sequencing

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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CNV and SV Detection

Luis Paulin from the Baylor College of Medicine presented at London Calling 2023 a short session entitled “The long and short of structural variants using Oxford Nanopore Sequencing.” Paulin described how genomic variation caused structural variants (SV) and copy number variants (CNV). Using long-read technology allows for access to difficult to sequence genomic regions, thus […]
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Improved DNA and RNA Sequencing with R10.4.1 and Duplex Reads

Miten Jain from Northeastern University presented at London Calling 2023 about “A complete analysis of human genomes and transcriptomes using nanopore sequencing.” They spoke about R10.4.1 ultralong DNA sequencing. Jain’s group has been using this sample prep and flow cells with N50s between 90-110 kb and throughput of >100 Gb per PromethION flow cell. The […]
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Enrichment and Sequencing for Carrier Screening

Tonight I watched a short London Calling 2023 session entitled “The dark side of carrier screening: illuminating hard-to-decipher genes in common genetic disorders with nanopore sequencing.” Bradley Hall from Asuragen in the US was the presenter. Hall is the director of research in Asuragen. They spoke about how carrier screening has evolved and more genes […]
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The Galapagos Genetic Barcode Project

Jaime A. Chaves from San Francisco State University and the Universidad San Francisco de Quito in Ecuador spoke at London Calling 2023 on “Galapagos Genetic Barcode: a model for island economic resilience during the COVID-19 pandemic.” Chaves explained how their interests in science and community merged with this project. Galapagos is a top tourist destination […]
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New and Annotated Medically-relevant Genes Expressed in the Frontal Cortex

Bernardo Aguzzoli Heberle from the University of Kentucky presented at London Calling 2023 on “Oxford Nanopore long-read RNA sequencing enables precise RNA isoform discovery and quantification in human brains.” They shared an example of how longer reads allow for better RNA isoform quantification and discovery. Aguzzoli Heberle also noted that Nanopore sequencing yields more uniquely […]
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Malaria Surveillance with Nanopore Sequencing

We are at the beach! What a week! Tonight I watched William Hamilton from the Wellcome Sanger Institute in the UK speak at London Calling 2023 on “Nanopore sequencing for real-time genomic surveillance of Plasmodium falciparum.” They are applying Nanopore sequencing to surveillance of malaria, assay development in Ghana, and training. Hamilton described malaria as […]
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Discovery of Novel Splice Sites

Ricardo De Paoli-Iseppi from the University of Melbourne in Australia spoke about the “Discovery of novel neuropsychiatric disorder risk-gene transcripts in the human brain” as part of London Calling 2023. They explained that different isoforms can lead to disease states. They extracted RNA from healthy control tissues and postmortem brain tissue. The team used long-read […]
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