Baettig F, Vlajnic T, Vetter M, Glatz K, Hench J, Frank S, Bihl M, Lopez R, Dobbie M, Heinzelmann-Schwarz V, Montavon C (2019) Nivolumab in chemotherapy-resistant cervical cancer: report of a vulvitis as a novel immune-related adverse event and molecular analysis of a persistent complete response. J Immunother Cancer 7:281. https://doi.org/10.1186/s40425-019-0742-6

Article  PubMed  PubMed Central  Google Scholar 

Capper D, Jones DTW, Sill M, Hovestadt V, Schrimpf D, Sturm D, Koelsche C, Sahm F, Chavez L, Reuss DE, Kratz A, Wefers AK, Huang K, Pajtler KW, Schweizer L, Stichel D, Olar A, Engel NW, Lindenberg K, Harter PN, Braczynski AK, Plate KH, Dohmen H, Garvalov BK, Coras R, Hölsken A, Hewer E, Bewerunge-Hudler M, Schick M, Fischer R, Beschorner R, Schittenhelm J, Staszewski O, Wani K, Varlet P, Pages M, Temming P, Lohmann D, Selt F, Witt H, Milde T, Witt O, Aronica E, Giangaspero F, Rushing E, Scheurlen W, Geisenberger C, Rodriguez FJ, Becker A, Preusser M, Haberler C, Bjerkvig R, Cryan J, Farrell M, Deckert M, Hench J, Frank S, Serrano J, Kannan K, Tsirigos A, Brück W, Hofer S, Brehmer S, Seiz-Rosenhagen M, Hänggi D, Hans V, Rozsnoki S, Hansford JR, Kohlhof P, Kristensen BW, Lechner M, Lopes B, Mawrin C, Ketter R, Kulozik A, Khatib Z, Heppner F, Koch A, Jouvet A, Keohane C, Mühleisen H, Mueller W, Pohl U, Prinz M, Benner A, Zapatka M, Gottardo NG, Driever PH, Kramm CM, Müller HL, Rutkowski S, von Hoff K, Frühwald MC, Gnekow A, Fleischhack G, Tippelt S, Calaminus G, Monoranu C-M, Perry A, Jones C, Jacques TS, Radlwimmer B, Gessi M, Pietsch T, Schramm J, Schackert G, Westphal M, Reifenberger G, Wesseling P, Weller M, Collins VP, Blümcke I, Bendszus M, Debus J, Huang A, Jabado N, Northcott PA, Paulus W, Gajjar A, Robinson GW, Taylor MD, Jaunmuktane Z, Ryzhova M, Platten M, Unterberg A, Wick W, Karajannis MA, Mittelbronn M, Acker T, Hartmann C, Aldape K, Schüller U, Buslei R, Lichter P, Kool M, Herold-Mende C, Ellison DW, Hasselblatt M, Snuderl M, Brandner S, Korshunov A, von Deimling A, Pfister SM (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 

Capper D, Stichel D, Sahm F, Jones DTW, Schrimpf D, Sill M, Schmid S, Hovestadt V, Reuss DE, Koelsche C, Reinhardt A, Wefers AK, Huang K, Sievers P, Ebrahimi A, Schöler A, Teichmann D, Koch A, Hänggi D, Unterberg A, Platten M, Wick W, Witt O, Milde T, Korshunov A, Pfister SM, von Deimling A (2018) Practical implementation of DNA methylation and copy-number-based CNS tumor diagnostics: the Heidelberg experience. Acta Neuropathol (Berl) 136:181–210. https://doi.org/10.1007/s00401-018-1879-y

Article  CAS  PubMed  Google Scholar 

Chen Y, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, Zanke BW, Gallinger S, Hudson TJ, Weksberg R (2013) Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics 8:203–209. https://doi.org/10.4161/epi.23470

Article  CAS  PubMed  PubMed Central  Google Scholar 

Djirackor L, Halldorsson S, Niehusmann P, Leske H, Capper D, Kuschel LP, Pahnke J, Due-Tønnessen BJ, Langmoen IA, Sandberg CJ, Euskirchen P, Vik-Mo EO (2021) Intraoperative DNA methylation classification of brain tumors impacts neurosurgical strategy. Neuro-Oncol Adv vdab149. https://doi.org/10.1093/noajnl/vdab149

Article  Google Scholar 

Euskirchen P, Bielle F, Labreche K, Kloosterman WP, Rosenberg S, Daniau M, Schmitt C, Masliah-Planchon J, Bourdeaut F, Dehais C, Marie Y, Delattre J-Y, Idbaih A (2017) Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing. Acta Neuropathol (Berl) 134:691–703. https://doi.org/10.1007/s00401-017-1743–5

Article  CAS  PubMed  Google Scholar 

Fortin J-P, Triche TJ, Hansen KD (2016) Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi. Bioinformatics btw691. https://doi.org/10.1093/bioinformatics/btw691

Gamaarachchi H, Lam CW, Jayatilaka G, Samarakoon H, Simpson JT, Smith MA, Parameswaran S (2020) GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis. BMC Bioinformatics 21:343. https://doi.org/10.1186/s12859-020-03697-x

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gamaarachchi H, Samarakoon H, Jenner SP, Ferguson JM, Amos TG, Hammond JM, Saadat H, Smith MA, Parameswaran S, Deveson IW (2022) Fast nanopore sequencing data analysis with SLOW5. Nat Biotechnol 40:1026–1029. https://doi.org/10.1038/s41587-021-01147–4

Article  CAS  PubMed  PubMed Central  Google Scholar 

Haefliger S, Tzankov A, Frank S, Bihl M, Vallejo A, Stebler J, Hench J (2021) NUT midline carcinomas and their differentials by a single molecular profiling method: a new promising diagnostic strategy illustrated by a case report. Virchows Arch Int J Pathol 478:1007–1012. https://doi.org/10.1007/s00428-020-02869–7

Article  CAS  Google Scholar 

Hench J, Vlajnic T, Soysal SD, Obermann EC, Frank S, Muenst S (2022) An Integrated Epigenomic and genomic view on Phyllodes and Phyllodes-like breast tumors. Cancers 14:667. https://doi.org/10.3390/cancers14030667

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jurmeister P, Schöler A, Arnold A, Klauschen F, Lenze D, Hummel M, Schweizer L, Bläker H, Pfitzner BM, Mamlouk S, Sers C, Denkert C, Stichel D, Frost N, Horst D, von Laffert M, Capper D (2019) DNA methylation profiling reliably distinguishes pulmonary enteric adenocarcinoma from metastatic colorectal cancer. Mod Pathol. https://doi.org/10.1038/s41379-019-0207-y

Article  PubMed  Google Scholar 

Jurmeister P, Bockmayr M, Seegerer P, Bockmayr T, Treue D, Montavon G, Vollbrecht C, Arnold A, Teichmann D, Bressem K, Schüller U, von Laffert M, Müller K-R, Capper D, Klauschen F (2019) Machine learning analysis of DNA methylation profiles distinguishes primary lung squamous cell carcinomas from head and neck metastases. Sci Transl Med 11:eaaw8513. https://doi.org/10.1126/scitranslmed.aaw8513

Article  CAS  PubMed  Google Scholar 

Jurmeister P, Glöß S, Roller R, Leitheiser M, Schmid S, Mochmann LH, Payá Capilla E, Fritz R, Dittmayer C, Friedrich C, Thieme A, Keyl P, Jarosch A, Schallenberg S, Bläker H, Hoffmann I, Vollbrecht C, Lehmann A, Hummel M, Heim D, Haji M, Harter P, Englert B, Frank S, Hench J, Paulus W, Hasselblatt M, Hartmann W, Dohmen H, Keber U, Jank P, Denkert C, Stadelmann C, Bremmer F, Richter A, Wefers A, Ribbat-Idel J, Perner S, Idel C, Chiariotti L, Della Monica R, Marinelli A, Schüller U, Bockmayr M, Liu J, Lund VJ, Forster M, Lechner M, Lorenzo-Guerra SL, Hermsen M, Johann PD, Agaimy A, Seegerer P, Koch A, Heppner F, Pfister SM, Jones DTW, Sill M, von Deimling A, Snuderl M, Müller K-R, Forgó E, Howitt BE, Mertins P, Klauschen F, Capper D (2022) DNA methylation-based classification of sinonasal tumors. Nat Commun 13:7148. https://doi.org/10.1038/s41467-022-34815–3

Article  CAS  PubMed  PubMed Central  Google Scholar 

Karimi S, Zuccato JA, Mamatjan Y, Mansouri S, Suppiah S, Nassiri F, Diamandis P, Munoz DG, Aldape KD, Zadeh G (2019) The central nervous system tumor methylation classifier changes neuro-oncology practice for challenging brain tumor diagnoses and directly impacts patient care. Clin Epigenetics 11:185. https://doi.org/10.1186/s13148-019-0766–2

Article  PubMed  PubMed Central  Google Scholar 

Koelsche C, Schrimpf D, Stichel D, Sill M, Sahm F, Reuss DE, Blattner M, Worst B, Heilig CE, Beck K, Horak P, Kreutzfeldt S, Paff E, Stark S, Johann P, Selt F, Ecker J, Sturm D, Pajtler KW, Reinhardt A, Wefers AK, Sievers P, Ebrahimi A, Suwala A, Fernández-Klett F, Casalini B, Korshunov A, Hovestadt V, Kommoss FKF, Kriegsmann M, Schick M, Bewerunge-Hudler M, Milde T, Witt O, Kulozik AE, Kool M, Romero-Pérez L, Grünewald TGP, Kirchner T, Wick W, Platten M, Unterberg A, Uhl M, Abdollahi A, Debus J, Lehner B, Thomas C, Hasselblatt M, Paulus W, Hartmann C, Staszewski O, Prinz M, Hench J, Frank S, Versleijen-Jonkers YMH, Weidema ME, Mentzel T, Griewank K, de Álava E, Martín JD, Gastearena MAI, Chang KT-E, Low SYY, Cuevas-Bourdier A, Mittelbronn M, Mynarek M, Rutkowski S, Schüller U, Mautner VF, Schittenhelm J, Serrano J, Snuderl M, Büttner R, Klingebiel T, Buslei R, Gessler M, Wesseling P, Dinjens WNM, Brandner S, Jaunmuktane Z, Lyskjær I, Schirmacher P, Stenzinger A, Brors B, Glimm H, Heining C, Tirado OM, Sáinz-Jaspeado M, Mora J, Alonso J, del Muro XG, Moran S, Esteller M, Benhamida JK, Ladanyi M, Wardelmann E, Antonescu C, Flanagan A, Dirksen U, Hohenberger P, Baumhoer D, Hartmann W, Vokuhl C, Flucke U, Petersen I, Mechtersheimer G, Capper D, Jones DTW, Fröhling S, Pfister SM, von Deimling A (2021) Sarcoma classification by DNA methylation profiling. Nat Commun 12:498. https://doi.org/10.1038/s41467-020-20603–4

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kuschel LP, Hench J, Frank S, Hench IB, Girard E, Blanluet M, Masliah-Planchon J, Misch M, Onken J, Czabanka M, Karau P, Ishaque N, Hain EG, Heppner F, Idbaih A, Behr N, Harms C, Capper D, Euskirchen P (2021) Robustmethylation-basedclassificationofbraintumorsusingnanoporesequencing.Oncology

Li H (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinforma Oxf Engl 34:3094–3100. https://doi.org/10.1093/bioinformatics/bty191

Article  CAS  Google Scholar 

Moran S, Martínez-Cardús A, Sayols S, Musulén E, Balañá C, Estival-Gonzalez A, Moutinho C, Heyn H, Diaz-Lagares A, de Moura MC (2016) othersEpigeneticprofilingtoclassifycancerofunknownprimary:amulticentre,retrospectiveanalysis.LancetOncol17:1386–1395

Moudgil-Joshi J, Kaliaperumal C (2021) Letter regarding Louis et al: the 2021 WHO classification of tumors of the Central Nervous System: a summary. Neuro-Oncol 23:2120–2121. https://doi.org/10.1093/neuonc/noab190

Article  PubMed  PubMed Central  Google Scholar 

Nestor CE, Ottaviano R, Reinhardt D, Cruickshanks HA, Mjoseng HK, McPherson RC, Lentini A, Thomson JP, Dunican DS, Pennings S, Anderton SM, Benson M, Meehan RR (2015) Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems. Genome Biol 16:11. https://doi.org/10.1186/s13059-014-0576-y

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sahm F, Schrimpf D, Stichel D, Jones DT, Hielscher T, Schefzyk S, Okonechnikov K, Koelsche C, Reuss DE, Capper D (2017) othersDNAmethylation-basedclassificationandgradingsystemformeningioma:amulticentre,retrospectiveanalysis.LancetOncol18:682–694

Saleh C, Jaszczuk P, Hund-Georgiadis M, Frank S, Cordier D, Hench IB, Todea A, Wasilewski A, Wilmes S, Grigioni G, Hench J (2020) Differentiation of rare brain tumors through unsupervised machine learning: clinical significance of in-depth methylation and copy number profiling illustrated through an unusual case of IDH wildtype glioblastoma. Clin Neuropathol. https://doi.org/10.5414/NP301305

Article  Google Scholar 

Samarakoon H, Ferguson JM, Jenner SP, Amos TG, Parameswaran S, Gamaarachchi H, Deveson IW (2023) Flexible and efficient handling of nanopore sequencing signal data with slow5tools. Genome Biol 24:69. https://doi.org/10.1186/s13059-023-02910–3

Article  PubMed  PubMed Central  Google Scholar 

Sittón-Candanedo I, Alonso RS, Corchado JM, Rodríguez-González S, Casado-Vara R (2019) A review of edge computing reference architectures and a new global edge proposal. Future Gener Comput Syst 99:278–294. https://doi.org/10.1016/j.future.2019.04.016

Article  Google Scholar 

Vaisvila R, Ponnaluri VKC, Sun Z, Langhorst BW, Saleh L, Guan S, Dai N, Campbell MA, Sexton BS, Marks K, Samaranayake M, Samuelson JC, Church HE, Tamanaha E, Corrêa IR, Pradhan S, Dimalanta ET, Evans TC, Williams L, Davis TB (2021) Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA. Genome Res 31:1280–1289. https://doi.org/10.1101/gr.266551.120

Article  PubMed  PubMed Central  Google Scholar 

van der Meulen R (2018) WhatEdgeComputingMeansforInfrastructureandOperationsLeaders.In:WhatEdgeComput.MeansInfrastruct.Oper.Lead.https://www.gartner.com/smarterwithgartner/what-edge-computing-means-for-infrastructure-and-operations-leaders.Accessed2Dec2022

Vermeulen C, Pagès-Gallego M, Kester L, Kranendonk MEG, Wesseling P, Verburg N, de Witt Hamer P, Kooi EJ, Dankmeijer L, van der Lugt J, van Baarsen K, Hoving EW, Tops BBJ, de Ridder J (2023) Ultra-fast deep-learned CNS tumour classification during surgery. Nature 622:842–849. https://doi.org/10.1038/s41586-023-06615–2

Article  CAS  PubMed  PubMed Central  Google Scholar 

Volker Hovestadt MZ (2017) conumee

WHO Classification of Tumours Editorial Board (2021) Centralnervoussystemtumours,5thedition.InternationalAgencyforResearchonCancer,Lyon(France)