Year: 2023

Methods for Exploring the Genotyping Haystack

The next Nanopore Community Meeting 2022 session I watched was a longer: 27 min. “Finding the needle: haplotype-resolved discovery and annotation of clinically relevant genetic and epigenetic variants using whole-genome nanopore sequencing” was presented by Sissel Juul and Phillipp Rescheneder, both from Oxford Nanopore Technologies. Juul described the work of their team to sequence genomes […]
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Methylation Profiles of Cell-Free DNA in Cancer Research

Billy Lau from Stanford University School of Medicine spoke at the Nanopore Community Meeting 2022. Lau’s 20-minute session was entitled “Single molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing.” The study had the goal of exploring the “potential utility of nanopore sequencing for assessing cancer in cfDNA.” Lau explained that the conventional […]
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Entering the T2T Era?

Telomere-to-telomere assembly has been coming up in Nanopore Community Meeting 2022 sessions frequently. The session I watched tonight had it in the title: “Expanding studies of global genomic diversity with complete, telomere-to-telomere assembly of diploid genomes” presented by Karen Miga from the University of California, Santa Cruz. Miga shared information about the release of the […]
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Variations in Cancer Susceptibility Identified through Long-read Sequencing

Katherine Dixon from The University of British Columbia in Canada spoke at the Nanopore Community Meeting 2022 about “Clinical and functional significance of germline variation in cancer susceptibility and disease.” Dixon spoke about the complexity of factors determining cancer. Between 15-20% of cancer show familial clustering, according to Dixon. In Canada, 300,000 are estimated to […]
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Identifying Complex Structural Variation with Nanopore Long-read Sequencing

“Long-read sequencing resolves cryptic structural variation in individuals with syndromic intellectual disability” was the title of the presentation Griet De Clercq from Ghent University in Belgium gave at the Nanopore Community Meeting 2022. De Clercq noted that “40% of people with intellectual disability (ID) remain without genetic diagnosis” and that current diagnostic tests used in […]
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STR Sequencing for Forensic Profiles with STRspy

Courtney Hall from the University of North Texas Health Science Center presented at the Nanopore Community Meeting 2022 on “STRspy-ing hidden variation in forensic DNA profiles using the MinION device.” Hall spoke about how short tendem repeats (STRs) are often used as the “gold standard for human identification in forensic investigations” due to their variability […]
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Sequencing of HCV for Identification of Resistance Mutations

Kame A. Galan-Huerta from the Autonomous University of Nuevo Leon in Mexico presented at the Nanopore Community Meeting 2022 a ten minute session entitled “Identification of resistance mutations to direct-acting antiviral agents against HCV in infected subjects in Mexico.” They spoke about adapting protocols to detect the RNA positive sense hepatitis C virus. Glan-Huerta explained […]
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Metagenomic Binning Considering Modifications

Soren Heidelbach spoke at the Nanopore Community Meeting 2022 about “Developing new bioinformatics methods to identify modifications from nanopore sequencing.” Heidelbach is from Aalborg University, Denmark. They did metagenomic binning: grouped contigs based on information from k-mers and coverage and also considered modification motifs. Their modification of metagenomic binning was to include base modification as […]
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Tilapia, ISKNV, and Tiled PCR

Shayma Alathari from the University of Exeter was the next presenter at the Nanopore Community Meeting 2022 that I watched present. Their five-minute session was very brief, and packed with information. The title of Alathari’s session was “Development and application of genomic tools for tracking viral outbreaks in fish.”Alathari is a Ph.D. student interested in […]
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Nanopore Sequencing to Investigate Splicing Order and Deadenylation Trends

Karine Choquet from Harvard Medical School spoke at the Nanopore Community Meeting 2022 about “Direct RNA sequencing reveals multi-intron splicing order and poly(A) tail lengths across subcellular compartments.” This five-minute session began by explaining RNA processing and removal of introns in eukaryotic gene expression. Choquet explained that “RNA processing is essential for eukaryotic gene expression” […]
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