Month: October 2023

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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Modeling Rare Variant Segregation

Min Wang from Murdoch Children’s Research Institute in Australia presented at the Nanopore Community Meeting in Singapore 2023 on “Variant segregation in rare disease singletons and duos using nanopore adaptive sampling.” They spoke about a method to learn about rare variants when samples from both parents are not available. When one DNA is not available, […]
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Myrtle Rust and Epitranscriptomics

Ashley Jones from The Australian National University in Australia presented at the Nanopore Community Meeting in Singapore on “Exploring post-transcriptional modifications during myrtle rust pathogen-plant interactions.” Myrtle rust is a biotrophic (needs a living plant to survive) fungus Austropuccinia psidii that infects plants in the Myrtaceae family and is spreading, according to Jones. Myrtle rust […]
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Ten Applications of Nanopore Technologies in Thailand

Thidathip Wongsurawat from the Siriraj Long-read Lab in the Mahidol University in Thailand, presented at the Nanopore Community Meeting in Singapore on “Ten case studies on the recent applications of nanopore sequencing in Thailand.” Number ten was nCNV-seq: Nanopore-based multiple copy number variation analyses. They developed the open access bioinformatics tool. Wongsurawat also spoke about […]
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