CpG

Methylation Distribution and RNA Sequencing: Insights from Large-Scale Studies

I continued watching the ONT “Empowering comprehensive sequencing at scale” session. The next speaker in this session was Brynja Sigurpalsdottir who spoke about large-scale methylation studies. They spoke about how base calling is used to detect methylation. The team sequenced 7,179 whole blood samples sequenced on 8906 PromethION R9.4 flowcells! Twenty-two samples were sequenced on […]
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Direct Sequencing of Cytosine Modification States from Nanopore Long-Read Data

Dominic Halliwell from the University of Bath in the UK presented at London Calling 2024 on “Direct sequencing of cytosine modification states from nanopore long-read data.” They are a doctoral student and were partially funded by Oxford Nanopore Technologies (ONT). Halliwell spoke about 5mC, 5hmC, and later oxidation derivatives, emphasizing that genome methylation can be […]
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Better Libraries and Improved Sequencing for Liquid Biopsy Samples

I continued watching the London Calling 2023 Showcase Stage sessions on liquid biopsies today. I watched the question and answer session. Panelists spoke about using amplicon panels and the Flongle. One panelist uses amplicon sequencing with Nanopore devices because they are able to go from sample to results in under eight hours. Another panelist answered […]
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Genome-wide Methylation Evaluation for Genetic Diagnosis

Miranda Galey from the University of Washington spoke at London Calling 2023 about “MeOW: genome-wide identification of differentially methylated regions using Oxford Nanopore long-read sequencing data.” Galey explained how long-read sequencing can shorten the time to diagnosis. The noted that methylated nucleotides have different current patterns that can be detected. The advantage of long-read sequencing […]
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Remora Brings the Mods

Marcus Stoiber, a Senior Data Analyst at Oxford Nanopore Technologies (ONT), presented on “Nanopore methylation: a better way to mods” at the Nanopore Community Meeting 2021. Stoiber and team devised the Remora modified base detection framework. Remora separates methylation/modified base calling from the basecalling neural networks. This separation provides high accuracy for methylation calls and […]
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Different Cytosine Methylations and DeepSignal-plant

Feng Luo from Clemson University presented at the Nanopore Community Meeting 2021 about “Genome-wide detection of cytosine methylations in plants from nanopore data using deep learning.” They are faculty in computer science at Clemson. They spoke about detecting methylation from nanopore signals. They developed the DeepSignal tool. Nanopore has developed Megalodon, and there is also […]
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