Genomics in the long-read sequencing era

EL van Dijk, D Naquin, K Gorrichon, Y Jaszczyszyn… - Trends in Genetics, 2023 - cell.com
Long-read sequencing (LRS) technologies have provided extremely powerful tools to
explore genomes. While in the early years these methods suffered technical limitations, they …

DNA methylation as a diagnostic tool

K Galbraith, M Snuderl - Acta Neuropathologica Communications, 2022 - Springer
DNA methylation of cytosines in CpG sites throughout the genome is an epigenetic mark
contributing to gene expression regulation. DNA methylation patterns are specific to tissue …

Ultra-fast deep-learned CNS tumour classification during surgery

C Vermeulen, M Pagès-Gallego, L Kester… - Nature, 2023 - nature.com
Central nervous system tumours represent one of the most lethal cancer types, particularly
among children. Primary treatment includes neurosurgical resection of the tumour, in which …

Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing

E Katsman, S Orlanski, F Martignano, I Fox-Fisher… - Genome Biology, 2022 - Springer
Abstract The Oxford Nanopore (ONT) platform provides portable and rapid genome
sequencing, and its ability to natively profile DNA methylation without complex sample …

Efficient real-time selective genome sequencing on resource-constrained devices

PJ Shih, H Saadat, S Parameswaran… - …, 2023 - academic.oup.com
Background Third-generation nanopore sequencers offer selective sequencing or “Read
Until” that allows genomic reads to be analyzed in real time and abandoned halfway if not …

Real‐time analysis of the cancer genome and fragmentome from plasma and urine cell‐free DNA using nanopore sequencing

Y van Der Pol, NA Tantyo, N Evander… - EMBO molecular …, 2023 - embopress.org
Cell‐free DNA (cfDNA) can be isolated and sequenced from blood and/or urine of cancer
patients. Conventional short‐read sequencing lacks deployability and speed and can be …

MGMT and whole-genome DNA methylation impacts on diagnosis, prognosis and therapy of glioblastoma multiforme

R Della Monica, M Cuomo, M Buonaiuto… - International Journal of …, 2022 - mdpi.com
Epigenetic changes in DNA methylation contribute to the development of many diseases,
including cancer. In glioblastoma multiforme, the most prevalent primary brain cancer and …

Methylation classifiers: Brain tumors, sarcomas, and what's next

C Koelsche, A von Deimling - Genes, Chromosomes and …, 2022 - Wiley Online Library
Tumor classification has evolved over the last decades with technical progress contributing
much to our current concepts. Among diagnostic hallmarks, novelties were immunostaining …

Applications of Nanopore sequencing in precision cancer medicine

SA Dyshlovoy, S Paigin, AK Afflerbach… - … Journal of Cancer, 2024 - Wiley Online Library
Abstract Oxford Nanopore Technologies sequencing, also referred to as Nanopore
sequencing, stands at the forefront of a revolution in clinical genetics, offering the potential …

DNA methylation subclasses predict the benefit from gross total tumor resection in IDH-wildtype glioblastoma patients

R Drexler, U Schüller, A Eckhardt, K Filipski… - Neuro …, 2023 - academic.oup.com
Background DNA methylation-based tumor classification allows an enhanced distinction into
subgroups of glioblastoma. However, the clinical benefit of DNA methylation-based …