Sample Information

  ID Sentrix ID Array type
RD-19-410 203282450137_R07C01 IlluminaHumanMethylationEPIC

Brain Tumor Methylation Classifier

Methylation Family Scores

Family Score Methylation Family
0.6923 MTGF_GBM
0.0733 MTGF_PLEX_T
0.0183 MTGF_IDH_GLM
0.0181 MTGF_MB_G3G4
0.0127 MNG

Methylation Class Scores

Class Score Methylation Class
0.3963 GBM, RTK I
0.2864 GBM, RTK II
0.0652 PLEX, PED B
0.0127 MNG
0.0121 MB, SHH CHL AD

Methylation Class Description

The methylation class “glioblastoma, IDH wildtype, subclass RTK I” is comprised of tumors with a histological diagnosis of glioblastoma, IDH wildtype. The tumors are located in the cerebral hemispheres. Median age is 64 years (range 29 to 84). Recurrent chromosomal alterations are gain of chromosome 7 with or without EGFR amplification (>80%), loss of 9p21 (CDKN2A/B; >50%) and chromosome 10 loss (>70%). Amplifications of the PDGFRA oncogene are enriched in this class (present in 20-30% of cases). Expression profiles often resemble the ‘Proneural’ subgroup according to the TCGA classification.

TSNE Clustering

Copy Number Variation Profile

Depiction of chromosome 1 to 22 (and X/Y if automatic prediction was successful). Gains/amplifications represent positive, losses negative deviations from the baseline. 29 brain tumor relevant gene regions are highlighted for easier assessment. (see Hovestadt & Zapatka, http://www.bioconductor.org/packages/devel/bioc/html/conumee.html)

MGMT Prediction

Status Estimated CI_Lower CI_Upper Cutoff
methylated 0.9922628 0.7251554 0.9998396 0.3582

see: Pierre Bady, Davide Sciuscio, Annie-Claire Diserens et al. MGMT methylation analysis of glioblastoma on the Infinium methylation BeadChip identifies two distinct CpG regions associated with gene silencing and outcome, yielding a prediction model for comparisons across datasets, tumor grades, and CIMP-status. Acta Neuropathologica, p.547-560, Number 4, 2012.

Raw and Calibrated Classification Scores

Quality Control

Reference

DNA methylation-based classification of central nervous system tumours

David Capper, David T. W. Jones, Martin Sill, Volker Hovestadt, Daniel Schrimpf, Dominik Sturm, Christian Koelsche, Felix Sahm, Lukas Chavez, David E. Reuss, Annekathrin Kratz, Annika K. Wefers, Kristin Huang, Kristian W. Pajtler, Leonille Schweizer, Damian Stichel, Adriana Olar, Nils W. Engel, Kerstin Lindenberg, Patrick N. Harter, Anne K. Braczynski, Karl H. Plate, Hildegard Dohmen, Boyan K. Garvalov, Roland Coras, Annett Hölsken, Ekkehard Hewer, Melanie Bewerunge-Hudler, Matthias Schick, Roger Fischer, Rudi Beschorner, Jens Schittenhelm, Ori Staszewski, Khalida Wani, Pascale Varlet, Melanie Pages, Petra Temming, Dietmar Lohmann, Florian Selt, Hendrik Witt, Till Milde, Olaf Witt, Eleonora Aronica, Felice Giangaspero, Elisabeth Rushing, Wolfram Scheurlen, Christoph Geisenberger, Fausto J. Rodriguez, Albert Becker, Matthias Preusser, Christine Haberler, Rolf Bjerkvig, Jane Cryan, Michael Farrell, Martina Deckert, Jürgen Hench, Stephan Frank, Jonathan Serrano, Kasthuri Kannan, Aristotelis Tsirigos, Wolfgang Brück, Silvia Hofer, Stefanie Brehmer, Marcel Seiz-Rosenhagen, Daniel Hänggi, Volkmar Hans, Stephanie Rozsnoki, Jordan R. Hansford, Patricia Kohlhof, Bjarne W. Kristensen, Matt Lechner, Beatriz Lopes, Christian Mawrin, Ralf Ketter, Andreas Kulozik, Ziad Khatib, Frank Heppner, Arend Koch, Anne Jouvet, Catherine Keohane, Helmut Mühleisen, Wolf Mueller, Ute Pohl, Marco Prinz, Axel Benner, Marc Zapatka, Nicholas G. Gottardo, Pablo Hernáiz Driever, Christof M. Kramm, Hermann L. Müller, Stefan Rutkowski, Katja von Hoff, Michael C. Frühwald, Astrid Gnekow, Gudrun Fleischhack, Stephan Tippelt, Gabriele Calaminus, Camelia-Maria Monoranu, Arie Perry, Chris Jones, Thomas S. Jacques, Bernhard Radlwimmer, Marco Gessi, Torsten Pietsch, Johannes Schramm, Gabriele Schackert, Manfred Westphal, Guido Reifenberger, Pieter Wesseling, Michael Weller, Vincent Peter Collins, Ingmar Blümcke, Martin Bendszus, Jürgen Debus, Annie Huang, Nada Jabado, Paul A. Northcott, Werner Paulus, Amar Gajjar, Giles W. Robinson, Michael D. Taylor, Zane Jaunmuktane, Marina Ryzhova, Michael Platten, Andreas Unterberg, Wolfgang Wick, Matthias A. Karajannis, Michel Mittelbronn, Till Acker, Christian Hartmann, Kenneth Aldape, Ulrich Schüller, Rolf Buslei, Peter Lichter, Marcel Kool, Christel Herold-Mende, David W. Ellison, Martin Hasselblatt, Matija Snuderl, Sebastian Brandner, Andrey Korshunov, Andreas von Deimling & Stefan M. Pfister

This result alone cannot be used for diagnosis of cancer and has to be interpreted in the context of all available clinical and pathological information. This test was developed, and its performance characteristics determined, by the NYU Molecular Diagnostic Pathology. It has not been cleared or approved by the U.S. Food and Drug Administration (FDA). The FDA has determined that such clearance is not necessary.