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The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
Open accessAbstract
The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (copy number variants and single nucleotide polymorphisms) and acquired somatic copy number aberrations (CNAs) were associated with expression in ~40% of genes, with the landscape dominated by cis- and trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP and MAP2K4. Unsupervised analysis of paired DNA–RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, oestrogen-receptor-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the ‘CNA-devoid’ subgroup and a basal-specific chromosome 5 deletion-associated mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic CNAs on the transcriptome.
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“Currently, numerous research efforts are focused on utilizing genetic data and artificial intelligence algorithms to develop diagnostic models to enhance the clinical efficiency and accuracy of breast cancer diagnosis [109,110,111].”
From A Comprehensive Review on Synergy of Multi-Modal Data and AI Technologies in Medical Diagnosis (2024) · cites this paper as [111]
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“This framework was also employed for a landmark study which used genomic and transcriptomic data from 2,000 breast tumours and discovered novel subgroups amongst them (Curtis et al., 2012).”
From Using machine learning approaches for multi-omics data analysis: A review (2021) · cites this paper as Curtis et al., 2012
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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
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
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
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
Li, J., Yen, C., Liaw, D., Podsypanina, K., Bose, S., Wang, S. I., Puc, J., Miliaresis, C., Rodgers, L., McCombie, R., et al. (1997) · Science · doi:10.1126/science.275.5308.1943 · Cited by 4,785
Ki67 expression in breast cancer
Elkablawy, M. A., Albasri, A. M., Mohammed, R. A., Hussainy, A. S., Nouh, M. M., & Alhujaily, A. S. (2016) · Saudi Medical Journal · doi:10.15537/smj.2016.2.12285 · Cited by 4,382
Diagnosis of multiple cancer types by shrunken centroids of gene expression
Tibshirani, R. J., Hastie, T. J., Narasimhan, B., & Chu, G. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.082099299 · Cited by 2,931
Tumor-Infiltrating CD8+Lymphocytes Predict Clinical Outcome in Breast Cancer
Mahmoud, S., Paish, E. C., Powe, D. G., Macmillan, R. D., Grainge, M. J., Lee, A. H. S., Ellis, I. O., & Green, A. R. (2011) · Journal of Clinical Oncology · doi:10.1200/jco.2010.30.5037 · Cited by 1,411
Self-citationGenomic and transcriptional aberrations linked to breast cancer pathophysiologies
Chin, K., DeVries, S., Fridlyand, J., Spellman, P. T., Roydasgupta, R., Kuo, W.-L., Lapuk, A. V., Neve, R. M., Qian, Z., Ryder, T., et al. (2006) · Cancer Cell · doi:10.1016/j.ccr.2006.10.009 · Cited by 1,309
Frequent Mutations of Chromatin Remodeling Gene ARID1A in Ovarian Clear Cell Carcinoma
Jones, S., Wang, T., Shih, I., Mao, T., Nakayama, K., Roden, R. B. S., Glas, R., Slamon, D. J., Diaz, L. A., Vogelstein, B., et al. (2010) · Science · doi:10.1126/science.1196333 · Cited by 1,218
Blows, F. M., Driver, K. E., Schmidt, M. K., Broeks, A., van Leeuwen, F. E., Wesseling, J., Cheang, M. C. U., Gelmon, K. A., Nielsen, T. O., BLOMQVIST, C. P., et al. (2010) · PLoS Medicine · doi:10.1371/journal.pmed.1000279 · Cited by 1,116
Self-citationVariations in DNA elucidate molecular networks that cause disease
Chen, Y., Zhu, J., Lum, P. Y., Yang, X., Pinto, S., MacNeil, D. J., Zhang, C., Lamb, J., Edwards, S., Sieberts, S. K., et al. (2008) · Nature · doi:10.1038/nature06757 · Cited by 887
Shen, R., Olshen, A. B., & Ladanyi, M. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp543 · Cited by 849
Signatures of mutation and selection in the cancer genome
Bignell, G. R., Greenman, C. D., Davies, H., Butler, A. P., Edkins, S., Andrews, J. M., Buck, G., Chen, L., Beare, D., Latimer, C., et al. (2010) · Nature · doi:10.1038/nature08768 · Cited by 707
Shen, R., Olshen, A. B., & Ladanyi, M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp659 · Cited by 564
Revealing the architecture of gene regulation: the promise of eQTL studies
Gilad, Y., Rifkin, S. A., & Pritchard, J. K. (2008) · Trends in Genetics · doi:10.1016/j.tig.2008.06.001 · Cited by 552
Genome-Wide Associations of Gene Expression Variation in Humans
Stranger, B. E., Forrest, M. S., Clark, A. G., Minichiello, M. J., Deutsch, S., Lyle, R., Hunt, S. E., Kahl, B. F., Antonarakis, S. E., Tavaré, S., et al. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010078 · Cited by 515
Self-citationA census of amplified and overexpressed human cancer genes
Santarius, T., Shipley, J., Brewer, D., Stratton, M. R., & Cooper, C. S. (2010) · Nature Reviews Cancer · doi:10.1038/nrc2771 · Cited by 482
EMSY Links the BRCA2 Pathway to Sporadic Breast and Ovarian Cancer
Hughes‐Davies, L., Huntsman, D. D., Ruas, M., Fuks, F., Bye, J. M., Chin, S., Milner, J., Brown, L. A., Hsu, F. D., Gilks, C. B., et al. (2003) · Cell · doi:10.1016/s0092-8674(03)00930-9 · Cited by 422
Self-citationChin, S., Teschendorff, A. E., Marioni, J. C., Wang, Y., Barbosa‐Morais, N. L., Thorne, N., Costa, J. L., Pinder, S. E., van de Wiel, M. A., Green, A. R., et al. (2007) · Genome biology · doi:10.1186/gb-2007-8-10-r215 · Cited by 323
Self-citationDistinct gene mutation profiles among luminal-type and basal-type breast cancer cell lines
Hollestelle, A., Nagel, J. H. A., Smid, M., Lam, S., Elstrodt, F., Wasielewski, M., Ng, S. S., French, P. J., Peeters, J. K., Rozendaal, M. J., et al. (2009) · Breast Cancer Research and Treatment · doi:10.1007/s10549-009-0460-8 · Cited by 308
Leary, R. J., Lin, J., Cummins, J. M., Boca, S. M., Wood, L. D., Parsons, D. W., Jones, S., Sjöblom, T., Park, B.-H., Parsons, R. E., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808041105 · Cited by 305
Human mitogen-activated protein kinase kinase 4 as a candidate tumor suppressor.
Teng, D. H. ‐., Perry, W. L., Hogan, J. K., Baumgard, M. L., Bell, R. N., Berry, S., Davis, T., Frank, D., Frye, C., Hattier, T., et al. (1997) · PubMed · Cited by 193
Are clusters found in one dataset present in another dataset?
Kapp, A. V., & Tibshirani, R. J. (2006) · Biostatistics · doi:10.1093/biostatistics/kxj029 · Cited by 180
High levels of the Mps1 checkpoint protein are protective of aneuploidy in breast cancer cells
Daniel, J. A., Coulter, J. B., Woo, J.-H., Wilsbach, K., & Gabrielson, E. W. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1007645108 · Cited by 166
Amplification of 11q13 in ovarian carcinoma
Brown, L. A., Kalloger, S. E., Miller, M. A., Shih, I., McKinney, S. E., Santos, J. L., Swenerton, K., Spellman, P. T., Gray, J. W., Gilks, C. B., et al. (2008) · Genes Chromosomes and Cancer · doi:10.1002/gcc.20549 · Cited by 160
Self-citationGenomic Architecture Characterizes Tumor Progression Paths and Fate in Breast Cancer Patients
Russnes, H. G., Vollan, H. K. M., Lingjærde, O. C., Krasnitz, A., Lundin, P., Naume, B., Sørlie, T., Borgen, E., Rye, I. H., Langerød, A., et al. (2010) · Science Translational Medicine · doi:10.1126/scitranslmed.3000611 · Cited by 150
Self-citationChristopher, S. A., Diegelman, P., Porter, C. W., & Kruger, W. D. (2002) · PubMed · Cited by 147
Holland, D. G., Burleigh, A., Git, A., Goldgraben, M. A., Pérez-Mancera, P. A., Chin, S., Hurtado, A., Bruna, A., Ali, H. R., Greenwood, W., et al. (2011) · EMBO Molecular Medicine · doi:10.1002/emmm.201100122 · Cited by 143
Self-citationSubtype‐specific mutation of PPP2R1A in endometrial and ovarian carcinomas
McConechy, M. K., Anglesio, M. S., Kalloger, S. E., Yang, W., Senz, J., Chow, C., Heravi‐Moussavi, A., Morin, G. B., Mes‐Masson, A., Chenevix‐Trench, G., et al. (2011) · The Journal of Pathology · doi:10.1002/path.2848 · Cited by 132
Self-citationTan, J. Y., Lee, P. L., Li, Z., Jiang, X., Lim, Y. C., Hooi, S. C., & Yu, Q. (2010) · Cancer Cell · doi:10.1016/j.ccr.2010.10.021 · Cited by 119
PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer
Teschendorff, A. E., Naderi, A., Barbosa‐Morais, N. L., & Caldas, C. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl174 · Cited by 67
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Comprehensive molecular portraits of human breast tumours
The Cancer Genome Atlas Network (2012) · Nature · doi:10.1038/nature11412 · Cited by 12,129
Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response
Jiang, P., Gu, S., Pan, D., Fu, J., Sahu, A., Hu, X., Li, Z., Traugh, N., Bu, X., Li, B., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0136-1 · Cited by 5,179
Profiling Tumor Infiltrating Immune Cells with CIBERSORT
Chen, B., Khodadoust, M. S., Liu, C. L., Newman, A. M., & Alizadeh, A. A. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7493-1_12 · Cited by 3,929
Triple-negative breast cancer: challenges and opportunities of a heterogeneous disease
Bianchini, G., Balko, J. M., Mayer, I. A., Sanders, M. E., & Gianni, L. (2016) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2016.66 · Cited by 3,079
Metadata
- Authors
- 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., Yuan, Y., Gräf, S., Ha, G., Haffari, G., Bashashati, A., Russell, R., McKinney, S., Langerød, A., Green, A., Provenzano, E., Wishart, G., Pinder, S., Watson, P., Markowetz, F., Murphy, L., Ellis, I., Purushotham, A., Børresen-Dale, A.-L., Brenton, J. D., Tavaré, S., Caldas, C., & Aparicio, S.
- Affiliations
- University of Cambridge (GB)
- University of British Columbia (CA)
- Oslo University Hospital (NO)
- University of Nottingham (GB)
- Cambridge University Hospitals NHS Foundation Trust (GB)
- King's College London (GB)
- University of Southern California (US)
- Corresponding author
- Caldas, Carlos
- Aparicio, Samuel
- ORCID
- Curtis, Christina
- Shah, Sohrab P.
- Chin, Suet-Feung
- Turashvili, Gulisa
- Rueda, Oscar M.
- Dunning, Mark J.
- Speed, Doug
- Lynch, Andy G.
- Samarajiwa, Shamith
- Yuan, Yinyin
- Gräf, Stefan
- Ha, Gavin
- Haffari, Gholamreza
- Bashashati, Ali
- Green, Andrew
- Provenzano, Elena
- Wishart, Gordon
- Pinder, Sarah
- Watson, Peter
- Markowetz, Florian
- Murphy, Leigh
- Ellis, Ian
- Purushotham, Arnie
- Brenton, James D.
- Tavaré, Simon
- Caldas, Carlos
- Aparicio, Samuel
- Venue
- Nature
- Published
- 2012-04-18
- Volume
- 486
- Issue
- 7403
- Pages
- 346-352
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3440846
- OpenAlex
- W2005895632
- Cited by
- 6,097
- References
- 32
- Citations by year
- 2026: 341 · 2025: 411 · 2024: 458 · 2023: 497 · 2022: 496 · 2021: 615 · 2020: 533 · 2019: 449 · 2018: 426 · 2017: 361 · 2016: 373 · 2015: 378 · 2014: 339 · 2013: 291 · 2012: 119
- FWCI
- 119.67
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Minerva Access (University of Melbourne) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion)
- Apollo
- Funders
- University of Southern California
- Michael Smith Health Research BC
- Cancer Research UK (A7199, 15601, 19556)
- National Institute for Health and Care Research (ACF-2012-14-006, NF-SI-0611-10154)
- University of Cambridge
- King's College London
- National Institutes of Health
- BC Cancer Agency
- NIHR Cambridge Biomedical Research Centre
- National Human Genome Research Institute (P50-HG02790, P50HG002790)
- Division of Mathematical Sciences
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Breast Cancer Treatment Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- breast cancer, copy number alterations, somatic copy number alterations, gene expression, single nucleotide polymorphisms, PPP2R2A, MTAP, MAP2K4, estrogen receptor-positive breast cancer, adaptive immune response, basal-like breast cancer, chromosome 5 deletion, molecular stratification, prognosis
- MeSH terms
- Breast Neoplasms, Female, Humans, Prognosis, Genome, Human, Gene Expression Regulation, Neoplastic, Treatment Outcome, Polymorphism, Single Nucleotide, Gene Expression Profiling, Genomics, MAP Kinase Kinase 4, Genes, Neoplasm, Kaplan-Meier Estimate, Gene Regulatory Networks, Protein Phosphatase 2, DNA Copy Number Variations
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