Softwares

Clinicians and Bioinformaticians Using Nanopore for Diagnostics

Tonight I watched the London Calling 2023 panel “The future of clinical genomics.” Four panelists were asked several questions. The first was about the role of bioinformaticians in clinical work. One panelist spoke about how clinicians work on the automation and presenting the data. The exchange with bioinformaticians has helped the clinicians make the most […]
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Liquid Biopsies for Longitudinal Non-invasive Cancer Monitoring

Tonight we started our first P2 run with two PromethION flow cells. I also continued watching the London Calling 2023 Showcase Stage on liquid biopsy. I watched them out of order! Today I watched Billy Lau from Stanford University School of Medicine do a quick presentation titled “Nanopore sequencing of cell-free DNA for methylation-based breast […]
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Better Libraries and Improved Sequencing for Liquid Biopsy Samples

I continued watching the London Calling 2023 Showcase Stage sessions on liquid biopsies today. I watched the question and answer session. Panelists spoke about using amplicon panels and the Flongle. One panelist uses amplicon sequencing with Nanopore devices because they are able to go from sample to results in under eight hours. Another panelist answered […]
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Multi-modal Liquid Biopsy Analysis in Children with Cancer

Tonight I watched the London Calling 2023 session entitled “The potential application of nanopore sequencing for liquid biopsy analysis in children with cancer.” The second speaker was Carolin Sauer, a public research fellow at EMBL-EBI in the UK. Sauer focused on pediatric cancers and noted that they are the leading cause of death in the […]
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ONT Duplex and HiFi Reads for T2T Assemblies

Dr. Sergey Koren from the National Institutes of Health presented at London Calling 2023 on “Automated telomere-to-telomere crop genome assembly using only Oxford Nanopore sequencing.” His background is in computer science. Dr. Koren began by mentioning that the telomere-to-telomere (T2T) human genome was recently completed, adding almost 8-10% to the genome. He described how Nanopore […]
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Methods to Study Mitochondrial DNA Variation

Mo Li from King Abdullah University of Science and Technology (KAUST) in Saudi Arabia presented a five-minute session about “Single-cell full-length nanopore sequencing for quantitative variant analysis of native and genome-edited mitochondria.” They explained that human mitochondrial DNA (mtDNA) has a circular genome of 16.5 kb. Mutant mtDNA has an uneven distribution in tissues, and […]
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tRNA Profiling with Nanopore Sequencing

Tsutomu Suzuki from the University of Tokyo in Japan presented at London Calling 2023 a fifteen-minute recorded session about “Nanopore sequencing of tRNA modifications.” Suzuki is a biochemist in the field of RNA biology. They began describing how RNA modification enriches the diversity of RNA. Suzuki noted that tRNA modifications have been studied for a […]
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VAX-seq for mRNA Vaccine Quality Analysis

Helen Gunter from the Australian Institute for Bioengineering and Nanotechnology at the University of Queensland in Australia spoke at London Calling 2023 about “Using nanopore sequencing to understand the manufacture, delivery, and action of mRNA vaccines.” Gunter explained how they use Oxford Nanopore Technologies devices and sequencing in vaccine development. They spoke about the mRNA […]
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The IsoMix Toolkit for Long-read RNA-seq

Michael Clark from The University of Melbourne in Australia presented at London Calling 2023 the session entitled “Investigating RNA isoform expression using the IsoMix toolkit.” They have created tools for RNA isoform analyses. Clark shared an example of a human gene expressed in multiple RNA isoforms. They explained that alternative isoforms can create RNAs and […]
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