Month: May 2023

Real-time Sequencing of Brain Samples

Franz-Josef Müller & Helene Kretzmer gave a presentation at the Nanopore Community Meeting 2021 about “Real-time cancer classification with nanopore sequencing.” Kretzmer defined real-time sequencing as “short time” sample processing from wet lab to bioinformatics. Muller explained that they have optimized a protocol for identification of brain cancers. They start with a rapid DNA extraction […]
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High-throughput Testing in Indonesia

Ariel Pradipta from the Genomik Solidaritas Indonesia Lab (GSI Lab) spoke at the Nanopore Community Meeting 2021 on “The First 100 days of establishing nanopore-based sequencing for national SARS-CoV-2 surveillance.” Pradipta is a senior researcher fellow assisting in the national genomic efforts. They recognized a gap in rapid sequencing. To address this, they worked on […]
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Starting Graduate School in a Sequencing Laboratory

Hannah Trivett from the University of Liverpool is a doctoral student who presented at the Nanopore Community Meeting 2021. The title of the presentation was “Highlights of a regional sequencing surveillance hub during a global pandemic.” They described the COVID-19 Genomics UK Consortium involved in a massive sequencing initiative. The University of Liverpool is involved, […]
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Hypermethylation Detection in Disease

Ulf Birkedal from Copenhagen University Hospital in Denmark spoke at the Nanopore Community Meeting in 2021 about “Nanopore sequencing increases resolution of DMPK hypermethylation in myotonic dystrophy type 1 patients.” Myotonic Dystrophy Type 1 (DM1), explained Birkedal, is an autosomal dominant multisystem disorder. Muscle degeneration, weakness, and myotonia are the symptoms, and Birkedal noted that […]
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Genomic Skimming on the MinION

I continue to watch Nanopore Community Meeting 2021 recordings and will spend some time later this week focusing on the London Calling 2023 Masterclasses. Tonight, I watched Joanna Malukiewicz from the German Primate Center present on “Genomic skimming on the MinION uncovers cryptic hybridization in the buffy-tufted marmoset, one of the world’s most threatened primates.” […]
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Org.one Collaborations for Sequencing Biodiversity

Tomas Marques-Bonet from the Institute of Evolutionary Biology in Spain presented at the Nanopore Community Meeting 2021 about “Org.one: a new program to promote sequencing biodiversity.” Tomorrow London Calling 2023 begins and I am continuing to watch previous sessions. Marques-Bonet highlighted how biodiversity is at risk, with more than 37,400 species threatened with extinction. Amphibians […]
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The Biological Implications of DNA and RNA Modifications

Ewan Birney from EMBL & EMBL-EBI in the UK presented at the Nanopore Community Meeting 2021 on “DNA and RNA modifications: how nanopore is giving us new biological insights -from COVID to gene expression.” They began by explaining that nanopore sequencing and sensing modification was recognized as feasible in 2014. DNA modifications such as CpG […]
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Signal Analysis with Uncalled4

Sam Kovaka, a PhD candidate from Johns Hopkins University, spoke at the Nanopore Community Meeting 2021 about “Visualization and analysis of nanopore RNA and DNA signal alignments with UNCALLED4.” They explained adaptive sampling (AKA “ReadUntil“): “software-based targeted sequencing via selective ejection of reads” Kovaka explained that this requires rapid identification based on the beginning of […]
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Bioprospecting in the Spanish Desert

Adriel Latorre-Perez from Darwin Bioprospecting Excellence S.L. in Spain presented at the Nanopore Community Meeting 2021 about “A round trip to the desert: in situ nanopore sequencing informs targeted bioprospecting.” They defined microbial bioprospecting as “the search for biotechnologically-relevant products from microbial communities.” The products could be enzymes, molecules, or microbiomes. The process starts with […]
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Characterization of Transgenic Constructs through Long-read Sequencing

Jolien D’aes from Sciensano, Belgium presented at the Nanopore Community Meeting 2021 on “Characterization of genetically modified microorganisms is facilitated by long-read whole-genome sequencing.” They explained that Sciensano is the Belgian science institute for food and animal safety. They monitor GMO-derived fermentation products. They may contain antimicrobial genes as resistance markers. Regulation prohibits the presence […]
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