Month: December 2023

GoT-Splice as Mutations Accumulate

Mariela Cortes Lopez from the Weil Cornell Medicine and New York Genome Center presented at the Nanopore Community Meeting in Houston about “GoT-Splice: unraveling cell-type-specific impact of splicing factor mutations.” Cortes Lopez is investigating mutations in splicing factors. They started by explaining that cells accumulate mutations with age and, therefore, the genomes of cells are […]
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Searching for Structural Variants of Interest in the 1000 Genomes Project

Gus Gustafson from the University of Washington spoke at the Nanopore Community Meeting in Houston about “Understanding normal patterns of human structural variation with nanopore sequencing.” Gustafson is a second-year graduate student. They provided background, including these statistics: >50% of suspected Mendelian conditions remain undiagnosed after clinical testing, and up to 2/3 of structural variants […]
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Phylogeny Reconstruction of Melanoma Sublines

Yuelin Liu from the University of Maryland and the National Cancer Institute spoke at the Nanopore Community Meeting in Houston about “Analysis of melanoma evolution using nanopore long-read sequencing data.” Liu spoke about melanoma and skin cancers. While melanoma makes up only about 2% of skin cancers, it is the most aggressive. Liu explained that […]
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Air Sampling and Metagenomic Sequencing

Christina Newman from the University of Wisconsin-Madison presented at the Nanopore Community Meeting in Houston on “Metagenomic sequencing of air samples to identify human viral pathogens.” Newman spoke about the loss of resolution of SARS-CoV-2 variants with the increased use of home kits. Newman noted that indoor air sampling could be used in schools to […]
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Exploring the Genetic Variants of Autism Spectrum Disorder

Sarah Dada from Canada’s Michael Smith Genome Sequence Center and the University of British Columbia in Canada presented at the Nanopore Community Meeting in Houston. The title of the session is “Potential personalized diagnosis and treatment of autism spectrum disorder in the era of long-read sequencing.” They presented three cases and started by acknowledging the […]
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Swab to Sequence in Space

Sarah Castro-Wallace from NASA spoke at the Nanopore Community Meeting in Houston. The title of their session is “2043: A Minion Space Odyssey.” Castro-Wallace helped the audience think about a Martian habitat and using Nanopore devices to monitor crew health, planetary protection (“forward and back contamination”), and microbial surveillance. Importantly, Castro-Wallace wanted us to consider […]
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Completing Genomes of Bacterial Isolates from Outbreaks

Erin L. Young from the Department of Health and Human Services in Utah presented at the Nanopore Community Meeting in Houston on “Nanopore sequencing for enhanced antimicrobial resistance gene surveillance.” I had watched Young present previously. They spoke about using whole genome sequencing (WGS) for surveillance and its use by the Centers for Disease Control. […]
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Assay Development for Bacterial Detection

Tonight, I watched the video for Kimberlee Musser’s session at the Nanopore Community Meeting Houston 2023. Kimberlee Musser works at Wadsworth Center in the New York State Department of Health. The session’s title is “Improving bacterial disease public health testing with nanopore sequencing.” Musser represents the work of many scientists from the Wadsworth Center, New […]
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Sequencing to Study Telomere Dynamics

Tobias T. Schmidt from the Salk Institute for Biological Studies presented at the Nanopore Community Meeting in Houston on “Telomere dynamics in aging and cancer by nanopore long-read sequencing.” Schmidt is a postdoc working on sequencing and described how telomeres protect the end of linear eukaryotic chromosomes. Telomeres shorten with every round of replication in […]
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Candida Clinical Isolates and Reference Genome

Per Aspera Adastra from the Baylor College of Medicine and Texas Children’s Hospital, presented at the Nanopore Community Meeting in Houston on “Using long-read sequencing to generate a case-specific reference genome for pathogen strain typing.” I had watched the longer session before and will watch this one to learn more! Aspera Adastra is a clinical […]
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