Alexander BM, Trippa L, Gaffey S, Arrillaga-Romany IC, Lee EQ, Rinne ML et al (2019) Individualized Screening Trial of Innovative Glioblastoma Therapy (INSIGhT): a Bayesian adaptive platform trial to develop precision medicines for patients with glioblastoma. JCO Precis Oncol. https://doi.org/10.1200/PO.18.00071

Article  PubMed  PubMed Central  Google Scholar 

Bates D, Machler M, Bolker B, Walker S (2015) Fitting linear mixe-effects models using lme4. J Stat Softw 67:1–48. https://doi.org/10.18637/jss.v067.i01

Article  Google Scholar 

Bender K, Perez E, Chirica M, Onken J, Kahn J, Brenner W et al (2021) High-grade astrocytoma with piloid features (HGAP): the Charite experience with a new central nervous system tumor entity. J Neurooncol 153:109–120. https://doi.org/10.1007/s11060-021-03749-z

Article  PubMed  PubMed Central  Google Scholar 

Capper D, Jones DTW, Sill M, Hovestadt V, Schrimpf D, Sturm D et al (2018) DNA methylation-based classification of central nervous system tumours. Nature 555:469–474. https://doi.org/10.1038/nature26000

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cimino PJ, McFerrin L, Wirsching HG, Arora S, Bolouri H, Rabadan R et al (2018) Copy number profiling across glioblastoma populations has implications for clinical trial design. Neuro Oncol 20:1368–1373. https://doi.org/10.1093/neuonc/noy108

Article  CAS  PubMed  PubMed Central  Google Scholar 

DeSisto J, Lucas JT Jr, Xu K, Donson A, Lin T, Sanford B et al (2021) Comprehensive molecular characterization of pediatric radiation-induced high-grade glioma. Nat Commun 12:5531. https://doi.org/10.1038/s41467-021-25709-x

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dodgshun AJ, Fukuoka K, Edwards M, Bianchi VJ, Das A, Sexton-Oates A et al (2020) Germline-driven replication repair-deficient high-grade gliomas exhibit unique hypomethylation patterns. Acta Neuropathol 140:765–776. https://doi.org/10.1007/s00401-020-02209-8

Article  CAS  PubMed  Google Scholar 

Ferreira R, Schneekloth JS Jr, Panov KI, Hannan KM, Hannan RD (2020) Targeting the RNA polymerase I transcription for cancer therapy comes of age. Cells. https://doi.org/10.3390/cells9020266

Article  PubMed  PubMed Central  Google Scholar 

Gu Z, Eils R, Schlesner M (2016) Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32:2847–2849. https://doi.org/10.1093/bioinformatics/btw313

Article  CAS  PubMed  Google Scholar 

Gutmann DH, McLellan MD, Hussain I, Wallis JW, Fulton LL, Fulton RS et al (2013) Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma. Genome Res 23:431–439. https://doi.org/10.1101/gr.142604.112

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kessler T, Berberich A, Sadik A, Sahm F, Gorlia T, Meisner C et al (2020) Methylome analyses of three glioblastoma cohorts reveal chemotherapy sensitivity markers within DDR genes. Cancer Med 9:8373–8385. https://doi.org/10.1002/cam4.3447

Article  CAS  PubMed  PubMed Central  Google Scholar 

Louis DN, Perry A, Wesseling P, Brat DJ, Cree IA, Figarella-Branger D et al (2021) The 2021 WHO Classification of Tumors of the Central Nervous System: a summary. Neuro Oncol. https://doi.org/10.1093/neuonc/noab106

Article  PubMed  PubMed Central  Google Scholar 

Lucas CG, Sloan EA, Gupta R, Wu J, Pratt D, Vasudevan HN et al (2022) Multiplatform molecular analyses refine classification of gliomas arising in patients with neurofibromatosis type 1. Acta Neuropathol. https://doi.org/10.1007/s00401-022-02478-5

Article  PubMed  PubMed Central  Google Scholar 

Mackay A, Burford A, Molinari V, Jones DTW, Izquierdo E, Brouwer-Visser J et al (2018) Molecular, pathological, radiological, and immune profiling of non-brainstem pediatric high-grade glioma from the HERBY Phase II Randomized Trial. Cancer Cell 33(829–842):e825. https://doi.org/10.1016/j.ccell.2018.04.004

Article  CAS  Google Scholar 

Min JL, Hemani G, Davey Smith G, Relton C, Suderman M (2018) Meffil: efficient normalization and analysis of very large DNA methylation datasets. Bioinformatics 34:3983–3989. https://doi.org/10.1093/bioinformatics/bty476

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pajtler KW, Witt H, Sill M, Jones DT, Hovestadt V, Kratochwil F et al (2015) Molecular classification of ependymal tumors across all CNS compartments, histopathological grades, and age groups. Cancer Cell 27:728–743. https://doi.org/10.1016/j.ccell.2015.04.002

Article  CAS  PubMed  PubMed Central  Google Scholar 

Parker KA, Robinson NJ, Schiemann WP (2022) The role of RNA processing and regulation in metastatic dormancy. Semin Cancer Biol 78:23–34. https://doi.org/10.1016/j.semcancer.2021.03.020

Article  CAS  PubMed  Google Scholar 

Pratt D, Abdullaev Z, Papanicolau-Sengos A, Ketchum C, Panneer Selvam P, Chung HJ et al (2022) High-grade glioma with pleomorphic and pseudopapillary features (HPAP): a proposed type of circumscribed glioma in adults harboring frequent TP53 mutations and recurrent monosomy 13. Acta Neuropathol 143:403–414. https://doi.org/10.1007/s00401-022-02404-9

Article  CAS  PubMed  Google Scholar 

Pratt D, Lucas CG, Selvam PP, Abdullaev Z, Ketchum C, Quezado M et al (2022) Recurrent ACVR1 mutations in posterior fossa ependymoma. Acta Neuropathol 144:373–376. https://doi.org/10.1007/s00401-022-02435-2

Article  CAS  PubMed  Google Scholar 

Raffeld M, Abdullaev Z, Pack SD, Xi L, Nagaraj S, Briceno N et al (2020) High level MYCN amplification and distinct methylation signature define an aggressive subtype of spinal cord ependymoma. Acta Neuropathol Commun 8:101. https://doi.org/10.1186/s40478-020-00973-y

Article  CAS  PubMed  PubMed Central  Google Scholar 

Reinhardt A, Stichel D, Schrimpf D, Koelsche C, Wefers AK, Ebrahimi A et al (2019) Tumors diagnosed as cerebellar glioblastoma comprise distinct molecular entities. Acta Neuropathol Commun 7:163. https://doi.org/10.1186/s40478-019-0801-8

Article  CAS  PubMed  PubMed Central  Google Scholar 

Reinhardt A, Stichel D, Schrimpf D, Sahm F, Korshunov A, Reuss DE et al (2018) Anaplastic astrocytoma with piloid features, a novel molecular class of IDH wildtype glioma with recurrent MAPK pathway, CDKN2A/B and ATRX alterations. Acta Neuropathol 136:273–291. https://doi.org/10.1007/s00401-018-1837-8

Article  CAS  PubMed  Google Scholar 

Ren X, Kuan PF (2019) methylGSA: a bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing. Bioinformatics 35:1958–1959. https://doi.org/10.1093/bioinformatics/bty892

Article  CAS  PubMed  Google Scholar 

Robinson JT, Thorvaldsdottir H, Wenger AM, Zehir A, Mesirov JP (2017) Variant review with the integrative genomics viewer. Cancer Res 77:e31–e34. https://doi.org/10.1158/0008-5472.CAN-17-0337

Article  CAS  PubMed  PubMed Central  Google Scholar 

Singh O, Pratt D, Aldape K (2021) Immune cell deconvolution of bulk DNA methylation data reveals an association with methylation class, key somatic alterations, and cell state in glial/glioneuronal tumors. Acta Neuropathol Commun 9:148. https://doi.org/10.1186/s40478-021-01249-9

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stanley RF, Abdel-Wahab O (2022) Dysregulation and therapeutic targeting of RNA splicing in cancer. Nat Cancer 3:536–546. https://doi.org/10.1038/s43018-022-00384-z

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sturm D, Orr BA, Toprak UH, Hovestadt V, Jones DTW, Capper D et al (2016) New brain tumor entities emerge from molecular classification of CNS-PNETs. Cell 164:1060–1072. https://doi.org/10.1016/j.cell.2016.01.015

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sturm D, Witt H, Hovestadt V, Khuong-Quang DA, Jones DT, Konermann C et al (2012) Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma. Cancer Cell 22:425–437. https://doi.org/10.1016/j.ccr.2012.08.024

Article  CAS  PubMed  Google Scholar 

Tanguturi SK, Trippa L, Ramkissoon SH, Pelton K, Knoff D, Sandak D et al (2017) Leveraging molecular datasets for biomarker-based clinical trial design in glioblastoma. Neuro Oncol 19:908–917. https://doi.org/10.1093/neuonc/now312

Article  CAS  PubMed  PubMed Central  Google Scholar 

Thomas C, Sill M, Ruland V, Witten A, Hartung S, Kordes U et al (2016) Methylation profiling of choroid plexus tumors reveals 3 clinically distinct subgroups. Neuro Oncol 18:790–796. https://doi.org/10.1093/neuonc/nov322

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yang B, Wang JQ, Tan Y, Yuan R, Chen ZS, Zou C (2021) RNA methylation and cancer treatment. Pharmacol Res 174:105937. https://doi.org/10.1016/j.phrs.2021.105937

Article  CAS  PubMed  Google Scholar