Predicting and elucidating the etiology of fatty liver disease: A machine learning modeling and validation study in the IMI DIRECT cohorts.

Journal: PLoS medicine
Published Date: Jun 19, 2020

Abstract

BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is highly prevalent and causes serious health complications in individuals with and without type 2 diabetes (T2D). Early diagnosis of NAFLD is important, as this can help prevent irreversible damage to the liver and, ultimately, hepatocellular carcinomas. We sought to expand etiological understanding and develop a diagnostic tool for NAFLD using machine learning.

Authors

  • Naeimeh Atabaki-Pasdar
    Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden.
  • Mattias Ohlsson
    Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
  • Ana Viñuela
    Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
  • Francesca Frau
    Sanofi-Aventis Deutschland, Frankfurt am Main, Germany.
  • Hugo Pomares-Millan
    Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden.
  • Mark Haid
    Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, Neuherberg, Germany.
  • Angus G Jones
    Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, United Kingdom.
  • E Louise Thomas
    Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, United Kingdom.
  • Robert W Koivula
    Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden.
  • Azra Kurbasic
    Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden.
  • Pascal M Mutie
    Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden.
  • Hugo Fitipaldi
    Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden.
  • Juan Fernandez
    Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden.
  • Adem Y Dawed
    Division of Population Health and Genomics, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom.
  • Giuseppe N Giordano
    Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden.
  • Ian M Forgie
    Division of Population Health and Genomics, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom.
  • Timothy J McDonald
    Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, United Kingdom.
  • Femke Rutters
    Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam UMC, Amsterdam, the Netherlands.
  • Henna Cederberg
    Department of Endocrinology, Abdominal Centre, Helsinki University Hospital, Helsinki, Finland.
  • Elizaveta Chabanova
    Department of Diagnostic Radiology, Copenhagen University Hospital Herlev Gentofte, Herlev, Denmark.
  • Matilda Dale
    Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden.
  • Federico De Masi
    Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.
  • Cecilia Engel Thomas
    Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden.
  • Kristine H Allin
    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
  • Tue H Hansen
    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
  • Alison Heggie
    Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom.
  • Mun-Gwan Hong
    Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden.
  • Petra J M Elders
    Department of General Practice, Amsterdam Public Health Research Institute, Amsterdam UMC, Amsterdam, the Netherlands.
  • Gwen Kennedy
    Immunoassay Biomarker Core Laboratory, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom.
  • Tarja Kokkola
    Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.
  • Helle Krogh Pedersen
    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
  • Anubha Mahajan
    Wellcome Centre for Human Genetics, Oxford, United Kingdom.
  • Donna McEvoy
    Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom.
  • Francois Pattou
    University of Lille, Inserm, UMR 1190, Translational Research in Diabetes, Department of Endocrine Surgery, CHU Lille, Lille, France.
  • Violeta Raverdy
    University of Lille, Inserm, UMR 1190, Translational Research in Diabetes, Department of Endocrine Surgery, CHU Lille, Lille, France.
  • Ragna S Häussler
    Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden.
  • Sapna Sharma
    German Center for Diabetes Research, Neuherberg, Germany.
  • Henrik S Thomsen
    Department of Radiology, Herlev Gentofte University Hospital, Herlev, Denmark.
  • Jagadish Vangipurapu
    Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.
  • Henrik Vestergaard
    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
  • Leen M 't Hart
    Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam UMC, Amsterdam, the Netherlands.
  • Jerzy Adamski
    Research Unit Molecular Endocrinology and Metabolism, Genome Analysis Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan 85350, Germany; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore.
  • Petra B Musholt
    Diabetes Division, Research and Development, Sanofi, Frankfurt, Germany.
  • Soren Brage
    MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom.
  • Søren Brunak
    NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
  • Emmanouil Dermitzakis
    Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
  • Gary Frost
    Section for Nutrition Research, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom.
  • Torben Hansen
    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
  • Markku Laakso
    Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.
  • Oluf Pedersen
    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
  • Martin Ridderstråle
    Department of Endocrinology, Clinical Obesity Research, Skåne University Hospital 214 28, Malmö, Sweden.
  • Hartmut Ruetten
    Sanofi-Aventis Deutschland, Frankfurt am Main, Germany.
  • Andrew T Hattersley
    Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, United Kingdom.
  • Mark Walker
    Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.
  • Joline W J Beulens
    Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam UMC, Amsterdam, the Netherlands.
  • Andrea Mari
  • Jochen M Schwenk
    Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden.
  • Ramneek Gupta
    Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.
  • Mark I McCarthy
    Wellcome Centre for Human Genetics, Oxford, United Kingdom.
  • Ewan R Pearson
    Division of Population Health and Genomics, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom.
  • Jimmy D Bell
    Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, United Kingdom.
  • Imre Pavo
    Eli Lilly Regional Operations, Vienna, Austria.
  • Paul W Franks
    Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden.

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