ArticleBreast cancer research and treatment2015
Cross-species DNA copy number analyses identifies multiple 1q21-q23 subtype-specific driver genes for breast cancer.
Article in Breast cancer research and treatment, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 49 citations in OpenAlex.
- Integrated Analysis of RNA and DNA from the Phase III Trial CALGB 40601 Identifies Predictors of Response to Trastuzumab-Based Neoadjuvant Chemotherapy in HER2-Positive Breast Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2018Trial
- Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer.The Journal of clinical investigation · 2018Trial
- Phosphatidylinositol 4-kinase α suppresses glioblastoma progression by inactivating YAP and PI3K/Akt signaling.The Journal of biological chemistry · 2026Article
- Golgi Drivers of Cancer.Sub-cellular biochemistry · 2026Review
- Prognostic and molecular multi-platform analysis of CALGB 40603 (Alliance) and public triple-negative breast cancer datasets.NPJ breast cancer · 2025Article
- Understanding metastasis mixed-treatment responses through genomic analyses.NPJ breast cancer · 2025Article
- Aneuploidy as a driver of human cancer.Nature genetics · 2024Review
- Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection.Breast cancer research : BCR · 2024Article
- Landscape of Genetic Alterations Underlying Hallmark Signature Changes in Cancer RevealsCancer research communications · 2023Article
- Molecular signatures of in situ to invasive progression for basal-like breast cancers: An integrated mouse model and human DCIS study.NPJ breast cancer · 2022Article
- The diaryl-imidazopyridazine anti-plasmodial compound, MMV652103, exhibits anti-breast cancer activity.EXCLI journal · 2022Article
- Single allele loss-of-function mutations select and sculpt conditional cooperative networks in breast cancer.Nature communications · 2021Article
- Prune-1 drives polarization of tumor-associated macrophages (TAMs) within the lung metastatic niche in triple-negative breast cancer.iScience · 2021Article
- Functional Genomics of PRUNE1 in Neurodevelopmental Disorders (NDDs) Tied to Medulloblastoma (MB) and Other Tumors.Frontiers in oncology · 2021Review
- In silico pathway analysis based on chromosomal instability in breast cancer patients.BMC medical genomics · 2020Article
- Using next-generation sequencing to redefine BRCAness in triple-negative breast cancer.Cancer science · 2020Article
- Genetic determinants of the molecular portraits of epithelial cancers.Nature communications · 2019Article
- Multi-omic Dissection of Oncogenically Active Epiproteomes Identifies Drivers of Proliferative and Invasive Breast Tumors.iScience · 2019Article
- Copy number alterations associated with clinical features in an underrepresented population with breast cancer.Molecular genetics & genomic medicine · 2019Article
- Breaking the chains: deubiquitylating enzyme specificity begets function.Nature reviews. Molecular cell biology · 2019Review
Corrections and comments
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Authors and funding
11 authors at 6 institutions in 1 country.
Funding
Abstract
A large number of DNA copy number alterations (CNAs) exist in human breast cancers, and thus characterizing the most frequent CNAs is key to advancing therapeutics because it is likely that these regions contain breast tumor 'drivers' (i.e., cancer causal genes). This study aims to characterize the genomic landscape of breast cancer CNAs and identify potential subtype-specific drivers using a large set of human breast tumors and genetically engineered mouse (GEM) mammary tumors. Using a novel method called SWITCHplus, we identified subtype-specific DNA CNAs occurring at a 15% or greater frequency, which excluded many well-known breast cancer-related drivers such as amplification of ERBB2, and deletions of TP53 and RB1. A comparison of CNAs between mouse and human breast tumors identified regions with shared subtype-specific CNAs. Additional criteria that included gene expression-to-copy number correlation, a DawnRank network analysis, and RNA interference functional studies highlighted candidate driver genes that fulfilled these multiple criteria. Numerous regions of shared CNAs were observed between human breast tumors and GEM mammary tumor models that shared similar gene expression features. Specifically, we identified chromosome 1q21-23 as a Basal-like subtype-enriched region with multiple potential driver genes including PI4KB, SHC1, and NCSTN. This step-wise computational approach based on a cross-species comparison is applicable to any tumor type for which sufficient human and model system DNA copy number data exist, and in this instance, highlights that a single region of amplification may in fact harbor multiple driver genes.
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