Oxford Nanopore Technologies

ONT Library Preparation Options

Tonight I continued watching the Nanopore Learning sessions about Metagenomics. The Metagenomics lessons I started with were “Library Preparation: An introduction and overview of the options available.” Hazel Johnson provided an overview of the library preparation protocols and kits offered. They defined library preparation as “converting sample into format compatible with the sequencing system” by […]
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RNA Structural Detection and Pore-CUPINE

Yue Wan from the Genome Institute of Singapore presented at the Nanopore Community Meeting in Singapore on “Detecting RNA structures using nanopore sequencing.” Wan’s lab has been using Nanopore to study RNA structures. Traditionally, chemical probes were used to determine structure. However, short-read high-throughput structure probing is challenging because of long complex protocols and RNAs […]
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Training for m6A Identification

Jonathan Goke from the Genome Institute of Singapore presented at the Nanopore Community Meeting in Singapore on “Identification of m6A RNA modifications at single molecule resolution using nanopore direct RNA-seq data.” They are working on methods to analyze transcriptomes and are interested in the epitranscriptome. Goke explained that m6A is one of the most frequent […]
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Population Genomics in Thailand and Australia

Tonight I watched the Population Genomics Showcase Stage from the Nanopore Community Meeting in Singapore 2023. Warren Bach, ONT Senior Strategic Account Manager in Australia, was the moderator. Hardip Patel spoke about Australia’s National Centre for Indigenous Genomics, and Manop Pithukaporn presented on Thailand were the speakers. Hardip Patel from The Australian National University presented […]
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Inactivation of X Chromosome

Tonight I watched Quentin Gouil from the Walter and Eliza Hall Institute of Medical Research in Australia speak at the Nanopore Community Meeting in Singapore about “Measuring skewed X inactivation by adaptive nanopore sequencing.” Gouil explained that there are ~2000 genes on the X chromosome, and males are more affected by X-linked diseases. They described […]
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Population-level Detection of Structural Variants and their Features

Fritz Sedlazeck from Baylor COllege of Medicine & Rice University, presented at the Nanopore Community Meeting in Singapore on “Comprehensive structural and copy number variant detection: from mosaic to population-level.” Sedlazeck and their team have developed numerous tools for structural variation (SV) detection. SV, Sedlazeck noted, are fewer than SNP but have profound impacts. Long […]
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Consensus Somatic SV Calling Using Long Reads

Tonight I watched a session from the Nanopore Community Meeting in Singapore entitled “Investigating structural variations and complex cancer genomes using Oxford Nanopore sequencing” presented by Marjan Naeini from the Garvan Institute of Medical Research in Australia. Naeini described the primary classes of structural variations (SVs) as deletions, duplications, inversions, insertions, and translocations. They studied […]
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Nanopore Sequencing for Detection of Modifications in Cancer Genomics

Genta Nagae from the University of Tokyo in Japan presented at the Nanopore Community Meeting in Singapore on “Direct detection of DNA modifications in human cancer genomes.” Nagae briefly spoke about the significance of DNA methylation in biology and cancer. They used the QIAamp and Puregene kits from QIAGEN to prepare tumor DNA for sequencing […]
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Early Warning: Every Second Counts

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 […]
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Algorithms for Long-read Analysis

Kai Ye from Xi’an Jiaotong University in China spoke at the Nanopore Community Meeting in Singapore about “Novel algorithms for long read analysis and applications.” They noted that long reads are “better for structural variant (SV) detection.” However, Ye explained that there are still challenges with long read. They converted the problem from text-based to […]
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