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000289293 1001_ $$aHench, Jürgen$$b0
000289293 245__ $$aEpiDiP/NanoDiP: a versatile unsupervised machine learning edge computing platform for epigenomic tumour diagnostics.
000289293 260__ $$aLondon$$bBiomed Central$$c2024
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000289293 520__ $$aDNA methylation analysis based on supervised machine learning algorithms with static reference data, allowing diagnostic tumour typing with unprecedented precision, has quickly become a new standard of care. Whereas genome-wide diagnostic methylation profiling is mostly performed on microarrays, an increasing number of institutions additionally employ nanopore sequencing as a faster alternative. In addition, methylation-specific parallel sequencing can generate methylation and genomic copy number data. Given these diverse approaches to methylation profiling, to date, there is no single tool that allows (1) classification and interpretation of microarray, nanopore and parallel sequencing data, (2) direct control of nanopore sequencers, and (3) the integration of microarray-based methylation reference data. Furthermore, no software capable of entirely running in routine diagnostic laboratory environments lacking high-performance computing and network infrastructure exists. To overcome these shortcomings, we present EpiDiP/NanoDiP as an open-source DNA methylation and copy number profiling suite, which has been benchmarked against an established supervised machine learning approach using in-house routine diagnostics data obtained between 2019 and 2021. Running locally on portable, cost- and energy-saving system-on-chip as well as gpGPU-augmented edge computing devices, NanoDiP works in offline mode, ensuring data privacy. It does not require the rigid training data annotation of supervised approaches. Furthermore, NanoDiP is the core of our public, free-of-charge EpiDiP web service which enables comparative methylation data analysis against an extensive reference data collection. We envision this versatile platform as a useful resource not only for neuropathologists and surgical pathologists but also for the tumour epigenetics research community. In daily diagnostic routine, analysis of native, unfixed biopsies by NanoDiP delivers molecular tumour classification in an intraoperative time frame.
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000289293 650_7 $$2Other$$aArtificial intelligence
000289293 650_7 $$2Other$$aCopy number profiling
000289293 650_7 $$2Other$$aCryptocurrency miner
000289293 650_7 $$2Other$$aDigital pathology
000289293 650_7 $$2Other$$aDimension reduction
000289293 650_7 $$2Other$$aEdge computing
000289293 650_7 $$2Other$$aEpigenetics
000289293 650_7 $$2Other$$aIntraoperative
000289293 650_7 $$2Other$$aMethylation
000289293 650_7 $$2Other$$aMethylation sequencing
000289293 650_7 $$2Other$$aMethylome
000289293 650_7 $$2Other$$aMicroarray
000289293 650_7 $$2Other$$aNanopore sequencing
000289293 650_7 $$2Other$$aOncology
000289293 650_7 $$2Other$$aSame-day classification
000289293 650_7 $$2Other$$aSoC
000289293 650_7 $$2Other$$aTumour
000289293 650_7 $$2Other$$aUMAP
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000289293 7001_ $$aHultschig, Claus$$b1
000289293 7001_ $$aBrugger, Jon$$b2
000289293 7001_ $$aMariani, Luigi$$b3
000289293 7001_ $$aGuzman, Raphael$$b4
000289293 7001_ $$aSoleman, Jehuda$$b5
000289293 7001_ $$aLeu, Severina$$b6
000289293 7001_ $$aBenton, Miles$$b7
000289293 7001_ $$aStec, Irenäus Maria$$b8
000289293 7001_ $$aHench, Ivana Bratic$$b9
000289293 7001_ $$aHoffmann, Per$$b10
000289293 7001_ $$aHarter, Patrick$$b11
000289293 7001_ $$0P:(DE-He78)832f5277c0186f22e7704f1930239636$$aWeber, Katharina$$b12
000289293 7001_ $$aAlbers, Anne$$b13
000289293 7001_ $$aThomas, Christian$$b14
000289293 7001_ $$aHasselblatt, Martin$$b15
000289293 7001_ $$aSchüller, Ulrich$$b16
000289293 7001_ $$aRestelli, Lisa$$b17
000289293 7001_ $$aCapper, David$$b18
000289293 7001_ $$aHewer, Ekkehard$$b19
000289293 7001_ $$aDiebold, Joachim$$b20
000289293 7001_ $$aKolenc, Danijela$$b21
000289293 7001_ $$aSchneider, Ulf C$$b22
000289293 7001_ $$aRushing, Elisabeth$$b23
000289293 7001_ $$aDella Monica, Rosa$$b24
000289293 7001_ $$aChiariotti, Lorenzo$$b25
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000289293 7001_ $$aKölsche, Christian$$b30
000289293 7001_ $$aTolnay, Markus$$b31
000289293 7001_ $$aFrank, Stephan$$b32
000289293 773__ $$0PERI:(DE-600)2715589-4$$a10.1186/s40478-024-01759-2$$gVol. 12, no. 1, p. 51$$n1$$p51$$tActa Neuropathologica Communications$$v12$$x2051-5960$$y2024
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