Year: 2024

Nanopore Sequencing for Clinical Labs: Case Studies from New Zealand

Tonight, I watched Rhys White from the Institute of Environmental Science and Research in New Zealand present “Real-time genomic surveillance with nanopore sequencing.” They have started a collaboration with the Wellington Regional Hospital. The goal was to make Nanopore sequencing accessible to the clinical lab. The team used a MinION device to sequence blood and […]
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Rady Children’s Institute: Discoveries in Genomic Methylation

Sergey Batalov from the Rady Children’s Institute for Genomic Medicine in the US presented at London Calling 2024 on “Patterns in genomic methylation determined with long-read sequencing.” Rady Children’s Institute is the only level four NICU in San Diego, Riverside, and Imperial counties. The Rady Children’s Hospital provides care to 256,000 kids/year! However, only 35% […]
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Detecting RNA Modifications with Nanopore Devices and IVT Reference Method

Logan Mulroney from the EMBL-EBI & Center for Genomic Science at the Italian Institute of Technology in Italy presented at London Calling 2024 “A survey of human RNA modifications by direct RNA nanopore sequencing.” Mulroney described RNA modifications as “chemical alterations to canonical nucleotides” and mentioned that they have been implicated in diseases such as […]
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Direct Amplification and Sequencing: Advancing Poliovirus Detection

Alex Shaw from the Imperial College London in the UK spoke at London Calling 2024 about “Early detection of poliovirus outbreaks in the DRC from 2021-2022.” They have been doing poliovirus sequencing training with partners for several years, focusing on direct sequencing methods with Nanopore: Direct molecular Detection and Nanopore Sequencing (DDNS). Shaw explained that […]
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Assembling a T2T Gyr Cattle Genome with Oxford Nanopore Reads

Temitayo A. Olagunju from the University of Idaho presented at London Calling 2024 on “Assembling a T2T cattle genome with Oxford Nanopore reads.”The breed of cattle they focused on is the gyr, with a characteristic hum on the back and important for milk production. They are often intercrossed/interbred with other bos cattle for their features […]
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Epitranscriptomics: Identifying m6A RNA Modifications in Neuroblastoma Cell Lines

Tonight, I watched Jade Foster from the University of Southampton in the UK present at London Calling 2024. The session’s title was “Identifying m6A RNA modifications in neuroblastoma cell lines.” They explained that epitranscriptomics describes the modification of RNA molecules. There are over 150 RNA modifications determined by readers, writers, and erasers! This process is […]
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NanoRay Platform: Autoscaling Resources & Cost-Benefit Analysis of Computational Needs

Sneha Geonka from Stanford University & Princeton presented on “Computational paradigm for scalable ultra-fast, & cost-efficient nanopore sequencing.” Goenka shared a graph showing the turnaround time for sequencing in the clinic. The world record is 7.3 hours at Stanford! To shorten the time to diagnosis, the pipeline included distributed computing and a lot of GPUs: […]
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Advancing Grapevine Breeding with Nanopore Sequencing

Tonight, I watched Max Schmidt from Geisenheim University in Germany speak about grapevine genomics at London Calling 2024. The title of the session is “Using Oxford Nanopore Sequencing in Grapevine Breeding.” The genome has 19 chromosomes and a total of 450 Mbp. Schmidt and team have been exploring variations and markers in the genome that […]
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Improving Lentiviral Gene Therapy Vectors through Direct RNA Sequencing

Tonight, I watched the London Calling 2024 session by Kathleen Zeglinski from the Walter and Eliza Hall Institute of Medical Research in Australia. The session title was “Quality Control of Gene Therapy Vectors using Nanopore Direct RNA Sequencing.” Zeglinski explained that lentiviruses are a type of RNA viruses that can integrate into the genome. Lentiviruses […]
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Alternative Splicing and Neurologic Disorders: Long-read CaptureSeq Findings

Sofia Kudasheva from Earlham Institute in the UK spoke at London Calling 2024 about “Long-read CaptureSeq identifies novel RNA isoforms of psychiatric risk genes.” They noted that alternative splicing is “a key regulator of neuronal differentiation,” occurring in 95% of human genes and involved in disorders. The team wanted to better understand the role of […]
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