Reflections

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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Swab-to-Sequencer in Space

Sarah Stahl-Rommel from NASA Health and Human Performance Contact & JES Tech in the USA presented at London Calling 2023 a session entitled “Unlocking the microbiome of the International Space Station.” Stahl-Rommel explained that NASA has been using culture-based approaches for decades. These assessments require samples transported back to earth. Now, they are preparing to […]
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Surveillance Efforts in New Zealand

Joep de Ligt from the Institute of Environmental Science and Research Limited (ESR) in New Zealand presented at London Calling 2023 a session entitled “The value of real-time, long-read sequencing for public health.” They talked about how they developed technologies during the COVID pandemic. The ESR uses genomics for public health. de Ligt described how […]
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Rapid Tuberculosis Drug Resistance Profiling from Sputum

Tonight the London Calling 2023 session I watched was presented by Tiana Schwab from the Institute of Social and Preventative Medicine at the University of Bern in Switzerland. The title is “Tuberculosis drug resistance profiling from native sputum using nanopore targeted sequencing: a field application study.” Schwab is working on a Ph.D. and described the […]
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Detection of Co-infections through Multiplex Assay Design

“Detection and differentiation of respiratory viral pathogens using near real-time sequencing” is the title of the London Calling 2023 session by Lukasz Rabalski from the University of Gdansk & Military Institute of Hygiene and Epidemiology in Poland. Rabalski is interested in co-infections and their prevalence and clinical impact. Co-infections can increase the severity of diseases […]
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nCATS to Sequence Mobile Element Insertions

Camille Mumm, a graduate student at the University of Michigan, presented at London Calling 2023 a five-minute session entitled “Exploring the impact of mobile elements on Alzheimer’s disease using targeted long-read sequencing. They explained that Alzheimer’s disease (AD) is a devastating neurodegenerative disease with not yet fully characterized genetic mechanisms. Somatic mutations in the brains […]
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ONT Masterclass 2023 for DNA/RNA Extraction

Tonight I watched a London Calling 2023 Masterclass on “How to extract high-quality DNA and RNA” with Vania Costa, a Field Applications Scientist with Oxford Nanopore Technologies. This is part of a series of Masterclasses. The learning objectives, Costa explained, were how to determine the right extraction method as well as common practices. Costa said […]
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Identifying and Plotting Short Tandem Repeats with Pathological Implications

Hagar Mor-Shaked from the Hadassah Medical Organization & Faculty of Medicine at the Hebrew University of Jerusalem in Israel presented at London Calling 2023 on “Pathological short tandem repeats analysis by long-read sequencing in affected individuals.” They explained that pathological repeat expansions can be found in coding and non-coding regions, and a few dozen have […]
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Using the PromethION for Human Genomics

The London Calling 2023 “Human genomics – from targeted to whole-genome sequencing” showcase recording is fifteen minutes long and highlights applications. Rachel Rubinstein, a technical product manager at Oxford Nanopore Technologies (ONT) shared various applications from targeted and whole genome de novo assembly. They spoke about the PromethION line of sequencing which can produce up […]
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