Comparing Methylation-Based CNS Tumor Classification

To compare our methylation-based classification of CNS tumours with described methylation classes of brain tumours by the Cancer Genome Atlas (TCGA) project, we downloaded the pre-processed methylation dataset described in Ceccarelli et al. 2016¹⁸ including methylation data of 418 low grade glioma and 377 glioblastoma samples analysed by using the Illumina 450k array or 27k array platforms. To classify our samples according to the TCGA pan-glioma DNA methylation classification, we trained a Random Forest classifier on this dataset using the 1,300 CpG probe signature provided by the authors and using the default settings of the Random Forest algorithms implemented in the R package randomForest. The results of this classification for astrocytomas, oligodendrogliomas and glioblastomas are shown in Extended Data Figure 3d and are given on a case-by-case basis in Supplementary Table 2 and 4.

Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link: Access Free Full Text.

Capper D., Jones D.T., Sill M., Hovestadt V., Schrimpf D., Sturm D., Koelsche C., Sahm F., Chavez L., Reuss D.E., Kratz A., Wefers A.K., Huang K., Pajtler K.W., Schweizer L., Stichel D., Olar A., Engel N.W., Lindenberg K., Harter P.N., Braczynski A., Plate K.H., Dohmen H., Garvalov B.K., Coras R., Hölsken A., Hewer E., Bewerunge-Hudler M., Schick M., Fischer R., Beschorner R., Schittenhelm J., Staszewski O., Wani K., Varlet P., Pages M., Temming P., Lohmann D., Selt F., Witt H., Milde T., Witt O., Aronica E., Giangaspero F., Rushing E., Scheurlen W., Geisenberger C., Rodriguez F.J., Becker A., Preusser M., Haberler C., Bjerkvig R., Cryan J., Farrell M., Deckert M., Hench J., Frank S., Serrano J., Kannan K., Tsirigos A., Brück W., Hofer S., Brehmer S., Seiz-Rosenhagen M., Hänggi D., Hans V., Rozsnoki S., Hansford J.R., Kohlhof P., Kristensen B.W., Lechner M., Lopes B., Mawrin C., Ketter R., Kulozik A., Khatib Z., Heppner F., Koch A., Jouvet A., Keohane C., Mühleisen H., Mueller W., Pohl U., Prinz M., Benner A., Zapatka M., Gottardo N.G., Driever P.H., Kramm C.M., Müller H.L., Rutkowski S., von Hoff K., Frühwald M.C., Gnekow A., Fleischhack G., Tippelt S., Calaminus G., Monoranu C.M., Perry A., Jones C., Jacques T.S., Radlwimmer B., Gessi M., Pietsch T., Schramm J., Schackert G., Westphal M., Reifenberger G., Wesseling P., Weller M., Collins V.P., Blümcke I., Bendszus M., Debus J., Huang A., Jabado N., Northcott P.A., Paulus W., Gajjar A., Robinson G., Taylor M.D., Jaunmuktane Z., Ryzhova M., Platten M., Unterberg A., Wick W., Karajannis M.A., Mittelbronn M., Acker T., Hartmann C., Aldape K., Schüller U., Buslei R., Lichter P., Kool M., Herold-Mende C., Ellison D.W., Hasselblatt M., Snuderl M., Brandner S., Korshunov A., von Deimling A, & Pfister S.M. (2018). DNA methylation-based classification of central nervous system tumours. Nature, 555(7697), 469-474.

Publication 2018

Astrocytomas Cancer Cancer of the brain Cns tumours Dna methylation Genome Glioblastoma Glioblastomas Glioma Methylation Oligodendrogliomas Tumours

Corresponding Organization :

Other organizations : University Hospital Heidelberg, Heidelberg University, Hopp Children's Cancer Center Heidelberg, National Center for Tumor Diseases, German Cancer Research Center, Humboldt-Universität zu Berlin, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Medical University of South Carolina, University Cancer Center Hamburg, Universität Hamburg, University Medical Center Hamburg-Eppendorf, Goethe University Frankfurt, University of Giessen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsklinikum Erlangen, University of Bern, University Children's Hospital Tübingen, University of Freiburg, The University of Texas MD Anderson Cancer Center, Centre Hospitalier Sainte-Anne, Essen University Hospital, University of Duisburg-Essen, University of Amsterdam, Sapienza University of Rome, University Hospital of Zurich, Cnopf´sche Kinderklinik, Johns Hopkins Medicine, Johns Hopkins University, University of Bonn, Comprehensive Cancer Center Vienna, Medical University of Vienna, University of Bergen, Beaumont Hospital, University Hospital Cologne, University Hospital of Basel, NYU Langone Health, Universitätsmedizin Göttingen, Luzerner Kantonsspital, University Medical Centre Mannheim, Evangelisches Krankenhaus Bielefeld, University Hospital Münster, Royal Children's Hospital, University of Melbourne, Katharinenhospital, University of Southern Denmark, Odense University Hospital, Royal London Hospital, University College London, London Cancer, University of Virginia, Otto-von-Guericke University Magdeburg, Saarland University, Miami Children's Hospital, Hospices Civils de Lyon, Cork University Hospital, Klinikum Ludwigsburg, Leipzig University, Queen's Hospital, Princess Margaret Hospital for Children, Klinikum Oldenburg, University Hospital Augsburg, Comprehensive Cancer Center Mainfranken, University of Würzburg, University of California, San Francisco, Institute of Cancer Research, Great Ormond Street Hospital for Children NHS Foundation Trust, University Hospital Carl Gustav Carus, TU Dresden, Heinrich Heine University Düsseldorf, Princess Máxima Center, University Medical Center Utrecht, University of Zurich, University of Cambridge, University of Toronto, McGill University, St. Jude Children's Research Hospital, SickKids Foundation, Hospital for Sick Children, National Hospital for Neurology and Neurosurgery, Burdenko Neurosurgery Institute, Memorial Sloan Kettering Cancer Center, Medizinische Hochschule Hannover, Ludwig-Maximilians-Universität München

Top 5 similar protocols

Protocol cited in 47 other protocols

Variable analysis

independent variables

Methylation-based classification of CNS tumours

dependent variables

Comparison of methylation-based classification with described methylation classes of brain tumours by the Cancer Genome Atlas (TCGA) project

control variables

Pre-processed methylation dataset described in Ceccarelli et al. 2016 including methylation data of 418 low grade glioma and 377 glioblastoma samples analysed by using the Illumina 450k array or 27k array platforms
Random Forest classifier trained on the dataset using the 1,300 CpG probe signature provided by the authors and using the default settings of the Random Forest algorithms implemented in the R package randomForest

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!