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Revolutionizing DNA Methylation Detection with Nanopore Sequencing

Dmitrijs Rots from Erasmus MC in the Netherlands presented at the Nanopore Community Meeting in Boston (NCM Boston 2024) on “DNA methylation signature detection using ultra-rapid, long-read nanopore genome sequencing.” Rots mentioned that Erasmus MC is one of the largest hospitals in Europe! The team wanted to implement nanopore sequencing to test for methylation and […]
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Understanding Human Variation and Cancer Genomics via EPI2ME

I started watching a core webinar from Oxford Nanopore Technologies (ONT) tonight. Nick Sisneros from ONT facilitated the presentation. The topic was scalable human genomic characterization with nanopore. The first presentation was by Philipp Rescheneder, Senior Director of Applications Bioinformatics at ONT. They described three end-to-end workflows using EPI2ME: the human variation, cancer genomics, and […]
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Evolution of MinION Technology in Microbiology: ASM Microbe 2024 Session Insights by Joshua Quick

Today, I watched the beginning of an Oxford Nanopore Technologies special recording. The title is “Celebrating a decade of DNA discoveries: 10 years of the MinION in microbiology.” This session was from June 14th, 2024, at the ASM Microbe meeting. Pomeranz began by introducing the ONT and noting that there have been over 13,000 publications […]
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Real-time Genomic Characterization of Pediatric Acute Leukemia: UNC Research

The second talk in the session I started watching yesterday was by a postdoctoral fellow from UNC. Julie Geyer from the University of North Carolina Chapel Hill School of Medicine described their research. The title of the talk was “Real-time genomic characterization of pediatric acute leukemia using adaptive sampling.” Leukemia is cancer of the blood. […]
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Long-read Sequencing and Structural Variants in Precision Oncology

“Accelerating precision oncology research with nanopore sequencing” is the name of the session I watched tonight. Anna Dysko, Associate Director of Business Development with Oxford Nanopore Technologies, facilitated the discussion on April 8, 2024. Dysko explained how nanopore sequencing works: DNA or RNA is passed through a nanopore thanks to the action of a motor […]
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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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Long-Read Sequencing and Methylation Pattern Characterization in 1000 Genomes Project

Sophia Gibson from the University of Washington presented at London Calling 2024 on “Haplotype-resolved repeat expansions & methylation patterns in 1000 Genome Project data.” Gibson noted that clinical genetic testing typically requires multiple tests and clinic visits… and is diagnostic in fewer than 50% of cases. This is described as the “diagnostic odyssey.” Long-read sequencing […]
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Investigating RNA Isoform Diversity in Colorectal Cancer at Single-Cell Level

Ping Lu from Peking University in China presented at London Calling 2024 on “Full-length RNA isoforms in human colorectal cancer at single-cell resolution.” Lu said colorectal cancer is the third most common cancer worldwide and the second leading cause of cancer death! Lu also mentioned that single-cell resolution is now necessary to better understand the […]
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Epigenetic Research on Methylation Patterns in Human Brain Samples

Darren Soanes from the University of Exeter in the UK spoke at London Calling about “DNA modifications in specific nuclei populations purified from human brain tissue.” Soanes is in the Complex Epigenetics Group at Exeter. They study cytosine modifications 5mC and 5hmC. The group has completed studies on methylation patterns in brain samples. Soanes noted […]
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Long-Read RNA Sequencing for Retina Transcript Isoform Identification

Rui Chen from Baylor College of Medicine presented at London Calling 2024 a session titled “Single-cell characterization of transcript isoforms with long-read RNA sequencing.” Their lab is interested in the retina since it is “the main target of irreversible blinding diseases.” In mice, there are over one hundred cell subtypes in the retina, noted Chen. […]
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