ArticleNature2012
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.
Article in Nature, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT04403984 (Investigation of the Prognostic Value of Genomic Alterations or Protein Expression in Patients With Operated Early Breast Cancer of Luminal A or Luminal B Subtypes), which is not on this map. Cited by 3,679 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Investigation of the Prognostic Value of Genomic Alterations or Protein Expression in Patients With Operated Early Breast Cancer of Luminal A or Luminal B Subtypes
Who cites it
3,679 citing papers in PubMed, 6,273 citations in OpenAlex.
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- Transcriptome-Based Synthetic Lethality Predictions to Improve Targeted Therapy/Immunotherapy Treatment Prioritization in Nonmetastatic Breast Cancer: BC-SELECT.Cancer research communications · 2026Article
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- TFAP2B and FOXC1 are associated with biologically and clinically distinct differentiation states in triple-negative breast cancer.Scientific reports · 2026Article
- Impact of Trastuzumab and Pertuzumab on HER2 Localization and the Estrogen Receptor Cistrome in ER+/HER2+ Breast Cancer.bioRxiv : the preprint server for biology · 2026Article
- CD1d remodels the tumor-infiltrating myeloid populations controlling antitumor immunity.The Journal of experimental medicine · 2026Article
- Metastasis of triple negative breast cancer is regulated by a targetable miR-342-E2F network.EMBO molecular medicine · 2026Article
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- Pan-cancer analysis identifies immunoproteasome as the predominant survival-associated component of antigen processing machinery.Translational oncology · 2026Article
- Article
3,619 more citing papers are in PubMed but not listed here.
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Authors and funding
32 authors at 8 institutions in 4 countries.
Funding
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.