sequencing

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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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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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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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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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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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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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The Serratia that Wasn’t Red… and Wasn’t marcescens

Levin Joe Klages from CeBiTec in Bielefeld University, Germany presented at the Nanopore Community Meeting 2022 on “Analysis of clinical research samples by nanopore sequencing with Q20+ chemistry reveals inaccurate classifications within the genus Serratia.” We used Q20+ chemistry to sequence a “red” isolate which ended up being Serratia according to our classification. I was […]
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Plasmids and Gene Transfers

Dr. Erin L. Young from the Utah Public Health Laboratory spoke a the Nanopore Community Meeting 2022. The ten-minute session was entitled “Long-read sequencing enables in-depth characterization of plasmids encoding KPC-2 in Citrobacter freundii outbreak. Young is a senior bioinformatician. Young explained that antimicrobial resistant (AMR) infections can be expensive and challenging to treat. Citrobacter […]
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Influenza WGS Surveillance and Direct RNA Sequencing of Brain Samples!

Tonight I watched two short Nanopore Community Meeting 2022 recordings. I started with Sarah Scott from the the Minnesota Public Health Laboratory, USA who presented on the “Exploration of Oxford Nanopore long-read sequencing to contribute to influenza surveillance at the state level.” Scott is an APHL and CDC Fellow. Scott explained that genomic surveillance of […]
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The Mortino Genome

Karla Estefania Rojas Lopez presented at the Nanopore Community Meeting 2022 a ten-minute session entitled “Draft genome of mortino (Vaccinium florib), a wild berry species of the Andean paramo.” Rojas Lopez works at the Universidad de San Francisco de Quito in Ecuador. This is the second session I watch presented by a researcher from this […]
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