All Outputs (5)

ROBIN: A unified nanopore-based assay integrating intraoperative methylome classification and next-day comprehensive profiling for ultra-rapid tumor diagnosis (2025)
Journal Article
Deacon, S., Cahyani, I., Holmes, N., Fox, G., Munro, R., Wibowo, S., Murray, T., Mason, H., Housley, M., Martin, D., Sharif, A., Patel, A., Goldspring, R., Brandner, S., Sahm, F., Smith, S., Paine, S., & Loose, M. (2025). ROBIN: A unified nanopore-based assay integrating intraoperative methylome classification and next-day comprehensive profiling for ultra-rapid tumor diagnosis. Neuro-Oncology, 27(8), 2035-2046. https://doi.org/10.1093/neuonc/noaf103

Background
Advances in our technological capacity to interrogate CNS tumor biology have led to the ever increasing use of genomic sequencing in diagnostic decision making. Presently, CNS tumors are classified based on their epigenetic signatures, le... Read More about ROBIN: A unified nanopore-based assay integrating intraoperative methylome classification and next-day comprehensive profiling for ultra-rapid tumor diagnosis.

Prospective, multicenter validation of a platform for rapid molecular profiling of central nervous system tumors (2025)
Journal Article
Patel, A., Göbel, K., Ille, S., Hinz, F., Schoebe, N., Bogumil, H., Meyer, J., Brehm, M., Kardo, H., Schrimpf, D., Lomakin, A., Ritter, M., Göller, P., Kerbs, P., Pfeifer, L., Hamelmann, S., Blume, C., Ippen, F. M., Berghaus, N., …Sahm, F. (2025). Prospective, multicenter validation of a platform for rapid molecular profiling of central nervous system tumors. Nature Medicine. https://doi.org/10.1038/s41591-025-03562-5

Molecular data integration plays a central role in central nervous system (CNS) tumor diagnostics but currently used assays pose limitations due to technical complexity, equipment and reagent costs, as well as lengthy turnaround times. We previously... Read More about Prospective, multicenter validation of a platform for rapid molecular profiling of central nervous system tumors.

An optimised toolkit for high molecular weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride (2025)
Journal Article
Cahyani, I., Tyson, J., Holmes, N., Quick, J., Moore, C., Loman, N., & Loose, M. (2025). An optimised toolkit for high molecular weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride. Genome Research, 35(5), 1154-1166. https://doi.org/10.1101/gr.279943.124

Since the advent of long-read sequencing, achieving longer read lengths has been a key goal for many users. Ultra-long-read sets (N50 ≥ 100 kb) produced from Oxford Nanopore sequencers have improved genome assemblies in recent years. However, despite... Read More about An optimised toolkit for high molecular weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride.

Enhancing nanopore adaptive sampling for PromethION using readfish at scale (2025)
Journal Article
Munro, R., Payne, A., Holmes, N., Moore, C., Cahyani, I., & Loose, M. (2025). Enhancing nanopore adaptive sampling for PromethION using readfish at scale. Genome Research, 35(4), 877-885. https://doi.org/10.1101/gr.279329.124

A unique feature of Oxford Nanopore Technologies sequencers, adaptive sampling, allows precise DNA molecule selection from sequencing libraries. Here, we present enhancements to our tool, readfish, enabling all features for the industrial scale Prome... Read More about Enhancing nanopore adaptive sampling for PromethION using readfish at scale.

Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements (2022)
Journal Article
Cahyani, I., Putro, E. W., Ridwanuloh, A. M., Wibowo, S., Hariyatun, H., Syahputra, G., Akbariani, G., Utomo, A. R., Ilyas, M., Loose, M., Kusharyoto, W., & Susanti, S. (2022). Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements. Viruses, 14(4), 778. https://doi.org/10.3390/v14040778

Whole-genome sequencing (WGS) has played a significant role in understanding the epidemiology and biology of SARS-CoV-2 virus. Here, we investigate the use of SARS-CoV-2 WGS in Southeast and East Asian countries as a genomic surveillance during the C... Read More about Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements.