Integrating Oxford Nanopore Sequencing with Epigenetic Analysis for Precision Medicine in Glioblastoma Multiforme

DOI

10.2991/978-94-6463-976-6_19How to use a DOI?

Keywords

Glioma; Glioblastoma Multiforme (GBM); DNA Methylation; 5-methylcytosine (5mC); 5-hydroxymethylcytosine (5hmC); Next- Generation Sequencing (NGS); Epigenetic Profiling; Precision Medicine; Biomarker Discovery; Basecalling; Genomic Feature Annotation

Abstract

Gliomas, particularly glioblastoma multiforme (GBM), are highly aggressive brain tumors with complex epigenetic landscapes involving DNA methylation modifications such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). These epigenetic marks regulate gene expression without altering the DNA sequence and are critical in tumor progression, therapeutic resistance, and prognosis. This study presents the development and implementation of a Next- Generation Sequencing (NGS)-based pipeline using Oxford Nanopore sequencing technology for simultaneous detection, annotation, and interpretation of 5mC and 5hmC modifications from a single glioma patient sample. The pipeline integrates advanced basecalling with Dorado software, alignment with Minimap2, methylation extraction using custom Python scripts, and genomic feature annotation via BEDTools. Functional and clinical relevance of methylated genes was assessed through pathway analysis tools (g:Profiler, DAVID). Gliomas, particularly glioblastoma multiforme (GBM), are highly aggressive brain tumors with complex epigenetic landscapes involving DNA methylation modifications such as 5-methylcytosine (5mC) and 5-hydroxymethyl cytosine (5hmC). These epigenetic marks regulate gene expression without altering the DNA sequence and are critical in tumor progression, therapeutic resistance, and prognosis. This study presents the development and implementation of a Next-Generation Sequencing (NGS)-based pipeline using Oxford Nanopore sequencing technology for simultaneous detection, annotation, and interpretation of 5mC and 5hmC modifications from a single glioma patient sample. The pipeline integrates advanced basecalling with Dorado software, alignment with Minimap2, methylation extraction using custom Python scripts, and genomic feature annotation via BEDTools. Functional and clinical relevance of methylated genes was assessed through pathway analysis tools (g:Profiler, DAVID, clusterProfiler) and cross-referencing with biomedical databases (ClinVar, COSMIC, DisGeNET). This approach enables precise mapping of methylation events to genomic features, fa- cilitating biomarker discovery and precision medicine strategies. The developed pipeline advances epigenetic profiling in gliomas, providing a robust framework for integrating methylation data into clinical decision-making and therapeutic targeting.

Copyright

© 2025 The Author(s)

Open Access

Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/), which permits any noncommercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.

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TY  - CONF
AU  - Vaibhavi Jain
AU  - Arpita Kharat
AU  - Abhinandan Yadav
AU  - Preenon Bagchi
PY  - 2025
DA  - 2025/12/29
TI  - Integrating Oxford Nanopore Sequencing with Epigenetic Analysis for Precision Medicine in Glioblastoma Multiforme
BT  - Proceedings of the International Conference on Intelligent Information Systems Design and Indian Knowledge System Applications (ICISDIKSA 2026)
PB  - Atlantis Press
SP  - 286
EP  - 295
SN  - 1951-6851
UR  - https://doi.org/10.2991/978-94-6463-976-6_19
DO  - 10.2991/978-94-6463-976-6_19
ID  - Jain2025
ER  -