Cited by 6,097Breast Cancer Treatment StudiesCancer Genomics and DiagnosticsGenomic variations and chromosomal abnormalities

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The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

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METABRIC Group, 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, Russell, Roslin, McKinney, Steven, Langerød, Anita, Green, Andrew, Provenzano, Elena, Wishart, Gordon, Pinder, Sarah, Watson, Peter, Markowetz, Florian, Murphy, Leigh, Ellis, Ian, Purushotham, Arnie, Børresen-Dale, Anne-Lise, Brenton, James D., Tavaré, Simon, Caldas, Carlos, Aparicio, Samuel·2012·Nature

DOI 10.1038/nature10983PMC PMC3440846

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Abstract

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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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
Publisher: Springer Science and Business Media LLC
Published: 2012-04-18
Volume: 486
Issue: 7403
Pages: 346-352
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature10983
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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