Tonight I watched another PAG Industry Workshop session by Oxford Nanopore Technologies. This one was titled “Pasteurized retail dairy enables genomic surveillance of H5N1 avian influenza in the United States.” Andrew Lail from the University of Wisconsin-Madison was the presenter. Lail explained that influenza is an RNA virus with 8 RNA segments. H5N1 influenza is […]
Tonight I continued watching the ONT webinar on advances in genomic profiling of respiratory viral pathogens. The second speaker was Nick Gauthier from BugSeq. The title of their session was “Translating metagenomics to the clinic.” The BugSeq team is working to develop clinical metagenomic pathogen agnostic approaches. BugSeq started working on an ONT mNGS platform […]
Serge Monpoeho from Regeneron Pharmaceuticals in the US presented at the ONT Biopharma Day in Boston. The title of the session was “Adventitious agent screening by long-read NGS.” They wanted to develop an Oxford Nanopore-driven adventitious agent detection system. They used the Ligation Sequencing Kit, heat extraction, and custom universal PCR primers. They ran for […]
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 […]
I started watching London Calling 2019 sessions to learn about fungal genomics and assembly. Sara D’Andreano from the Autonomous University of Barcelona in Spain gave a “lightning talk” on “MinION application: performing long-fragment analysis on pure fungal cultures (3.5 kb and 6 kb) and genome analysis of Malassezia pachydermatis.” D’Andreano is a Ph.D. student working […]
Hagar Mor-Shaked from the Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, presented a lightning talk at London Calling 2023. The title of the session is “Pathological short tandem repeats analysis by long-read sequencing in affected individuals.” They were also an employee of the Geneyx company that did genomic analysis. Mor-Shaked spoke […]
Marcela Aguilera Flores from Virginia Tech presented at the Nanopore Community Meeting 2019 on “Culture-free detection of boxwood blight to improve disease diagnosis and prevention.” Aguilera Flores spoke about the use of the MinION for metagenomics to detect the fungi that cause blight in the boxwood. According to Aguilera Flores, boxwood is an important ornamental […]
Tonight I watched the next video of the Human Genome Sequencing and Analysis course that is part of Nanopore Learning. The lesson is an “Introduction to SNP and Indel Detection,” and Anthony Doran, a Technical Services Scientist, from ONT discussed bioinformatics tools for SNP and indel detection. Doran spoke about the need to map/align reads […]
Erik Karlsson from the Institut Pasteur du Cambodge in Cambodia, presented at the Nanopore Community Meeting in Singapore 2023 on “Advances in rapid, accurate, field-forward sequencing to respond to avian influenza virus at the animal-human interface.” Their work focuses on warning and detection systems to detect infectious diseases. Karlsson noted that active surveillance is expensive […]
Ji Wang from the Chinese Center for Disease Control and Prevention in China presented at the Nanopore Community Meeting in Singapore this year on “Application and history of nanopore sequencing in helping China’s CDC system.” They described extensive network of the CDC in China with 3,000 units. Wang shared data from a survey of lab […]