sequencing

Nanomonsv

Yuichi Shiraishi from the National Cancer Center in Japan presented at London Calling 2023 on “Precise characterization of somatic complex structural variations from paired long-read sequencing using nanomonsv.” Shiraishi explained that long-read sequencing is effective for detecting somatic structural variations (SVs), though there are few tools for systematically detecting somatic SVs using paired tumor and […]
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Personalized OncoGenomics Program Trials using Long-Read Sequencing

Tonight I watched the London Calling 2023 session by Kieran O’Neil from Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Canada. The session title is “The potential of nanopore sequencing for personalised genomics.” They have been supporting a Personalized OncoGenomics Program (POG) that has focused on short-read whole genomes and interested in long-read sequencing […]
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The Genomics England Long-read Sequencing Program

I am at the Gordon Research Conference in Maine. This is my first GRC! I was able to rest a little this afternoon and watched the London Calling 2023 session entitled “Genomics England long-read cancer whole -genome sequencing pilot” presented by Helen Webb from Genomics England, UK. Genomics England is also called GEL. Webb disclosed […]
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Deconvoluting Methylomes with Nanomix

Tonight I started watching videos from London Calling 2023! I started with the presentation by Jonathan Broadbent from the Ontario Institute for Cancer Research & the University of Toronto, Canada. Broadbent presented about “Nanomix: methylation-based cell-type deconvolution for low-pass nanopore sequencing.” They defined cell-free DNA (cfDNA) as “a mix of DNA from blood cells and […]
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Direct RNA Sequencing Identifies NMD Targets

Anna Glushkevich from the Shmyakin-Ovchinnikov Institute of Bioorganic Chemistry in the Russian Federation, presented at the Nanopore Community Meeting 2021 on “Direct RNA sequencing reveals unusual NMD targets in plants.” They study nonsense-mediated RNA decay (NMD), a mechanism that regulates up to 10% of cellular transcripts! This is the second time I hear about Nanopore […]
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Profiling Gene Expression of Pediatric Leukemia Samples

Jeremy Wang from the University of North Carolina at Chapel Hill presented at the Nanopore Community Meeting 2021 on “Classification of pediatric acute leukemia using full-length transcriptomics.” This research was a collaboration for a pediatric oncologist also at UNC. They spoke about the variation in treatment of pediatric cancers based on local. Cellular and genetic […]
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Cas9 Enrichment for KIR Haplotype Analysis

Tonight I watched the Nanopore Community Meeting 2021 session by Jesse Bruijnesteijn from the Biomedical Primate Research Center in the Netherlands. Their session was entitled “Rapid characterization of complex killer cell immunoglobulin-like receptor regions using Cas9 enrichment and nanopore sequencing.” They began by explaining the role of NK cell activation in recognizing inhibitory and activating […]
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CanMAGs from Long-read Assemblies

Anna Cusco from Vetgenomics in Spain spoke at the 2021 Nanopore Community Meeting about “Long-read metagenomics and Hi-C proximity ligation to characterize a canine fecal microbiome.” They have been characterizing microbiomes using metagenomics and Hi-C. The (now) classical approach is amplicon sequencing; however, it allows for taxonomic classification but not everything can be detected. With […]
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Barcode-aware Sequencing

Alexander Payne from the University of Nottingham in the UK presented at the 2021 Nanopore Community Meeting about “Barcode-specific adaptive sampling – from human gene panels to viral amplicons.” They spoke about ReadFish or “Read Until” which is an adaptive sampling toolkit. They ran an experiment with four different species to test adaptive sampling for […]
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