methylation

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Epigenetics and DNA Methylation Detection with ONT

Continuing with the Human genome sequencing and analysis Nanopore Learning course, tonight I watched the video on “Methylation Detection: Sample to Answer Workflow Overview.” Dilrini De Silva from the Technical Services Team at Oxford Nanopore started by defining epigenetics as the study of gene activity caused by chemical modification of nucleic acids, both DNA and […]
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Identifying Methylation States with MinKNOW

Dilrini De Silva, a Technical Applications Scientist in Bioinformatics at Oxford Nanopore Technologies, spoke about Methylation Detection on MinKNOW as part of the Human genome sequencing and analysis Nanopore Learning course. They discussed approaches for detecting methylation states with Nanopore sequencing and the MinKNOW software. MinKNOW includes models for methylation detection and mapping of reads. […]
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Inactivation of X Chromosome

Tonight I watched Quentin Gouil from the Walter and Eliza Hall Institute of Medical Research in Australia speak at the Nanopore Community Meeting in Singapore about “Measuring skewed X inactivation by adaptive nanopore sequencing.” Gouil explained that there are ~2000 genes on the X chromosome, and males are more affected by X-linked diseases. They described […]
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Nanopore Sequencing for Detection of Modifications in Cancer Genomics

Genta Nagae from the University of Tokyo in Japan presented at the Nanopore Community Meeting in Singapore on “Direct detection of DNA modifications in human cancer genomes.” Nagae briefly spoke about the significance of DNA methylation in biology and cancer. They used the QIAamp and Puregene kits from QIAGEN to prepare tumor DNA for sequencing […]
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Using Nanopore Sequencing for Liquid Biopsies

The recording for the London Calling 2023 Liquid Biopsy session was posted, and I watched it tonight. The first panel member was Billy Lau who spoke about “Nanopore sequencing of cell-free DNA for methylation-based breast cancer detection in a case-control research cohort.” I had watched the individual talks previously but not the complete session. Lau […]
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Liquid Biopsies for Longitudinal Non-invasive Cancer Monitoring

Tonight we started our first P2 run with two PromethION flow cells. I also continued watching the London Calling 2023 Showcase Stage on liquid biopsy. I watched them out of order! Today I watched Billy Lau from Stanford University School of Medicine do a quick presentation titled “Nanopore sequencing of cell-free DNA for methylation-based breast […]
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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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Sequencing Improvements for Diagnosis of Acutely Unwell Children in the UK

Emma Baple from the Royal Devon University Healthcare NHS Foundation Trust & the University of Exeter spoke at London Calling 2023 about “Empowering NHS rapid diagnostic testing with long-read sequencing.” They explained how rapid genetic tests for acutely ill children with rare diseases is critical, and they shared some intriguing statistics about the prevalence of […]
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Sequencing Borg Genomes

Marie Charlotte Schoelmerich from the University of California, Berkley presented at London Calling 2023 about “Confirmation of borg extrachromosomal genomes: analysis of their methylation patterns, metabolism, and tandem repeats.” Schoelmerich is a postdoc in Jill Banfield’s lab and spoke about the key role of microorganisms in methane cycles. Methane emissions are driving climate change, and […]
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