biostudies-literatureRonchi CBreast Cancer NowEC | Horizon 2020 Framework ProgrammeEC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)56https://www.ebi.ac.uk/biostudies/studies/S-EPMC11233672biostudies-literatureUnknown10(1)Transcriptomics has revolutionized biomedical research and refined breast cancer subtyping and diagnostics. However, wider use in clinical practice is hampered for a number of reasons including the application of transcriptomic signatures as single sample predictors. Here, we present an embedding approach called EMBER that creates a unified space of 11,000 breast cancer transcriptomes and predicts phenotypes of transcriptomic profiles on a single sample basis. EMBER accurately captures the five molecular subtypes. Key biological pathways, such as estrogen receptor signaling, cell proliferation, DNA repair, and epithelial-mesenchymal transition determine sample position in the space. We validate EMBER in four independent patient cohorts and show with samples from the window trial, POETIC, tNPJ breast cancerEMBER creates a unified space for independent breast cancer transcriptomic datasets enabling precision oncology.PMC11233672859860Brisken CHaider SRonchi CfalseEMBER creates a unified space for independent breast cancer transcriptomic datasets enabling precision oncology.Transcriptomics has revolutionized biomedical research and refined breast cancer subtyping and diagnostics. However, wider use in clinical practice is hampered for a number of reasons including the application of transcriptomic signatures as single sample predictors. Here, we present an embedding approach called EMBER that creates a unified space of 11,000 breast cancer transcriptomes and predicts phenotypes of transcriptomic profiles on a single sample basis. EMBER accurately captures the five molecular subtypes. Key biological pathways, such as estrogen receptor signaling, cell proliferation, DNA repair, and epithelial-mesenchymal transition determine sample position in the space. We validate EMBER in four independent patient cohorts and show with samples from the window trial, POETIC, t2024-01-01T00:00:00Z2024 Jul2026-07-15T05:15:41.603Z2024-11-09T15:16:06.682ZS-EPMC112336723898208610.1038/s41523-024-00665-z