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1. Additional file 3 of Pleomorphic xanthoastrocytoma is a heterogeneous entity with pTERT mutations prognosticating shorter survival

Author

Ebrahimi, Azadeh, Korshunov, Andrey, Reifenberger, Guido, Capper, David, Felsberg, Joerg, Trisolini, Elena, Pollo, Bianca, Calatozzolo, Chiara, Prinz, Marco, Staszewski, Ori, Schweizer, Leonille, Schittenhelm, Jens, Harter, Patrick N., Paulus, Werner, Thomas, Christian, Kohlhof-Meinecke, Patricia, Seiz-Rosenhagen, Marcel, Milde, Till, Casalini, Bel��n M., Suwala, Abigail, Wefers, Annika K., Reinhardt, Annekathrin, Sievers, Philipp, Kramm, Christof M., Etminam, Nima, Unterberg, Andreas, Wick, Wolfgang, Herold-Mende, Christel, Sturm, Dominik, Pfister, Stefan M., Sill, Martin, Jones, David T. W., Schrimpf, Daniel, Reuss, David E., Aldape, Ken, Abdullaev, Zied, Sahm, Felix, von Deimling, Andreas, and Stichel, Damian

Abstract

Additional file 3. Composition of cohorts mcPXA and histPXA in numbers.

Published
2022
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2. Additional file 5 of Pleomorphic xanthoastrocytoma is a heterogeneous entity with pTERT mutations prognosticating shorter survival

Author

Ebrahimi, Azadeh, Korshunov, Andrey, Reifenberger, Guido, Capper, David, Felsberg, Joerg, Trisolini, Elena, Pollo, Bianca, Calatozzolo, Chiara, Prinz, Marco, Staszewski, Ori, Schweizer, Leonille, Schittenhelm, Jens, Harter, Patrick N., Paulus, Werner, Thomas, Christian, Kohlhof-Meinecke, Patricia, Seiz-Rosenhagen, Marcel, Milde, Till, Casalini, Bel��n M., Suwala, Abigail, Wefers, Annika K., Reinhardt, Annekathrin, Sievers, Philipp, Kramm, Christof M., Etminam, Nima, Unterberg, Andreas, Wick, Wolfgang, Herold-Mende, Christel, Sturm, Dominik, Pfister, Stefan M., Sill, Martin, Jones, David T. W., Schrimpf, Daniel, Reuss, David E., Aldape, Ken, Abdullaev, Zied, Sahm, Felix, von Deimling, Andreas, and Stichel, Damian

Abstract

Additional file 5. Histological features observed in pleomorphic xanthoastrocytomas, (a) classical giant pleomorphic cells with multiple nuclei and prominent nucleolus, (b) extensive perivascular inflammatory infiltrates, (c) endothelial proliferations, (d) extensive myxoid matrix, (e) pseudopalisading necrosis, (f) pseudopapillary growth pattern, (g) biphasic pattern with spindle cell component and giant pleomorphic cell component, (h) extensive calcification, (i) small round blue cell morphology, (j) a thrombosed vessel; all depicted tumors had a maximum calibrated score above 0.9 for mcPXA; Supplementary figure 2 Overall survival (Kaplan-Meier curve) of patients in cohort mcPXA stratified after initial histological diagnosis (a) and BRAF V600E status (b); Supplementary figure 3 Typical copy number profile of mcPXA (upper panel) compared to that of mcGBM (lower panel); Supplementary figure 4 Copy number summary of cohort mcPXA altogether and stratified after WHO grade; Supplementary figure 5: The composition of cohorts histPXA and mcPXA, (a) 220 mcPXA cases with their histological composition, (b) 144 histPXA cases with their methylation class assignments (v11b4).

Published
2022
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3. Additional file 6 of Pleomorphic xanthoastrocytoma is a heterogeneous entity with pTERT mutations prognosticating shorter survival

Author

Ebrahimi, Azadeh, Korshunov, Andrey, Reifenberger, Guido, Capper, David, Felsberg, Joerg, Trisolini, Elena, Pollo, Bianca, Calatozzolo, Chiara, Prinz, Marco, Staszewski, Ori, Schweizer, Leonille, Schittenhelm, Jens, Harter, Patrick N., Paulus, Werner, Thomas, Christian, Kohlhof-Meinecke, Patricia, Seiz-Rosenhagen, Marcel, Milde, Till, Casalini, Bel��n M., Suwala, Abigail, Wefers, Annika K., Reinhardt, Annekathrin, Sievers, Philipp, Kramm, Christof M., Etminam, Nima, Unterberg, Andreas, Wick, Wolfgang, Herold-Mende, Christel, Sturm, Dominik, Pfister, Stefan M., Sill, Martin, Jones, David T. W., Schrimpf, Daniel, Reuss, David E., Aldape, Ken, Abdullaev, Zied, Sahm, Felix, von Deimling, Andreas, and Stichel, Damian

Subjects
TheoryofComputation_MATHEMATICALLOGICANDFORMALLANGUAGES, ComputingMethodologies_SYMBOLICANDALGEBRAICMANIPULATION, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Data_FILES, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries)
Abstract

Additional file 6. List of abbreviations.

Published
2022
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4. Additional file 4 of Pleomorphic xanthoastrocytoma is a heterogeneous entity with pTERT mutations prognosticating shorter survival

Author

Ebrahimi, Azadeh, Korshunov, Andrey, Reifenberger, Guido, Capper, David, Felsberg, Joerg, Trisolini, Elena, Pollo, Bianca, Calatozzolo, Chiara, Prinz, Marco, Staszewski, Ori, Schweizer, Leonille, Schittenhelm, Jens, Harter, Patrick N., Paulus, Werner, Thomas, Christian, Kohlhof-Meinecke, Patricia, Seiz-Rosenhagen, Marcel, Milde, Till, Casalini, Bel��n M., Suwala, Abigail, Wefers, Annika K., Reinhardt, Annekathrin, Sievers, Philipp, Kramm, Christof M., Etminam, Nima, Unterberg, Andreas, Wick, Wolfgang, Herold-Mende, Christel, Sturm, Dominik, Pfister, Stefan M., Sill, Martin, Jones, David T. W., Schrimpf, Daniel, Reuss, David E., Aldape, Ken, Abdullaev, Zied, Sahm, Felix, von Deimling, Andreas, and Stichel, Damian

Abstract

Additional file 4. tSNE plot of histPXA cases with the set of reference samples underlying the classifier version v11b4; ���histPXA a��� represents cases with a calibrated score less than 0.9 in v11b4 classifier, ���histPXA b��� represents cases with a calibrated score of 0.9 or higher in v11b4 classifier.

Published
2022
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5. Additional file 2 of Molecular analysis of pediatric CNS-PNET revealed nosologic heterogeneity and potent diagnostic markers for CNS neuroblastoma with FOXR2-activation

Author

Korshunov, Andrey, Okonechnikov, Konstantin, Schmitt-Hoffner, Felix, Ryzhova, Marina, Sahm, Felix, Stichel, Damian, Schrimpf, Daniel, Reuss, David E., Sievers, Philipp, Suwala, Abigail Kora, Kumirova, Ella, Zheludkova, Olga, Golanov, Andrey, Jones, David T. W., Pfister, Stefan M., Kool, Marcel, and Deimling, Andreas Von

Subjects
Data_FILES
Abstract

Additional file 2.

Published
2021
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6. Additional file 1 of Molecular analysis of pediatric CNS-PNET revealed nosologic heterogeneity and potent diagnostic markers for CNS neuroblastoma with FOXR2-activation

Author

Korshunov, Andrey, Okonechnikov, Konstantin, Schmitt-Hoffner, Felix, Ryzhova, Marina, Sahm, Felix, Stichel, Damian, Schrimpf, Daniel, Reuss, David E., Sievers, Philipp, Suwala, Abigail Kora, Kumirova, Ella, Zheludkova, Olga, Golanov, Andrey, Jones, David T. W., Pfister, Stefan M., Kool, Marcel, and Deimling, Andreas Von

Subjects
Data_FILES
Abstract

Additional file 1.

Published
2021
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7. Additional file 4: of Tumors diagnosed as cerebellar glioblastoma comprise distinct molecular entities

Author

Reinhardt, Annekathrin, Stichel, Damian, Schrimpf, Daniel, Koelsche, Christian, Wefers, Annika, Azadeh Ebrahimi, Sievers, Philipp, Huang, Kristin, M. Casalini, Fernández-Klett, Francisco, Suwala, Abigail, Weller, Michael, Gramatzki, Dorothee, Joerg Felsberg, Reifenberger, Guido, Becker, Albert, Hans, Volkmar, Prinz, Marco, Staszewski, Ori, Acker, Till, Dohmen, Hildegard, Hartmann, Christian, Paulus, Werner, Heß, Katharina, Brokinkel, Benjamin, Schittenhelm, Jens, Buslei, Rolf, Deckert, Martina, Mawrin, Christian, Hewer, Ekkehard, Pohl, Ute, Jaunmuktane, Zane, Brandner, Sebastian, Unterberg, Andreas, HäNggi, Daniel, Platten, Michael, Pfister, Stefan, Wick, Wolfgang, Herold-Mende, Christel, Korshunov, Andrey, Reuss, David, Sahm, Felix, Jones, David, Capper, David, and Deimling, Andreas

Subjects
body regions, nervous system, fungi, sense organs, eye diseases
Abstract

Average CNV loads of cerebellar and reference glioma methylation classes. (PDF 135 kb)

Published
2019
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8. Additional file 2: of Tumors diagnosed as cerebellar glioblastoma comprise distinct molecular entities

Author

Reinhardt, Annekathrin, Stichel, Damian, Schrimpf, Daniel, Koelsche, Christian, Wefers, Annika, Azadeh Ebrahimi, Sievers, Philipp, Huang, Kristin, M. Casalini, Fernández-Klett, Francisco, Suwala, Abigail, Weller, Michael, Gramatzki, Dorothee, Joerg Felsberg, Reifenberger, Guido, Becker, Albert, Hans, Volkmar, Prinz, Marco, Staszewski, Ori, Acker, Till, Dohmen, Hildegard, Hartmann, Christian, Paulus, Werner, Heß, Katharina, Brokinkel, Benjamin, Schittenhelm, Jens, Buslei, Rolf, Deckert, Martina, Mawrin, Christian, Hewer, Ekkehard, Pohl, Ute, Jaunmuktane, Zane, Brandner, Sebastian, Unterberg, Andreas, HäNggi, Daniel, Platten, Michael, Pfister, Stefan, Wick, Wolfgang, Herold-Mende, Christel, Korshunov, Andrey, Reuss, David, Sahm, Felix, Jones, David, Capper, David, and Deimling, Andreas

Subjects
body regions, nervous system, fungi, nervous system diseases
Abstract

Methylation-based clustering analysis of 86 cerebellar glioblastomas (cGBMs) with 707 reference cases. (PDF 16356 kb)

Published
2019
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9. Additional file 5: of Tumors diagnosed as cerebellar glioblastoma comprise distinct molecular entities

Author

Reinhardt, Annekathrin, Stichel, Damian, Schrimpf, Daniel, Koelsche, Christian, Wefers, Annika, Azadeh Ebrahimi, Sievers, Philipp, Huang, Kristin, M. Casalini, Fernández-Klett, Francisco, Suwala, Abigail, Weller, Michael, Gramatzki, Dorothee, Joerg Felsberg, Reifenberger, Guido, Becker, Albert, Hans, Volkmar, Prinz, Marco, Staszewski, Ori, Acker, Till, Dohmen, Hildegard, Hartmann, Christian, Paulus, Werner, Heß, Katharina, Brokinkel, Benjamin, Schittenhelm, Jens, Buslei, Rolf, Deckert, Martina, Mawrin, Christian, Hewer, Ekkehard, Pohl, Ute, Jaunmuktane, Zane, Brandner, Sebastian, Unterberg, Andreas, HäNggi, Daniel, Platten, Michael, Pfister, Stefan, Wick, Wolfgang, Herold-Mende, Christel, Korshunov, Andrey, Reuss, David, Sahm, Felix, Jones, David, Capper, David, and Deimling, Andreas

Subjects
body regions, nervous system, fungi, sense organs, eye diseases
Abstract

Summary copy number variation (CNV) profiles. (PDF 1900 kb)

Published
2019
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10. MOESM2 of Genome-wide methylation profiling and copy number analysis in atypical fibroxanthomas and pleomorphic dermal sarcomas indicate a similar molecular phenotype

Author

Koelsche, Christian, Stichel, Damian, Griewank, Klaus, Schrimpf, Daniel, Reuss, David, Bewerunge-Hudler, Melanie, Vokuhl, Christian, Dinjens, Winand, Petersen, Iver, Mittelbronn, Michel, Cuevas-Bourdier, Adrian, Buslei, Rolf, Pfister, Stefan, Flucke, Uta, Mechtersheimer, Gunhild, Mentzel, Thomas, and Deimling, Andreas

Abstract

Additional file 2: Figure S1. Histologic and immunohistochemical features of a pleomorphic dermal sarcoma with a DNA-methylation pattern resembling melanoma. This highly cellular tumor (ID 101138) with brisk mitotic activity (green arrows) predominantly presented with a polygonal to spindle-shape appearance and a fascicular growth pattern (a). In a circumscribed area the tumor cells were epithelioid (b). Adjacent subcutaneous fat tissue was infiltrated (c) and vascular invasion was observed (d). Parts of the tumor were necrotic (e). The tumor cells did not bind S100 specific antibody, whereas peripheral nerve and few histiocytes were positive (f). The tumor cells were negative for nuclear SOX10 expression with peripheral nerve as positive internal control (g), negative for HMB45 (h) and MelanA (i) protein expression. Scale-bars equal 100Â Âľm.

Published
2019
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11. Additional file 1: of Tumors diagnosed as cerebellar glioblastoma comprise distinct molecular entities

Author

Reinhardt, Annekathrin, Stichel, Damian, Schrimpf, Daniel, Koelsche, Christian, Wefers, Annika, Azadeh Ebrahimi, Sievers, Philipp, Huang, Kristin, M. Casalini, Fernández-Klett, Francisco, Suwala, Abigail, Weller, Michael, Gramatzki, Dorothee, Joerg Felsberg, Reifenberger, Guido, Becker, Albert, Hans, Volkmar, Prinz, Marco, Staszewski, Ori, Acker, Till, Dohmen, Hildegard, Hartmann, Christian, Paulus, Werner, Heß, Katharina, Brokinkel, Benjamin, Schittenhelm, Jens, Buslei, Rolf, Deckert, Martina, Mawrin, Christian, Hewer, Ekkehard, Pohl, Ute, Jaunmuktane, Zane, Brandner, Sebastian, Unterberg, Andreas, HäNggi, Daniel, Platten, Michael, Pfister, Stefan, Wick, Wolfgang, Herold-Mende, Christel, Korshunov, Andrey, Reuss, David, Sahm, Felix, Jones, David, Capper, David, and Deimling, Andreas

Subjects
body regions, nervous system, fungi
Abstract

Primary antibodies used for immunohistochemistry. (PDF 52 kb)

Published
2019
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12. MOESM4 of Genome-wide methylation profiling and copy number analysis in atypical fibroxanthomas and pleomorphic dermal sarcomas indicate a similar molecular phenotype

Author

Koelsche, Christian, Stichel, Damian, Griewank, Klaus, Schrimpf, Daniel, Reuss, David, Bewerunge-Hudler, Melanie, Vokuhl, Christian, Dinjens, Winand, Petersen, Iver, Mittelbronn, Michel, Cuevas-Bourdier, Adrian, Buslei, Rolf, Pfister, Stefan, Flucke, Uta, Mechtersheimer, Gunhild, Mentzel, Thomas, and Deimling, Andreas

Subjects
integumentary system
Abstract

Additional file 4: Figure S2. Copy number profiles of the three atypical fibroxanthomas and the two pleomorphic dermal sarcomas carrying gene amplifications.

Published
2019
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13. Additional file 2 of TTCA: an R package for the identification of differentially expressed genes in time course microarray data

Author

Albrecht, Marco, Stichel, Damian, Mßller, Benedikt, Merkle, Ruth, Sticht, Carsten, Gretz, Norbert, Klingmßller, Ursula, Breuhahn, Kai, and MatthäUs, Franziska

Abstract

Method comparison. A table summarises the methods mentioned in the introduction, method shortcomings are further discussed and TTCA is compared with some applicable methods. Includes Table S1-S3 and Figures S1-S8. (PDF 2165 kb)

Published
2017
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