Self-supervised deep learning for pan-cancer mutation prediction from histopathology

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract The histopathological phenotype of tumors reflects the underlying genetic makeup. Deep learning can predict genetic alterations from tissue morphology, but it is unclear how well these predictions generalize to external datasets. Here, we present a deep learning pipeline based on self-supervised feature extraction which achieves a robust predictability of genetic alterations in two large multicentric datasets of seven tumor types.

Authors 11

1. Oliver Lester Saldanha Aachen Department of Medicine III

   Universitätsklinikum Aachen · Else Kröner Fresenius Center for Digital Health · Technische Universität Dresden · RWTH Aachen University

   Affiliation as printed

   Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany

   Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany

2. Chiara Maria Lavinia Loeffler Aachen Department of Medicine III

   Universitätsklinikum Aachen · Else Kröner Fresenius Center for Digital Health · Technische Universität Dresden · RWTH Aachen University

   Affiliation as printed

   Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany

   Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany

3. Jan Niehues Aachen Department of Medicine III

   Universitätsklinikum Aachen · Else Kröner Fresenius Center for Digital Health · Technische Universität Dresden · RWTH Aachen University

   Affiliation as printed

   Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany

   Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany

4. Marko van Treeck Aachen Department of Medicine III

   Universitätsklinikum Aachen · Else Kröner Fresenius Center for Digital Health · Technische Universität Dresden · RWTH Aachen University

   Affiliation as printed

   Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany

   Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany

5. Tobias Paul Seraphin

   Düsseldorf University Hospital · Heinrich Heine University Düsseldorf

   Affiliation as printed

   Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, Medical Faculty at Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany.t

6. Katherine Jane Hewitt Aachen Department of Medicine III

   Universitätsklinikum Aachen · Else Kröner Fresenius Center for Digital Health · Technische Universität Dresden · RWTH Aachen University

   Affiliation as printed

   Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany

   Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany

7. Didem Çifçi Aachen Department of Medicine III

   Universitätsklinikum Aachen · Else Kröner Fresenius Center for Digital Health · Technische Universität Dresden · RWTH Aachen University

   Affiliation as printed

   Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany

   Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany

8. Gregory Patrick Veldhuizen Aachen Department of Medicine III

   Universitätsklinikum Aachen · Else Kröner Fresenius Center for Digital Health · Technische Universität Dresden · RWTH Aachen University

   Affiliation as printed

   Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany

   Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany

9. Siddhi Ramesh

   University of Chicago

   Affiliation as printed

   Pritzker School of Medicine, University of Chicago, Chicago, IL, USA

10. Alexander T. Pearson

    University of Chicago · University of Chicago Medicine Comprehensive Cancer Center

    Affiliation as printed

    Biological Sciences Division, University of Chicago, Chicago, IL, USA

    University of Chicago Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA

11. Jakob Nikolas Kather corresponding Aachen Department of Medicine III

    University of Leeds · University Hospital Heidelberg · National Center for Tumor Diseases · Universitätsklinikum Aachen · University Hospital Carl Gustav Carus · Else Kröner Fresenius Center for Digital Health · Technische Universität Dresden · RWTH Aachen University

    Affiliation as printed

    Department of Medicine 1, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany

    Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany

    Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany

    Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany

    Pathology & Data Analytics, Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, United Kingdom

    Pathology & Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom