Tonight I watched the Oxford Nanopore Technologies (ONT) PAG Industry Workshop session titled “A single-platform solution for plant de novo genome assembly.” Jeannie Mounger, a field applications scientist with ONT, was the presenter. They noted that for plant genome assembly there are several considerations. Plant genome size varies greatly: from Mb to Gb. Polyploidy varies […]
Fritz Sedlazeck from Baylor College of Medicine spoke at the Nanopore Community Meeting in Boston on the “Detection of mosaic and somatic structural variants with Sniffles2.”Sedlazeck spoke about the advantages of long-read sequencing for structural variant detection. Their team is improving Sniffles2 for insertions and deletions and larger structural variants. Full structural variant genotyping requires […]
J. (Gus) Gustafson from the University of Washington spoke at the Nanopore Community Meeting in Boston about “needLR: a structural variant filtering and prioritization tool for long-read sequencing data.” They noted that half of suspected Mendelian conditions remain undiagnosed after current clinical testing methods. The Miller Lab at the University of Washington uses Oxford Nanopore […]
Matthew Jones from Stanford University presented at London Calling 2024 a session titled “CoRAL accurately resolves extrachromosomal DNA structures with long-read sequencing.” This toolkit can be used to study extrachromosomal or ecDNA, a form of oncogene amplification in cancers. ecDNA is not found in normal cells, is associated with shorter patient survival, and is large: […]
Tonight, I watched the London Calling 2024 session on “breaking boundaries in neurodegenerative disease research.” Cora Vacher from Oxford Nanopore Technologies (ONT) introduced the speakers and facilitated the question and answer session. Joanne Trinh from the Institute of Neurogenetics at the University of Lubeck in Germany was the first presenter. Trinh works with a research […]
My Linh Thibodeau from the University of British Columbia in Canada presented at London Calling 2019 on “Resolution of germline hereditary cancer structural variants using nanopore sequencing.” They began talking about the Personalized OncoGenomics Program (POG), which is an initiative of BC Cancer. The study enrolls participants and conducts extensive genomic analyses. The team evaluated […]
I am continuing to watch the London Calling 2023 on-demand lightning talks. Tonight, I watched the session “Discovering the missing variation: a long-read sequencing study into the structural variation in two dairy breeds” by Tuan Viet Nguyen, a research scientist from Agriculture Victoria in Australia. They spoke about structural variants, defined as genomic variants larger […]
Tuan Viet Nguyen, a research scientist from Agriculture Victoria in Australia, presented at London Calling 2023 on “Discovering the missing variation: a long-read sequencing study into the structural variation in two dairy breeds.” They defined structural variants (SVs) as larger than 50 bps and can be deletions, duplications, and inversions. Structural variants, Nguyen noted, are […]
Luis Paulin from the Baylor College of Medicine presented at London Calling 2023 a short session entitled “The long and short of structural variants using Oxford Nanopore Sequencing.” Paulin described how genomic variation caused structural variants (SV) and copy number variants (CNV). Using long-read technology allows for access to difficult to sequence genomic regions, thus […]
Kieran O’Neill from Canada’s Michael Smith Genome Sciences Center (GSC), BC Cancer, Canada presented at London Calling 2022 on “Nanopore sequencing shows potential for personalised oncogenomics.” O’Neill spoke about the GSC’s work on genome research and sequencing. They have a Personalized Oncogenomics Program (POG) that consists of taking a biopsy, whole genome transcriptome analysis, reporting, […]