7
views
0
recommends
+1 Recommend
1 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Sarcoma classification by DNA methylation profiling

      research-article
      1 , 2 , 3 , 1 , 2 , 2 , 4 , 5 , 1 , 2 , 1 , 2 , 4 , 6 , 4 , 6 , 7 , 8 , 8 , 9 , 8 , 8 , 4 , 6 , 7 , 4 , 6 , 7 , 4 , 6 , 7 , 4 , 7 , 10 , 4 , 7 , 10 , 4 , 6 , 7 , 4 , 5 , 7 , 1 , 2 , 1 , 2 , 1 , 2 , 2 , 1 , 2 , 1 , 2 , 2 , 1 , 2 , 11 , 12 , 3 , 3 , 13 , 13 , 4 , 7 , 10 , 4 , 7 , 10 , 4 , 7 , 4 , 5 , 14 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 21 , 22 , 23 , 24 , 21 , 22 , 23 , 24 , 25 , 26 , 26 , 26 , 27 , 28 , 29 , 28 , 30 , 31 , 32 , 32 , 33 , 33 , 34 , 35 , 36 , 37 , 36 , 38 , 39 , 40 , 41 , 41 , 42 , 43 , 44 , 45 , 45 , 45 , 46 , 47 , 48 , 49 , 50 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 59 , 60 , 61 , 3 , 3 , 62 , 63 , 64 , 65 , 66 , 64 , 65 , 66 , 67 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 76 , 77 , 76 , 78 , 79 , 80 , 81 , 82 , 83 , 84 , 85 , 86 , 87 , 88 , 3 , 89 , 4 , 6 , 8 , 4 , 5 , 7 , 1 , 2 ,
      Nature Communications
      Nature Publishing Group UK
      Sarcoma, Computational biology and bioinformatics, Classification and taxonomy, Databases

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Sarcomas are malignant soft tissue and bone tumours affecting adults, adolescents and children. They represent a morphologically heterogeneous class of tumours and some entities lack defining histopathological features. Therefore, the diagnosis of sarcomas is burdened with a high inter-observer variability and misclassification rate. Here, we demonstrate classification of soft tissue and bone tumours using a machine learning classifier algorithm based on array-generated DNA methylation data. This sarcoma classifier is trained using a dataset of 1077 methylation profiles from comprehensively pre-characterized cases comprising 62 tumour methylation classes constituting a broad range of soft tissue and bone sarcoma subtypes across the entire age spectrum. The performance is validated in a cohort of 428 sarcomatous tumours, of which 322 cases were classified by the sarcoma classifier. Our results demonstrate the potential of the DNA methylation-based sarcoma classification for research and future diagnostic applications.

          Abstract

          Sarcomas are morphologically heterogeneous tumours rendering their classification challenging. Here the authors developed a classifier using DNA methylation data from several soft tissue and bone sarcoma subtypes, which has the potential to improve classification for research and clinical purposes.

          Related collections

          Most cited references42

          • Record: found
          • Abstract: not found
          • Article: not found

          Random Forests

            Bookmark
            • Record: found
            • Abstract: not found
            • Article: not found

            Regularization Paths for Generalized Linear Models via Coordinate Descent

              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              High-performance medicine: the convergence of human and artificial intelligence

              Eric Topol (2019)
              The use of artificial intelligence, and the deep-learning subtype in particular, has been enabled by the use of labeled big data, along with markedly enhanced computing power and cloud storage, across all sectors. In medicine, this is beginning to have an impact at three levels: for clinicians, predominantly via rapid, accurate image interpretation; for health systems, by improving workflow and the potential for reducing medical errors; and for patients, by enabling them to process their own data to promote health. The current limitations, including bias, privacy and security, and lack of transparency, along with the future directions of these applications will be discussed in this article. Over time, marked improvements in accuracy, productivity, and workflow will likely be actualized, but whether that will be used to improve the patient-doctor relationship or facilitate its erosion remains to be seen.
                Bookmark

                Author and article information

                Contributors
                andreas.vondeimling@med.uni-heidelberg.de
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                21 January 2021
                21 January 2021
                2021
                : 12
                Affiliations
                [1 ]GRID grid.5253.1, ISNI 0000 0001 0328 4908, Department of Neuropathology, , Institute of Pathology, Heidelberg University Hospital, ; Heidelberg, Germany
                [2 ]GRID grid.7497.d, ISNI 0000 0004 0492 0584, Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), , German Cancer Research Center (DKFZ), ; Heidelberg, Germany
                [3 ]GRID grid.5253.1, ISNI 0000 0001 0328 4908, Department of General Pathology, , Institute of Pathology, Heidelberg University Hospital, ; Heidelberg, Germany
                [4 ]Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
                [5 ]GRID grid.7497.d, ISNI 0000 0004 0492 0584, Division of Pediatric Neurooncology, , German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), ; Heidelberg, Germany
                [6 ]GRID grid.7497.d, ISNI 0000 0004 0492 0584, Pediatric Glioma Research Group, , German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), ; Heidelberg, Germany
                [7 ]GRID grid.5253.1, ISNI 0000 0001 0328 4908, Department of Pediatric Oncology, Hematology and Immunology, , Heidelberg University Hospital, ; Heidelberg, Germany
                [8 ]GRID grid.5253.1, ISNI 0000 0001 0328 4908, Division of Translational Medical Oncology, , National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), ; Heidelberg, Germany
                [9 ]GRID grid.7497.d, ISNI 0000 0004 0492 0584, Heidelberg Center for Personalized Oncology (HIPO), , German Cancer Research Center (DKFZ), ; Heidelberg, Germany
                [10 ]GRID grid.7497.d, ISNI 0000 0004 0492 0584, Clinical Cooperation Unit Pediatric Oncology, German Cancer Consortium (DKTK), , German Cancer Research Center (DKFZ), ; Heidelberg, Germany
                [11 ]GRID grid.66859.34, Broad Institute of MIT and Harvard, ; Cambridge, MA USA
                [12 ]GRID grid.32224.35, ISNI 0000 0004 0386 9924, Department of Pathology and Center for Cancer Research, , Massachusetts General Hospital and Harvard Medical School, ; Boston, MA USA
                [13 ]GRID grid.7497.d, ISNI 0000 0004 0492 0584, Genomics and Proteomics Core Facility, , German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), ; Heidelberg, Germany
                [14 ]GRID grid.5252.0, ISNI 0000 0004 1936 973X, Max-Eder Research Group for Pediatric Sarcoma Biology, , Institute of Pathology, Faculty of Medicine, LMU Munich, ; Munich, Germany
                [15 ]GRID grid.5252.0, ISNI 0000 0004 1936 973X, Institute of Pathology, Faculty of Medicine, LMU Munich, ; Munich, Germany
                [16 ]GRID grid.5253.1, ISNI 0000 0001 0328 4908, Neurology Clinic and National Center for Tumor Diseases, , University Hospital Heidelberg, ; Heidelberg, Germany
                [17 ]GRID grid.7497.d, ISNI 0000 0004 0492 0584, Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), , German Cancer Research Center (DKFZ), ; Heidelberg, Germany
                [18 ]GRID grid.7700.0, ISNI 0000 0001 2190 4373, Department of Neurology, , Mannheim University Medical Center, University of Heidelberg, ; Mannheim, Germany
                [19 ]GRID grid.7497.d, ISNI 0000 0004 0492 0584, Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Consortium (DKTK), , German Cancer Research Center (DKFZ), ; Heidelberg, Germany
                [20 ]GRID grid.5253.1, ISNI 0000 0001 0328 4908, Department of Neurosurgery, , Heidelberg University Hospital, ; Heidelberg, Germany
                [21 ]GRID grid.5253.1, ISNI 0000 0001 0328 4908, Department of Radiation Oncology, , Heidelberg University Hospital, ; Heidelberg, Germany
                [22 ]GRID grid.488831.e, Heidelberg Institute of Radiation Oncology (HIRO), , National Center for Radiation Research in Oncology (NCRO), ; Heidelberg, Germany
                [23 ]Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg, Germany
                [24 ]GRID grid.5253.1, ISNI 0000 0001 0328 4908, Translational Radiation Oncology, German Cancer Consortium (DKTK), , National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), ; Heidelberg, Germany
                [25 ]GRID grid.5253.1, ISNI 0000 0001 0328 4908, Department of Orthopaedics, Trauma Surgery and Paraplegiology, , Heidelberg University Hospital, ; Heidelberg, Germany
                [26 ]GRID grid.16149.3b, ISNI 0000 0004 0551 4246, Institute of Neuropathology, , University Hospital Münster, ; Münster, Germany
                [27 ]GRID grid.10423.34, ISNI 0000 0000 9529 9877, Department of Neuropathology, , Institute of Pathology, Hannover Medical School (MHH), ; Hannover, Germany
                [28 ]GRID grid.5963.9, Institute of Neuropathology, Faculty of Medicine, , University of Freiburg, ; Freiburg, Germany
                [29 ]GRID grid.5963.9, Berta-Ottenstein-Programme for Clinician Scientists, Faculty of Medicine, , University of Freiburg, ; Freiburg, Germany
                [30 ]GRID grid.5963.9, Signalling Research Centers BIOSS and CIBSS, University of Freiburg, ; Freiburg, Germany
                [31 ]GRID grid.5963.9, Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, , University of Freiburg, ; Freiburg, Germany
                [32 ]GRID grid.410567.1, Department of Neuropathology, Institute of Pathology, , Basel University Hospital, ; Basel, Switzerland
                [33 ]GRID grid.10417.33, ISNI 0000 0004 0444 9382, Department of Medical Oncology, , Radboud University Medical Center, ; Nijmegen, The Netherlands
                [34 ]Dermatopathology Bodensee, Friedrichshafen, Germany
                [35 ]Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
                [36 ]GRID grid.411109.c, ISNI 0000 0000 9542 1158, Department of Pathology, Institute of Biomedicine of Sevilla (IBiS), , Virgen del Rocio University Hospital, CSIC/University of Sevilla/CIBERONC, ; Seville, Spain
                [37 ]GRID grid.9224.d, ISNI 0000 0001 2168 1229, Department of Normal and Pathological Cytology and Histology, , School of Medicine. University of Seville, ; Seville, Spain
                [38 ]GRID grid.5924.a, ISNI 0000000419370271, Department of Pathological Anatomy, Clínica Universidad de Navarra, , University of Navarra, ; Pamplona, Spain
                [39 ]GRID grid.414963.d, ISNI 0000 0000 8958 3388, Department of Pathology and Laboratory Medicine, , KK Women’s and Children’s Hospital, ; Singapore, Republic of Singapore
                [40 ]GRID grid.276809.2, ISNI 0000 0004 0636 696X, Department of Neurosurgery, , National Neuroscience Institute, ; Singapore, Republic of Singapore
                [41 ]GRID grid.419123.c, ISNI 0000 0004 0621 5272, National Center of Pathology (NCP), , Laboratoire National de Santé (LNS), ; Dudelange, Luxembourg
                [42 ]Luxembourg Center of Neuropathology (LCNP), Luxembourg, Luxembourg
                [43 ]GRID grid.16008.3f, ISNI 0000 0001 2295 9843, Luxembourg Centre for Systems Biomedicine (LCSB), , University of Luxembourg, ; Luxembourg, Luxembourg
                [44 ]GRID grid.451012.3, ISNI 0000 0004 0621 531X, Department of Oncology (DONC), , Luxembourg Institute of Health (LIH), ; Luxembourg, Luxembourg
                [45 ]GRID grid.13648.38, ISNI 0000 0001 2180 3484, Department of Pediatric Hematology and Oncology, , University Medical Center Hamburg-Eppendorf, ; Hamburg, Germany
                [46 ]GRID grid.13648.38, ISNI 0000 0001 2180 3484, Institute of Neuropathology, , University Medical Center Hamburg-Eppendorf, ; Hamburg, Germany
                [47 ]GRID grid.470174.1, Research Institute Children’s Cancer Center Hamburg, ; Hamburg, Germany
                [48 ]GRID grid.13648.38, ISNI 0000 0001 2180 3484, Department of Neurology, , University Medical Center Hamburg-Eppendorf, ; Hamburg, Germany
                [49 ]GRID grid.411544.1, ISNI 0000 0001 0196 8249, Department of Neuropathology, Institute of Pathology and Neuropathology, , University Hospital of Tübingen, ; Tübingen, Germany
                [50 ]GRID grid.137628.9, ISNI 0000 0004 1936 8753, Department of Pathology, , New York University School of Medicine, ; New York, NY USA
                [51 ]GRID grid.411097.a, ISNI 0000 0000 8852 305X, Institute of Pathology, , Cologne University Hospital, ; Cologne, Germany
                [52 ]GRID grid.411088.4, ISNI 0000 0004 0578 8220, Department of Pediatric Hematology and Oncology, , University Children’s Hospital, ; Frankfurt/Main, Germany
                [53 ]GRID grid.419802.6, ISNI 0000 0001 0617 3250, Institute of Pathology, Sozialstiftung Bamberg, Klinikum am Bruderwald, ; Bamberg, Germany
                [54 ]GRID grid.8379.5, ISNI 0000 0001 1958 8658, Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Würzburg University, ; Würzburg, Germany
                [55 ]GRID grid.487647.e, Princess Máxima Center for Pediatric Oncology, ; Utrecht, The Netherlands
                [56 ]GRID grid.7177.6, ISNI 0000000084992262, Department of Pathology, , Amsterdam University Medical Centers/VUmc, ; Amsterdam, The Netherlands
                [57 ]GRID grid.508717.c, ISNI 0000 0004 0637 3764, Department of Pathology, , Erasmus MC Cancer Institute, ; Rotterdam, The Netherlands
                [58 ]GRID grid.83440.3b, ISNI 0000000121901201, Department of Neurodegeneration, Institute of Neurology, , University College London, ; London, UK
                [59 ]GRID grid.52996.31, ISNI 0000 0000 8937 2257, Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, , University College London Hospitals NHS Foundation Trust, ; London, UK
                [60 ]GRID grid.83440.3b, ISNI 0000000121901201, Department of Molecular Neuroscience, UCL Queen Square Institute of Neurology, , University College London, ; London, UK
                [61 ]GRID grid.83440.3b, ISNI 0000000121901201, Research Department of Pathology, , University College London, ; London, UK
                [62 ]GRID grid.7497.d, ISNI 0000 0004 0492 0584, Division of Applied Bioinformatics, German Cancer Consortium (DKTK), , German Cancer Research Center (DKFZ), ; Heidelberg, Germany
                [63 ]GRID grid.5253.1, ISNI 0000 0001 0328 4908, Translational and Functional Cancer Genomics, , National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), ; Heidelberg, Germany
                [64 ]Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), Dresden, Germany
                [65 ]GRID grid.4488.0, ISNI 0000 0001 2111 7257, Center for Personalized Oncology, , National Center for Tumor Diseases (NCT) Dresden and University Hospital Carl Gustav Carus Dresden at TU Dresden, ; Dresden, Germany
                [66 ]GRID grid.7497.d, ISNI 0000 0004 0492 0584, German Cancer Consortium (DKTK), ; Dresden, Germany
                [67 ]GRID grid.418284.3, ISNI 0000 0004 0427 2257, Sarcoma Research Group, Oncobell Program, , Bellvitge Biomedical Research Institute (IDIBELL), CIBERONC, ; Barcelona, Catalonia Spain
                [68 ]GRID grid.411160.3, ISNI 0000 0001 0663 8628, Department of Pediatric Onco-Hematology and Developmental Tumor Biology Laboratory, , Hospital Sant Joan de Déu, ; Barcelona, Catalonia Spain
                [69 ]GRID grid.413448.e, ISNI 0000 0000 9314 1427, Pediatric Solid Tumor Laboratory, , Human Genetic Department, Research Institute of Rare Diseases, Instituto de Salud Carlos III (ISCIII), ; Madrid, Spain
                [70 ]GRID grid.5841.8, ISNI 0000 0004 1937 0247, Medical Oncology Service, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), , University of Barcelona, ; Barcelona, Catalonia Spain
                [71 ]GRID grid.418284.3, ISNI 0000 0004 0427 2257, Cancer Epigenetics and Biology Program (PEBC), , Bellvitge Biomedical Research Institute (IDIBELL), ; Barcelona, Catalonia Spain
                [72 ]GRID grid.429289.c, Josep Carreras Leukaemia Research Institute (IJC), Badalona, ; Barcelona, Catalonia Spain
                [73 ]GRID grid.413448.e, ISNI 0000 0000 9314 1427, Centro de Investigacion Biomedica en Red Cancer (CIBERONC), ; Madrid, Spain
                [74 ]GRID grid.425902.8, ISNI 0000 0000 9601 989X, Institucio Catalana de Recerca i Estudis Avançats (ICREA), ; Barcelona, Catalonia Spain
                [75 ]GRID grid.5841.8, ISNI 0000 0004 1937 0247, Physiological Sciences Department, School of Medicine and Health Sciences, , University of Barcelona (UB), ; Barcelona, Catalonia Spain
                [76 ]GRID grid.51462.34, ISNI 0000 0001 2171 9952, Department of Pathology, , Memorial Sloan Kettering Cancer Center, ; New York, NY USA
                [77 ]GRID grid.16149.3b, ISNI 0000 0004 0551 4246, Gerhard Domagk Institute of Pathology, , University Hospital Münster, ; Münster, Germany
                [78 ]GRID grid.412945.f, ISNI 0000 0004 0467 5857, Department of Histopathology, , Royal National Orthopaedic Hospital NHS Trust, ; Stanmore, Middlesex UK
                [79 ]GRID grid.83440.3b, ISNI 0000000121901201, University College London Cancer Institute, ; London, UK
                [80 ]GRID grid.410718.b, ISNI 0000 0001 0262 7331, Pediatrics III Pediatric Hematology, Oncology, Immunology, Cardiology, Pulmonology, West German Cancer Center, , University Hospital Essen, ; Essen, Germany
                [81 ]GRID grid.5718.b, ISNI 0000 0001 2187 5445, International Ewing Sarcoma Study Group, German Cancer Consortium (DKTK), West German Cancer Center (WTZ), University Duisburg-Essen, ; Essen, Germany
                [82 ]GRID grid.7700.0, ISNI 0000 0001 2190 4373, Division of Surgical Oncology and Thoracic Surgery, Mannheim University Medical Center, , University of Heidelberg, ; Mannheim, Germany
                [83 ]GRID grid.410567.1, Bone Tumour Reference Centre at the Institute of Pathology, , University Hospital Basel and University of Basel, ; Basel, Switzerland
                [84 ]GRID grid.16149.3b, ISNI 0000 0004 0551 4246, Division of Translational Pathology, Gerhard Domagk Institute of Pathology, , University Hospital Münster, ; Münster, Germany
                [85 ]GRID grid.412468.d, ISNI 0000 0004 0646 2097, Department of Pediatric Pathology, , University Hospital of Schleswig-Holstein, ; Kiel, Germany
                [86 ]GRID grid.10417.33, ISNI 0000 0004 0444 9382, Department of Pathology, , Radboud University Medical Center, ; Nijmegen, The Netherlands
                [87 ]Institute of Pathology, SRH Poliklinik Gera GmbH, Gera, Germany
                [88 ]GRID grid.6363.0, ISNI 0000 0001 2218 4662, Institute of Pathology, ; Jena University Hospital Jena, Germany
                [89 ]GRID grid.6363.0, ISNI 0000 0001 2218 4662, Department of Neuropathology, , Charité Universitätsmedizin Berlin, ; Berlin, Germany
                Article
                20603
                10.1038/s41467-020-20603-4
                7819999
                33479225
                84e54f64-a565-460b-8fcb-bb00f49a0027
                © The Author(s) 2021

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                Funding
                Funded by: FundRef https://doi.org/10.13039/501100005972, Deutsche Krebshilfe (German Cancer Aid);
                Award ID: 70112499
                Award Recipient :
                Categories
                Article
                Custom metadata
                © The Author(s) 2021

                Uncategorized
                sarcoma,computational biology and bioinformatics,classification and taxonomy,databases

                Comments

                Comment on this article