Carlos C. Goller

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2023 Dorado Updates

Joyjit Daw, a Principal Machine Learning Engineer at Oxford Nanopore Technologies (ONT), provided a Dorado update at the Nanopore Community Meeting Houston meeting. The Dorado v0.5.0 release supports core Guppy features, custom barcodes, read splitting, and Minimap2 alignment. Dorado has been integrated into MinKNOW. They have also extended features such as hemi methylation for the […]
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Dog Patients, Osteosarcoma, and Severus Structural Variant Analyses

Mikhail Kolmogorov from the National Cancer Institute, NIH, spoke at the Nanopore Community Meeting Houston about “Nanopore sequencing reveals structural heterogeneity in canine osteosarcoma.” Structural variants are any alterations greater than 50 bp. These events can affect one or multiple genes… or whole chromosomes! NCI has a comparative osteosarcoma (OS) program that recruits dogs nationwide. […]
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Streamlined Nanopore Sequencing

“Reveal more: bring streamlined nanopore sequencing into your lab” is the title of the Nanopore Community Meeting Houston session I watched tonight. Rachel Rubinstein, a Technical Product Manager, explained new developments to streamline nanopore sequencing. Rubinstein emphasized “end-to-end” processes. They began describing the range of the PromethION devices, from the P2 to the PromethION 48. […]
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Carrier Analyses using ONT

Bradley Hall from Asuragen presented at the Nanopore Community Meeting in Houston. The session was titled “AmplideX PCR and nanopore sequencing for accessible carrier screening for any lab.” Hall started by stating that “everyone is a genetic carrier of a disease or condition.” There are >2000 conditions, and carrier screening is often challenging for some […]
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ONT Workflows for the GREGoR Project

Medhat Mahmoud from the Baylor College of Medicine’s Human Genome Sequencing Center presented at the Nanopore Community Meeting in Houston a session titled “Unraveling complex Mendelian diseases with nanopore sequencing.” They are in the Sedlacek lab and spoke about GREGoR: Genomics Research to Elucidate the Genetics of Rare Diseases project. GREGoR includes five research centers […]
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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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