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Integrating copy number, methylation, and fusion detection in one assay: A Nanopore sequencing approach for pediatric and adults’ rare tumors diagnosis

ABSTRACT: Recent advances in sequencing technologies have significantly refined tumor characterization by enabling detailed analysis of genetic alterations, transcriptomic profiles, and DNA methylation patterns. Combined with pathological data, these molecular insights have become essential for accurate tumor classification at diagnosis, allowing for more precise prognostic assessment and the implementation of the most appropriate therapeutic strategies. Currently, obtaining this comprehensive molecular information requires the use of multiple techniques, often leading to extended turnaround times and high cost. A key challenge is therefore the development of an integrated method capable of simultaneously detecting copy number variations, structural rearrangements, and methylation-based classifications in a time-efficient manner. In this study, we applied Nanopore long-read sequencing combined with adaptive sampling to a series of 20 pediatric and rare tumors previously characterized using conventional short-read panels and RNA sequencing. Our approach successfully detected all clinically relevant and classifying structural variants, including gene fusions and internal tandem duplications, previously identified by traditional short read sequencing. In addition, we generated high-quality genome-wide copy number profiles and methylation data from the same DNA sample, enabling integrated molecular classification. These findings demonstrate the strong concordance of this unified method with standard approaches and highlight the value of Nanopore sequencing as a powerful and time-efficient tool for comprehensive tumor profiling. Requiring only a single sample and offering rapid technical processing, this approach aligns with the clinical objective of accelerating diagnostic workflows and improving patient care.

ORGANISM(S): Homo sapiens

PROVIDER: GSE320108 | GEO | 2026/02/27

REPOSITORIES: GEO

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Project description:Probing epigenetic features on long molecules of DNA has tremendous potential to advance our understanding of the phased epigenome. In this study, we evaluate CpG methylation and chromatin accessibility simultaneously on long strands of DNA using GpC methyltransferase to exogenously label open chromatin, coupled with nanopore sequencing technology. We performed nanopore sequencing of Nucleosome Occupancy and Methylome (nanoNOMe) on four human cell lines (GM12878, MCF-10A, MCF-7, MDA-MB-231), and demonstrate the ability to directly measure methylation and chromatin accessibility in genomic features such as structural variations and repetitive elements. The long single-molecule resolution allows footprinting of protein and nucleosome binding and determining the combinatorial promoter epigenetic state on individual molecules. Long-read sequencing makes it possible to robustly assign reads to haplotypes, enabling allele-specific epigenetic analysis across the genome. We use existing SNV data on GM12878 to present the first fully phased human Probing epigenetic features on long molecules of DNA has tremendous potential to advance our understanding of the phased epigenome. We evaluate CpG methylation and chromatin accessibility simultaneously on long strands of DNA using GpC methyltransferase to exogenously label open chromatin, coupled with nanopore sequencing technology. We performed nanopore sequencing of Nucleosome Occupancy and Methylome (nanoNOMe) on four human cell lines (GM12878, MCF-10A, MCF-7, MDA-MB-231), and demonstrate the ability to directly measure methylation and chromatin accessibility in genomic features such as structural variations and repetitive elements. The long single-molecule resolution allows footprinting of protein and nucleosome binding and determining the combinatorial promoter epigenetic state on individual molecules. Long-read sequencing makes it possible to robustly assign reads to haplotypes, enabling allele-specific epigenetic analysis across the genome. We use existing SNV data on GM12878 to present the first fully phased human epigenome, consisting of chromosome-level allele-specific profiles of CpG methylation and chromatin accessibility.mosome-level allele-specific profiles of CpG methylation and chromatin accessibility.

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Integrating copy number, methylation, and fusion detection in one assay: A Nanopore sequencing approach for pediatric and adults’ rare tumors diagnosis

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