DNA methylation profiling was performed as described previously6 (link),7 (link). DNA was extracted in the same manner as described for WGS using 500ng as input material for fresh frozen tissue and 250ng input material for FFPE tissue. Array data was created using the Infinium HumanMethylation450 BeadChip array (450k array) according to the manufacturer’s instructions (Illumina, San Diego, USA) at the DKFZ Genomics and Proteomics Core Facility (Heidelberg, Germany). For a subset of samples (described in Supplementary Table 1) Methylation BeadChip (EPIC) arrays were used. CpG probes that were used for the analysis were filtered based on presence of a common SNP within five bases of the probe, reads not mapping uniquely to the reference genome, probes mapping to the X and Y chromosome and reads not overlapping between 450K arrays and EPIC arrays. Clustering was performed after correction of samples for the origin of the DNA (FFPE or Fresh frozen) using Surrogate Variable Analysis (sva)40 (link) and only the 10000 most variable probes based on the full dataset after correction were selected for clustering. Distance was calculated using 1-Pearson correlation and linkage was calculated using average as measure. Subsequently, t-stochastic neighbourhood embedding (t-SNE) analysis using RTSNE (v0.13) was applied to generate the figures41 .
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Lambo S., Gröbner S.N., Rausch T., Waszak S.M., Schmidt C., Gorthi A., Romero C., Mauermann M., Brabetz S., Krausert S., Buchhalter I., Koster J., Zwijnenburg D.A., Sill M., Hübner J.M., Mack N., Schwalm B., Ryzhova M., Hovestadt V., Papillon-Cavanagh S., Chan J.A., Landgraf P., Ho B., Milde T., Witt O., Ecker J., Sahm F., Sumerauer D., Ellison D.W., Orr B.A., Darabi A., Haberler C., Figarella-Branger D., Wesseling P., Schittenhelm J., Remke M., Taylor M.D., Gil-da-Costa M.J., Łastowska M., Grajkowska W., Hasselblatt M., Hauser P., Pietsch T., Uro-Coste E., Bourdeaut F., Masliah-Planchon J., Rigau V., Alexandrescu S., Wolf S., Li X.N., Schüller U., Snuderl M., Karajannis M.A., Giangaspero F., Jabado N., von Deimling A., Jones D.T., Korbel J.O., von Hoff K., Lichter P., Huang A., Bishop A., Pfister S.M., Korshunov A, & Kool M. (2019). The Molecular Landscape of ETMR at Diagnosis and Relapse. Nature, 576(7786), 274-280.
Corresponding Organization : Hopp Children's Cancer Center Heidelberg
Other organizations :
European Molecular Biology Laboratory, The University of Texas Health Science Center at San Antonio, The University of Texas at San Antonio, Academic Medical Center, Burdenko Neurosurgery Institute, McGill University, University of Calgary, University Hospital Cologne, University of Cologne, Hospital for Sick Children, University Hospital Heidelberg, University Hospital in Motol, St. Jude Children's Research Hospital, Lund University, Medical University of Vienna, Centre National de la Recherche Scientifique, Assistance Publique Hôpitaux de Marseille, Institut de Neurophysiopathologie, Aix-Marseille Université, Princess Máxima Center, Amsterdam University Medical Centers, University of Toronto, Düsseldorf University Hospital, Heinrich Heine University Düsseldorf, Hospital de São João, Children's Memorial Health Institute, University Hospital Münster, Semmelweis University, University of Bonn, Université de Toulouse, Centre de Recherche en Cancérologie de Toulouse, Inserm, Institut Curie, Université Paris Sciences et Lettres, Université de Montpellier, Institute for Neurosciences of Montpellier, Centre Hospitalier Universitaire de Montpellier, Harvard University, Boston Children's Hospital, Lurie Children's Hospital, Children's Cancer Center, Northwestern University, Baylor College of Medicine, Universität Hamburg, University Medical Center Hamburg-Eppendorf, Kinderkrebs-Zentrum Hamburg, NYU Langone Health, Center for Cancer and Blood Disorders, Children's Center, Istituto Neurologico Mediterraneo, Sapienza University of Rome, Charité - Universitätsmedizin Berlin
Probes filtering criteria (presence of common SNP, reads not mapping uniquely, probes mapping to X and Y chromosome, reads not overlapping between 450K arrays and EPIC arrays)
controls
Positive control: Not specified
Negative control: Not specified
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