A Machine Learning-Driven Virtual Biopsy System For Kidney Transplant Patients
Nature Communications, vol. 15, pp. 554
Abstract
In kidney transplantation, day-zero biopsies are used to assess organ quality and discriminate between donor-inherited lesions and those acquired post-transplantation. However, many centers do not perform such biopsies since they are invasive, costly and may delay the transplant procedure. We aim to generate a non-invasive virtual biopsy system using routinely collected donor parameters. Using 14,032 day-zero kidney biopsies from 17 international centers, we develop a virtual biopsy system. 11 basic donor parameters are used to predict four Banff kidney lesions: arteriosclerosis, arteriolar hyalinosis, interstitial fibrosis and tubular atrophy, and the percentage of renal sclerotic glomeruli. Six machine learning models are aggregated into an ensemble model. The virtual biopsy system shows good performance in the internal and external validation sets. We confirm the generalizability of the system in various scenarios. This system could assist physicians in assessing organ quality, optimizing allograft allocation together with discriminating between donor derived and acquired lesions post-transplantation.
Authors 39
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Inserm · Université Paris Cité · Paris Cardiovascular Research Center
Affiliation as printed
Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration, F-75015, Paris, France
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Inserm · Université Paris Cité · Assistance Publique – Hôpitaux de Paris · Paris Cardiovascular Research Center · Hôpital Saint-Louis
Affiliation as printed
Kidney Transplant Department, Saint-Louis Hospital, Assistance Publique - Hôpitaux de Paris, Paris, France
Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration, F-75015, Paris, France
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Inserm · Université Paris Cité · Paris Cardiovascular Research Center
Affiliation as printed
Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration, F-75015, Paris, France
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Affiliation as printed
OneLegacy, Los Angeles, CA, USA
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Affiliation as printed
OneLegacy, Los Angeles, CA, USA
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University of California, Los Angeles
Affiliation as printed
David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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Affiliation as printed
Division of Nephrology and Hypertension, Mayo Clinic Transplant Center, Rochester, MN, USA
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Affiliation as printed
Department of Surgery, Mayo Clinic, Rochester, MN, USA
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Affiliation as printed
Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
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Sun Yat-sen University · The First Affiliated Hospital, Sun Yat-sen University
Affiliation as printed
Organ Transplant Center, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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Sun Yat-sen University · The First Affiliated Hospital, Sun Yat-sen University
Affiliation as printed
Organ Transplant Center, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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Centre Hospitalier Universitaire de Tours
Affiliation as printed
Néphrologie-Immunologie Clinique, Hôpital Bretonneau, CHU Tours, Tours, France
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Université Toulouse III - Paul Sabatier · Inserm
Affiliation as printed
Department of Nephrology and Organ Transplantation, Paul Sabatier University, INSERM, Toulouse, France
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Centre Hospitalier Universitaire de Liège
Affiliation as printed
Department of Nephrology-Dialysis-Transplantation, Centre hospitalier universitaire de Liège, Liège, Belgium
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Columbia University Irving Medical Center · Columbia University
Affiliation as printed
Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
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Columbia University Irving Medical Center · Columbia University
Affiliation as printed
Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
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University of British Columbia
Affiliation as printed
Division of Nephrology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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Affiliation as printed
Kidney Transplant Department, Hospital Clínic i Provincial de Barcelona, Barcelona, Spain
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Affiliation as printed
Kidney Transplant Department, Hospital Clínic i Provincial de Barcelona, Barcelona, Spain
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Affiliation as printed
Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
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Centre Hospitalier Universitaire Henri-Mondor · Assistance Publique – Hôpitaux de Paris · Hôpitaux Universitaires Henri-Mondor
Affiliation as printed
Department of Nephrology, AP-HP Hôpital Henri Mondor, Créteil, Île de France, France
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Universitat Autònoma de Barcelona · Vall d'Hebron Hospital Universitari
Affiliation as printed
Nephrology Department, Hospital Vall d'Hebrón, Autonomous University of Barcelona, Barcelona, Spain
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Hôpital Necker-Enfants Malades · Assistance Publique – Hôpitaux de Paris
Affiliation as printed
Department of Pathology, Necker-Enfants Malades Hospital, Assistance Publique - Hôpitaux de Paris, Paris, France
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Hôpital Necker-Enfants Malades · Inserm · Université Paris Cité · Assistance Publique – Hôpitaux de Paris · Paris Cardiovascular Research Center
Affiliation as printed
Department of Pathology, Necker-Enfants Malades Hospital, Assistance Publique - Hôpitaux de Paris, Paris, France
Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration, F-75015, Paris, France
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Affiliation as printed
Faculty of Medicine & Dentistry - Laboratory Medicine & Pathology Dept, University of Alberta, Edmonton, AB, Canada
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Affiliation as printed
Faculty of Medicine & Dentistry - Laboratory Medicine & Pathology Dept, University of Alberta, Edmonton, AB, Canada
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Affiliation as printed
Faculty of Medicine & Dentistry - Laboratory Medicine & Pathology Dept, University of Alberta, Edmonton, AB, Canada
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Universitat Autònoma de Barcelona · Vall d'Hebron Hospital Universitari
Affiliation as printed
Nephrology Department, Hospital Vall d'Hebrón, Autonomous University of Barcelona, Barcelona, Spain
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University Hospital Centre Zagreb
Affiliation as printed
Department of nephrology, arterial hypertension, dialysis and transplantation, University Hospital Centre Zagreb, Zagreb, Croatia
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University Hospital Centre Zagreb
Affiliation as printed
Department of nephrology, arterial hypertension, dialysis and transplantation, University Hospital Centre Zagreb, Zagreb, Croatia
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Universitätsklinikum Aachen · RWTH Aachen University
Affiliation as printed
Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany
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Affiliation as printed
Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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Affiliation as printed
Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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Royal Adelaide Hospital · The University of Adelaide
Affiliation as printed
Department of Renal and Transplantation, University of Adelaide, Royal Adelaide Hospital Campus, Adelaide, SA, Australia
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Hôpital Necker-Enfants Malades · Inserm · Université Paris Cité · Assistance Publique – Hôpitaux de Paris · Paris Cardiovascular Research Center
Affiliation as printed
Department of Kidney Transplantation, Necker-Enfants Malades Hospital, Assistance Publique - Hôpitaux de Paris, Paris, France
Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration, F-75015, Paris, France
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Inserm · Université Paris Cité · Paris Cardiovascular Research Center · University of Pennsylvania
Affiliation as printed
Renal-Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadephia, PA, USA
Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration, F-75015, Paris, France
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Inserm · Université Paris Cité · Assistance Publique – Hôpitaux de Paris · Paris Cardiovascular Research Center · Hôpital Saint-Louis
Affiliation as printed
Kidney Transplant Department, Saint-Louis Hospital, Assistance Publique - Hôpitaux de Paris, Paris, France
Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration, F-75015, Paris, France
Kidney Transplant Department, Saint-Louis Hospital, Assistance Publique – Hôpitaux de Paris, Paris, France
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Hôpital Necker-Enfants Malades · Inserm · Université Paris Cité · Assistance Publique – Hôpitaux de Paris · Paris Cardiovascular Research Center
Affiliation as printed
Department of Kidney Transplantation, Necker-Enfants Malades Hospital, Assistance Publique - Hôpitaux de Paris, Paris, France
Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration, F-75015, Paris, France
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Alexandre Loupy corresponding
Hôpital Necker-Enfants Malades · Inserm · Université Paris Cité · Assistance Publique – Hôpitaux de Paris · Paris Cardiovascular Research Center
Affiliation as printed
Department of Kidney Transplantation, Necker-Enfants Malades Hospital, Assistance Publique - Hôpitaux de Paris, Paris, France. alexandre.loupy@inserm.fr
Université Paris Cité, INSERM U970 PARCC, Paris Institute for Transplantation and Organ Regeneration, F-75015, Paris, France. alexandre.loupy@inserm.fr
Department of Kidney Transplantation, Necker-Enfants Malades Hospital, Assistance Publique - Hôpitaux de Paris, Paris, France
Cited by 40 stored of 40
Cited by patents worldwide 1 (Lens.org)
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Method for evaluating organ histological data and associated deviceCN115989551A 2023-04-18 Pending