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Prognostic RNA-splicing archetypes in breast cancer identified by extended pre-training of histopathology foundation models.

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Title: Prognostic RNA-splicing archetypes in breast cancer identified by extended pre-training of histopathology foundation models.
Authors: Fournier L; Idiap Research Institute, Martigny, Switzerland.; Center of Translational Research in Onco-Hematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Haefliger G; Idiap Research Institute, Martigny, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Vernhes A; Idiap Research Institute, Martigny, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Jung V; Idiap Research Institute, Martigny, Switzerland.; Signal Processing Laboratory (LTS4), School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland., Loye L; Department for BioMedical Research, University of Bern, Bern, Switzerland.; Department of Digital Medicine, University of Bern, Bern, Switzerland., Du Bois V; Department of Oncology, Hôpitaux Universitaires de Genève, Geneva, Switzerland.; Faculty of Medicine, Université de Genève, Geneva, Switzerland., Labidi-Galy I; Department of Oncology, Hôpitaux Universitaires de Genève, Geneva, Switzerland.; Faculty of Medicine, Université de Genève, Geneva, Switzerland., Frossard P; Signal Processing Laboratory (LTS4), School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland., Letovanec I; Department of Histopathology, Central Institute, Valais Hospital, Sion, Switzerland.; Institute of Pathology, Centre Hospitalier Universitaire Vaudois CHUV, Lausanne, Switzerland., Vincent-Cuaz C; Signal Processing Laboratory (LTS4), School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. cedric.vincent-cuaz@unibe.ch.; Department for BioMedical Research, University of Bern, Bern, Switzerland. cedric.vincent-cuaz@unibe.ch.; Department of Digital Medicine, University of Bern, Bern, Switzerland. cedric.vincent-cuaz@unibe.ch., Luisier R; Swiss Institute of Bioinformatics, Lausanne, Switzerland. raphaelle.luisier@unibe.ch.; Department for BioMedical Research, University of Bern, Bern, Switzerland. raphaelle.luisier@unibe.ch.; Department of Digital Medicine, University of Bern, Bern, Switzerland. raphaelle.luisier@unibe.ch.
Source: Nature communications [Nat Commun] 2026 Jul 07. Date of Electronic Publication: 2026 Jul 07.
Publication Type: Journal Article
Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
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  Data: <searchLink fieldCode="AU" term="%22Fournier+L%22">Fournier L</searchLink>; Idiap Research Institute, Martigny, Switzerland.; Center of Translational Research in Onco-Hematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Haefliger+G%22">Haefliger G</searchLink>; Idiap Research Institute, Martigny, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Vernhes+A%22">Vernhes A</searchLink>; Idiap Research Institute, Martigny, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Jung+V%22">Jung V</searchLink>; Idiap Research Institute, Martigny, Switzerland.; Signal Processing Laboratory (LTS4), School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Loye+L%22">Loye L</searchLink>; Department for BioMedical Research, University of Bern, Bern, Switzerland.; Department of Digital Medicine, University of Bern, Bern, Switzerland.<br /><searchLink fieldCode="AU" term="%22Du+Bois+V%22">Du Bois V</searchLink>; Department of Oncology, Hôpitaux Universitaires de Genève, Geneva, Switzerland.; Faculty of Medicine, Université de Genève, Geneva, Switzerland.<br /><searchLink fieldCode="AU" term="%22Labidi-Galy+I%22">Labidi-Galy I</searchLink>; Department of Oncology, Hôpitaux Universitaires de Genève, Geneva, Switzerland.; Faculty of Medicine, Université de Genève, Geneva, Switzerland.<br /><searchLink fieldCode="AU" term="%22Frossard+P%22">Frossard P</searchLink>; Signal Processing Laboratory (LTS4), School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Letovanec+I%22">Letovanec I</searchLink>; Department of Histopathology, Central Institute, Valais Hospital, Sion, Switzerland.; Institute of Pathology, Centre Hospitalier Universitaire Vaudois CHUV, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Vincent-Cuaz+C%22">Vincent-Cuaz C</searchLink>; Signal Processing Laboratory (LTS4), School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. cedric.vincent-cuaz@unibe.ch.; Department for BioMedical Research, University of Bern, Bern, Switzerland. cedric.vincent-cuaz@unibe.ch.; Department of Digital Medicine, University of Bern, Bern, Switzerland. cedric.vincent-cuaz@unibe.ch.<br /><searchLink fieldCode="AU" term="%22Luisier+R%22">Luisier R</searchLink>; Swiss Institute of Bioinformatics, Lausanne, Switzerland. raphaelle.luisier@unibe.ch.; Department for BioMedical Research, University of Bern, Bern, Switzerland. raphaelle.luisier@unibe.ch.; Department of Digital Medicine, University of Bern, Bern, Switzerland. raphaelle.luisier@unibe.ch.
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