Sample Information

  ID Sentrix ID Array type
RD-19-527 203550290019_R05C01 IlluminaHumanMethylationEPIC

Brain Tumor Methylation Classifier

Methylation Family Scores

Family Score Methylation Family
0.773 MTGF_GBM
0.0973 DMG, K27
0.0285 MTGF_PA
0.0065 MTGF_IDH_GLM
0.0062 MTGF_PLEX_T

Methylation Class Scores

Class Score Methylation Class
0.7256 GBM, MID
0.0973 DMG, K27
0.0429 GBM, RTK I
0.0242 LGG, PA PF
0.0052 CNS NB, FOXR2

Methylation Class Description

The methylation class “glioblastoma, IDH wildtype, subclass midline” is comprised of tumors with a histological diagnosis of glioblastoma, located in midline structures (thalamus, cerebellum, spine). Median age is 13 years (range 2 to 79). Tumors of this class share epigenetic similarities with histone 3 K27M-mutated tumors, but lack this mutation. Mutations of FGFR1 are relatively common, particularly in thalamic tumors. Copy number changes are numerous, the most frequent changes being gain/amplification of PDGFR-alpha and loss of CDKN2A/B (both in over 70% of cases).

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
unmethylated 0.0102351 0.0011153 0.0873987 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.