival Outcomes in Patients With Metastatic Triple-Negative Breast Cancer
Lehmann, B. D., Abramson, V. G., Dees, E. C., Shah, P. D., Ballinger, T. J., Isaacs, C. J., Santa-Maria, C. A., An, H., Ericsson, P. I. G., Sanders, M. E., et al. (2023) · JAMA Oncology · doi:10.1001/jamaoncol.2023.5424 · Cited by 40
Molecular markers for breast cancer diagnosis, prognosis and targeted therapy
Lang, J. E., Wecsler, J. S., Press, M. F., & Tripathy, D. (2014) · Journal of Surgical Oncology · doi:10.1002/jso.23732 · Cited by 37
Establishing the origin of metastatic deposits in the setting of multiple primary malignancies: The role of massively parallel sequencing
Mattos‐Arruda, L. D., Bidard, F., Won, H. H., Cortés, J., Ng, C. K. Y., Peg, V., Nuciforo, P. G., Jungbluth, A. A., Weigelt, B., Berger, M. F., et al. (2013) · Molecular Oncology · doi:10.1016/j.molonc.2013.10.006 · Cited by 37
Next-Generation Genotyping by Digital PCR to Detect and Quantify the BRAF V600E Mutation in Melanoma Biopsies
Lamy, P., Castan, F., Lozano, N., Montélion, C., Audran, P., Bibeau, F., Roques, S., Montels, F., & Laberenne, A.-C. (2015) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2015.02.004 · Cited by 37
EGFR/Notch Antagonists Enhance the Response to Inhibitors of the PI3K-Akt Pathway by Decreasing Tumor-Initiating Cell Frequency
Fu, W., Lei, C., Yu, Y., Liu, S., Li, T., Lin, F., Fan, X., Shen, Y., Ding, M., Tang, Y. F., et al. (2019) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-2732 · Cited by 37
DNA methylation exploration for ARDS: a multi-omics and multi-microarray interrelated analysis
Zhang, S., Wu, Z., Xie, J., Yang, Y., Wang, L., & Qiu, H. (2019) · Journal of Translational Medicine · doi:10.1186/s12967-019-2090-1 · Cited by 36
Tumor membrane-based vaccine immunotherapy in combination with anti-CTLA-4 antibody confers protection against immune checkpoint resistant murine triple-negative breast cancer
Pack, C. D., Bommireddy, R., Muñoz, L. E., Patel, J. M., Bozeman, E. N., Dey, P., Radhakrishnan, V., Vartabedian, V. F., Venkat, K., Ramachandiran, S., et al. (2020) · Human Vaccines & Immunotherapeutics · doi:10.1080/21645515.2020.1754691 · Cited by 37
BCL2 is an independent predictor of outcome in basal-like triple-negative breast cancers treated with adjuvant anthracycline-based chemotherapy
Bouchalová, K., Svoboda, M., Kharaishvili, G., Vrbková, J., Bouchal, J., Trojanec, R., Koudeláková, V., Radová, L., Cwiertka, K., Hajdúch, M., et al. (2015) · Tumor Biology · doi:10.1007/s13277-015-3061-7 · Cited by 37
Heterogeneity of tertiary lymphoid structures predicts the response to neoadjuvant therapy and immune microenvironment characteristics in triple-negative breast cancer
Wang, Q., Yu, Y.-S., Wang, C.-X., Jiang, Z., Li, J.-L., Li, X.-F., Huang, X.-W., Song, Y., Li, Z.-H., Tang, S., et al. (2024) · British Journal of Cancer · doi:10.1038/s41416-024-02917-y · Cited by 38
Predicting censored survival data based on the interactions between meta-dimensional omics data in breast cancer
Kim, D., Li, R., DUDEK, S. M., & Ritchie, M. D. (2015) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2015.05.019 · Cited by 36
Characterizing the heterogeneity of triple-negative breast cancers using microdissected normal ductal epithelium and RNA-sequencing
Radovich, M., Clare, S. E., Atale, R. V., Pardo, I., Hancock, B. A., Solzak, J. P., Kassem, N., Mathieson, T., Storniolo, A. M., Rufenbarger, C., et al. (2013) · Breast Cancer Research and Treatment · doi:10.1007/s10549-013-2780-y · Cited by 36
On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly
Rizzi, R., Tomescu, A. I., & Mäkinen, V. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-s9-s5 · Cited by 38
MEL-18 loss mediates estrogen receptor–α downregulation and hormone independence
Lee, J., Won, H., Park, J., Kim, H., Choi, H., Shin, D., Kang, J., Woo, J. K., Oh, S.-H., Son, T., et al. (2015) · Journal of Clinical Investigation · doi:10.1172/jci73743 · Cited by 36
Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments
Smith, E. N., Jepsen, K., Khosroheidari, M., Rassenti, L. Z., D’Antonio, M., Ghia, E. M., Carson, D. A., Jamieson, C. H. M., Kipps, T. J., & Frazer, K. A. (2014) · Genome biology · doi:10.1186/preaccept-1251182501124451 · Cited by 35
MET and ERBB2 Are Coexpressed in ERBB2+ Breast Cancer and Contribute to Innate Resistance
Paulson, A. K., Linklater, E. S., Berghuis, B. D., App, C. A., Oostendorp, L. D., Paulson, J. E., Pettinga, J., Melnik, M. K., Woude, G. F. V., & Graveel, C. R. (2013) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-13-0042 · Cited by 38
Gene regulatory networks by transcription factors and microRNAs in breast cancer
Qin, S., Ma, F., & Chen, L. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu597 · Cited by 36
Cancer cells exhibit clonal diversity in phenotypic plasticity
Mathis, R. A., Sokol, E. S., & Gupta, P. B. (2017) · Open Biology · doi:10.1098/rsob.160283 · Cited by 34
Orai1 is critical for Notch-driven aggressiveness under hypoxic conditions in triple-negative breast cancers
Liu, X., Wang, T., Wang, Y., Chen, Z., Hua, D., Yao, X., Ma, X., & Zhang, P. (2018) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2018.01.003 · Cited by 36
State of art of advanced triple negative breast cancer
Khosravi‐Shahi, P., Cabezón‐Gutiérrez, L., & Salcedo, M. I. A. (2019) · The Breast Journal · doi:10.1111/tbj.13369 · Cited by 36
Profiling molecular regulators of recurrence in chemorefractory triple-negative breast cancers
Hancock, B. A., Chen, Y.-H., Solzak, J. P., Ahmad, M. N., Wedge, D. C., Brinza, D., Scafe, C., Veitch, J. M., Gottimukkala, R., Short, W., et al. (2019) · Breast Cancer Research · doi:10.1186/s13058-019-1171-7 · Cited by 37
The HER2 S310F Mutant Can Form an Active Heterodimer with the EGFR, Which Can Be Inhibited by Cetuximab but Not by Trastuzumab as well as Pertuzumab
Shin, J. W., Kim, S., Ha, S., Choi, B., Kim, S., Im, S., Yoon, T., & Chung, J. (2019) · Biomolecules · doi:10.3390/biom9100629 · Cited by 36
Integrative analysis of genomic amplification-dependent expression and loss-of-function screen identifies ASAP1 as a driver gene in triple-negative breast cancer progression
He, J., McLaughlin, R. P., van der Beek, L., Canisius, S., Wessels, L. F. A., Smid, M., Martens, J. W. M., Foekens, J. A., Zhang, Y.-H., & van de Water, B. (2020) · Oncogene · doi:10.1038/s41388-020-1279-3 · Cited by 36
Sporadic activation of an oxidative stress–dependent NRF2-p53 signaling network in breast epithelial spheroids and premalignancies
Pereira, E. J., Burns, J. S., Lee, C. Y., Marohl, T., Calderon, D., Wang, L., Atkins, K. A., Wang, C., & Janes, K. A. (2020) · Science Signaling · doi:10.1126/scisignal.aba4200 · Cited by 36
Triple-Negative Breast Cancer Comparison With Canine Mammary Tumors From Light Microscopy to Molecular Pathology
Namagerdi, A. A., d’Angelo, D., Ciani, F., Iannuzzi, C. A., Napolitano, F., Avallone, L., Laurentiis, M. D., & Giordano, A. (2020) · Frontiers in Oncology · doi:10.3389/fonc.2020.563779 · Cited by 36
Cancer in the parasitic protozoans Trypanosoma brucei and Toxoplasma gondii
Lun, Z., Lai, D., Wen, Y., Zheng, L., Shen, J.-L., Yang, T.-B., Zhou, W., Qu, L., Hide, G., & Ayala, F. J. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1502599112 · Cited by 39
Self-citation
Constitutively activated PI3K accelerates tumor initiation and modifies histopathology of breast cancer
Sheen, M. R., Marotti, J. D., Allegrezza, M. J., Rutkowski, M. R., Conejo-Garcia, J. R., & Fiering, S. (2016) · Oncogenesis · doi:10.1038/oncsis.2016.65 · Cited by 36
Delayed Sequential Co-Delivery of Gefitinib and Doxorubicin for Targeted Combination Chemotherapy
Zhou, Z., Jafari, M., Sriram, V., Kim, J., Lee, J., Ruiz-Torres, S. J., & Waltz, S. E. (2017) · Molecular Pharmaceutics · doi:10.1021/acs.molpharmaceut.7b00669 · Cited by 36
Tumor-infiltrating lymphocytes and ductal carcinoma in situ of the breast: friends or foes?
Agahozo, M. C., Hammerl, D., Debets, R., Kok, M., & van Deurzen, C. H. M. (2018) · Modern Pathology · doi:10.1038/s41379-018-0030-x · Cited by 36
The Mutant p53-Targeting Compound APR-246 Induces ROS-Modulating Genes in Breast Cancer Cells
Synnott, N. C., Madden, S. F., Bykov, V. J. N., Crown, J., Wiman, K. G., & Duffy, M. J. (2018) · Translational Oncology · doi:10.1016/j.tranon.2018.08.009 · Cited by 35
Cancer stem cell-driven efficacy of trastuzumab (Herceptin): towards a reclassification of clinically HER2-positive breast carcinomas
Martín-Castillo, B., López‐Bonet, E., Cuyàs, E., Viñas, G., Pernas, S., Dorca, J., & Menéndez, J. A. (2015) · Oncotarget · doi:10.18632/oncotarget.6094 · Cited by 35
Genetically engineered mouse models of PI3K signaling in breast cancer
Klarenbeek, S., van Miltenburg, M. H., & Jonkers, J. (2013) · Molecular Oncology · doi:10.1016/j.molonc.2013.02.003 · Cited by 36
Individualizing breast cancer treatment—The dawn of personalized medicine
Nandy, A., Gangopadhyay, S., & Mukhopadhyay, A. (2013) · Experimental Cell Research · doi:10.1016/j.yexcr.2013.09.002 · Cited by 36
Aldehyde dehydrogenase 1/epidermal growth factor receptor coexpression is characteristic of a highly aggressive, poor-prognosis subgroup of high-grade serous ovarian carcinoma
Liebscher, C. A., Prinzler, J., Sinn, B. V., Budczies, J., Denkert, C., Noske, A., Sehouli, J., Braicu, E. I., Dietel, M., & Darb‐Esfahani, S. (2013) · Human Pathology · doi:10.1016/j.humpath.2012.12.016 · Cited by 35
Prognostic value of circulating tumor cells and disseminated tumor cells in patients with ovarian cancer: a systematic review and meta-analysis
Cui, L., Kwong, J., & Wang, C. C. (2015) · Journal of Ovarian Research · doi:10.1186/s13048-015-0168-9 · Cited by 35
Targeting a Cancer-Specific Epitope of the Epidermal Growth Factor Receptor in Triple-Negative Breast Cancer
Simon, N. C., Antignani, A., Sarnovsky, R. J., Hewitt, S. M., & FitzGerald, D. (2016) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djw028 · Cited by 33
Discovering potential cancer driver genes by an integrated network-based approach
Shi, K., Gao, L., & Wang, B. (2016) · Molecular BioSystems · doi:10.1039/c6mb00274a · Cited by 35
NOTCH and DNA repair pathways are more frequently targeted by genomic alterations in inflammatory than in non‐inflammatory breast cancers
Bertucci, F., Rypens, C., Finetti, P., Guillé, A., Adélaı̈de, J., Monneur, A., Carbuccia, N., Garnier, S., Dirix, P. R., Gonçalvès, A., et al. (2019) · Molecular Oncology · doi:10.1002/1878-0261.12621 · Cited by 35
HDAC6 inhibitors sensitize non-mesenchymal triple-negative breast cancer cells to cysteine deprivation
Alothaim, T., Charbonneau, M., & Tang, X. (2021) · Scientific Reports · doi:10.1038/s41598-021-90527-6 · Cited by 36
Genomic sequencing in cancer
Tuna, M., & Amos, C. I. (2012) · Cancer Letters · doi:10.1016/j.canlet.2012.11.004 · Cited by 37
Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles
Li, W., Calder, R. B., Mar, J. C., & Vijg, J. (2015) · Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis · doi:10.1016/j.mrfmmm.2015.01.002 · Cited by 34
Metabolic Flexibility Is a Determinant of Breast Cancer Heterogeneity and Progression
Fukano, M., Park, M., & Deblois, G. (2021) · Cancers · doi:10.3390/cancers13184699 · Cited by 36
Translating Genomics to the Clinic: Implications of Cancer Heterogeneity
Samuel, N., & Hudson, T. J. (2012) · Clinical Chemistry · doi:10.1373/clinchem.2012.184580 · Cited by 34
Analysis of Paired Primary-Metastatic Hormone-Receptor Positive Breast Tumors (HRPBC) Uncovers Potential Novel Drivers of Hormonal Resistance
Manso, L., Mouron, S. A., Tress, M. L., Goméz-López, G., Morente, M. M., Ciruelos, E., Rubio-Camarillo, M., Rodríguez‐Peralto, J. L., Pujana, M. Á., Pisano, D. G., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0155840 · Cited by 34
A Transposon-based Analysis Reveals RASA1 Is Involved in Triple-Negative Breast Cancer
Suárez-Cabrera, C., Quintana, R. M., Bravo, A., Casanova, M., Page, A., Alameda, J. P., Paramio, J. M., Maroto, A., Salamanca, J., Dupuy, A. J., et al. (2017) · Cancer Research · doi:10.1158/0008-5472.can-16-1586 · Cited by 34

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
Publisher: Springer Science and Business Media LLC
Published: 2012-04-04
Volume: 486
Issue: 7403
Pages: 395-399
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature10933
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

The clonal and mutational evolution spectrum of primary triple-negative breast cancers

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks