Year: 2023

Strand-seq for Haplotyping and Parent-of-origin Assignments

Vahid Akbari is a Ph.D. student at BC Cancer in the Genome Sciences Centre in Canada. They presented at the Nanopore Community Meeting 2022 a session entitled “Simultaneous haplotyping and parent-of-origin assignment of homologous chromosomes without parental sequence data.” The approach they developed allows researchers to haplotype chromosomes and assign parent-of-origin without parent data. They […]
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The Advantages of POD5

I have been thinking and learning about POD5 files. Tonight, I watched a relevant Nanopore Community Meeting 2022 session by Alex Merry, Instrument Software Fellow at Oxford Nanopore Technologies. The session was entitled “Arrow: pointing the way forward for high-performance nanopore signal handling with POD5.” They began talking about FAST5 files to store signal data […]
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Fungal Symbioses and Nanopore Sequencing

Jessica Allen from Eastern Washington University presented at the Nanopore Community Meeting 2022 on “Using nanopore sequencing to investigate genome evolution in fungal symbioses: ploidy, repetitive elements, and reproduction.” Allen studies fungi and mentioned that human fungal pathogens and those affecting plant systems are on the rise. Allen studies lichens. Lichenized fungi are diverse, abundant, […]
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Targeted Sequencing of Mycobacterium tuberculosis Resistance Genes with Nanopore

“Profiling drug-resistant Mycobacterium tuberculosis with targeted nanopore sequencing” was the title of the sessionn Shannon Murphy from the Wadsworth Center – New York State Department of Health presented at the Nanopore Community Meeting 2022. Murphy spoke about how they are planning on using Nanopore sequencing to address some of the challenges of Mycobacterium tuberculosis (MTB). […]
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Branching Out to Sequence Single-cell Transcript Isoforms with Nanopore

Tonight I watched Sheridan Cavalier from The John Hopkins University School of Medicine present at the Nanopore Community Meeting 2022. The title of the session was “Single-cell transcript isoform sequencing of the activated adult mouse hippocampus with 10x Genomics and Oxford Nanopore.” Cavalier is a graduate student and developed an approach to sequence mouse hippocampus […]
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Dimelo-seq and CENP-A to Determine the Centromere Protein A Landscape

Yuan (Daniel) Xu from the University of California, Santa Cruz, spoke about the “Determination of the centromere protein A landscape at single-molecule resolution” during the Nanopore Community Meeting 2022. Their five-minute session was based on their work as a graduate student. They spoke about centromere localization and how CENP-A helps determine the region. The objective […]
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Sniffles2 and Structural Variations

Tonight I watched Fritz Sedlazeck from The Baylor College of Medicine Human Genome Sequencing Center present at the Nanopore Community Meeting 2022 on “Rapid structural variant calling across AllOfUs using Oxford Nanopore sequencing.” Sedlazeck spoke about structural variations (SV) that are 50bp+ genomic alterations. Long read sequencing SV calling improves detection. Sedlazeck and team created […]
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Exploring Isoform Diversity

Tonight I watched the Nanopore Community Meeting 2022 session by Alisa MacCalman from the University of Exeter in the UK. The title of the session was “Ultra-deep targeted transcript sequencing identifies isoform diversity across human pancreatic development.” MacCalman spoke about pancreatic development and that most of the knowledge is from mouse models. They are interested […]
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Mapping Chromosomal Translocations

“Can nanopore long-read sequencing replace current cytogenetic methods in clinical genetic diagnostics” was the title of Emilie Boye Lester’s session at the Nanopore Community Meeting 2022. Lester is from Odense University Hospital in Denmark and explained that the aim of their study was to “explore the capability of long-read whole genome sequencing to detect structural […]
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exRNA in Blood!?

Jasper Verwilt from Ghent University in Belgium presented at the Nanopore Community Meeting 2022 on “Revealing plasma exRNA’s deepest secrets.” The title of this ten-minute session was intriguing. Verwilt explained that human blood is a very unfriendly environment, yet some exRNA exist! I had never thought about this! There are, Verwilt shared, linear and circular […]
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