methylation

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Oxford Nanopore Technologies Innovations for Rapid Tumor Classification – London Calling 2024

The London Calling 2024 studio interview session I watched tonight was about rapid tumor classification. Zoe McDougall spoke to Simon Paine from Nottingham University Hospitals NHS Trust in the UK. Paine is a neuropathologist and analyzes samples to predict patient outcomes. They are excited about discovering ways to classify tumors using Oxford Nanopore Technologies. The […]
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Epstein-Barr Virus and Methylation Patterns

Christopher Oakes from The Ohio State University spoke at London Calling 2019 on “Discerning the origin of Epstein-Barr virus in patients using nanopore-derived DNA methylation signatures.” Oakes spoke about how they study tumor viruses and cancer. The Epstein-Barr virus is common, the “prototypical cancer virus,” according to Oakes. Immune cells suppress the virus, but the […]
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Targeting Mobile Elements in Alzheimer’s

I started watching the on-demand lighting talk recordings from London Calling 2023 tonight. I started with Camille Mumm’s session. Mumm is from the University of Michigan and presented on “Exploring the impact of mobile elements on Alzheimer’s disease using targeted long-read sequencing.”Mumm is also a graduate student (at the time of recording). They spoke about […]
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MethPhaser and Improved Haplotype Phasing of Human Genomes

“MetaPhaser: methylation-based haplotype phasing of human genomes” is the title of the NCM Houston session I watched tonight. Yilei Fu from Rice University was the presenter. They began sharing how long reads provide more information about structural variations (SV) and help with assembly and phasing. Fu explained an example of thiopurine methyltransferase (TMPT) and how […]
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ONT Workflows for the GREGoR Project

Medhat Mahmoud from the Baylor College of Medicine’s Human Genome Sequencing Center presented at the Nanopore Community Meeting in Houston a session titled “Unraveling complex Mendelian diseases with nanopore sequencing.” They are in the Sedlacek lab and spoke about GREGoR: Genomics Research to Elucidate the Genetics of Rare Diseases project. GREGoR includes five research centers […]
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Phylogeny Reconstruction of Melanoma Sublines

Yuelin Liu from the University of Maryland and the National Cancer Institute spoke at the Nanopore Community Meeting in Houston about “Analysis of melanoma evolution using nanopore long-read sequencing data.” Liu spoke about melanoma and skin cancers. While melanoma makes up only about 2% of skin cancers, it is the most aggressive. Liu explained that […]
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NCM Houston Applications Update

Tonight I watched the NCM Houston Update from Sissel Juul from Oxford Nanopore Technologies. The session is entitled “Covering all bases,” and Juul is the director of the applications team. The talk focused on variant calling mostly on the PromethION. About a year and a half ago, the telomere-to-telomere consortium published the T2T assembly in […]
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Nextflow and EPI2ME Labs Workflows in a Terminal

I want to learn how to use EPI2ME and EPI2ME Labs effectively. The Nanopore Learning course has several videos about EPI2ME Labs. The one I watched tonight was about “EPI2ME Labs Nextflow Workflows demonstration” by Dilrini De Silva, a Technical Applications Scientists in Bioinformatics at Oxford Nanopore Technologies. In the video, De Silva demonstrated running […]
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