sequencing

Use of Long-read Sequencing in a Contract Food Laboratory

Andrzej A. Benkowski from Eurofins Microbiology Laboratories in Madison, WI, presented at London Calling 2023 a lightning talk on the “Practical uses of nanopore long-read sequencing in a high-throughput contract food laboratory.” They presented a few case studies from the contract lab. The first case study was from a client who experienced an increase in […]
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Highly Multiplex Aptamer-based Biomarker Detection with ONT

Caroline Koch from the Imperial College in London, UK, presented at London Calling 2023 a lightning talk on “Novel screening platform for highly multiplexed biomarker analysis.” Koch was a Ph.D. student and explained why we need methods for multiplexed biomarker detection by emphasizing how we all express diseases differently and need sensitive diagnostic methods. They […]
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Identification of Extrachromosomal Circular DNA Molecules in Cancer Patients

Fei Xiao from the Beijing Hospital in China presented at London Calling 2023 a lightning talk on “Small extrachromosomal circular DNAs as biomarkers for potential pan-cancer diagnosis and prognosis.” Xiao noted that extrachromosomal circular DNA (eccDNA) are circular DNA molecules that are independent of conventional chromosomes and most are smaller than 10 kb. The study […]
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Structural Variants from the Bovine Long Read Consortium

I am continuing to watch the London Calling 2023 on-demand lightning talks. Tonight, I watched the session “Discovering the missing variation: a long-read sequencing study into the structural variation in two dairy breeds” by Tuan Viet Nguyen, a research scientist from Agriculture Victoria in Australia. They spoke about structural variants, defined as genomic variants larger […]
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Targeting Mobile Elements in Alzheimer’s

I started watching the on-demand lighting talk recordings from London Calling 2023 tonight. I started with Camille Mumm’s session. Mumm is from the University of Michigan and presented on “Exploring the impact of mobile elements on Alzheimer’s disease using targeted long-read sequencing.”Mumm is also a graduate student (at the time of recording). They spoke about […]
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Accuracy Improvements in Crop Genome Assembly

Tonight, I watched a recording from the Nanopore Community Meeting 2021 featuring Alexander Wittenberg from KeyGene in the Netherlands. They presented “Accuracy improvements in crop genome assembly using the Q20+ chemistry.” KeyGene is a crop innovation company, and they are generating new tools for genome assembly and structural variant analysis, among other analyses. They built […]
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Studying Centromere Structure with ONT

I continue to watch the YouTube “Assembly” playlist from the Oxford Nanopore Technologies (ONT) channel. Tonight, I watched session #8! Ian Henderson from the University of Cambridge in the UK presented at the Nanopore Community Meeting 2021. The session was titled “Assembling the centromeres – the ‘black holes’ of the genome.” Henderson said the centromeres […]
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Liftoff and Novel Gene Annotation

Alaina Shumate from Johns Hopkins University was a speaker at the Nanopore Community Meeting 2021. Shumate was a graduate student and worked on “The annotation of novel genes in a complete human genome.” They noted that in 2003, scientists “finished” the human genome, but reions were still incomplete. In 2021, the Telomere-to-Telomere (T2T) Consortium was […]
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CanSeq150 to Sequence Canada’s Most Endangered Species

The London Calling 2021 session “CanSeq150: high-resolution genomic sequencing and assembly of 150 Canadian species” caught my attention today. Jahanshah Ashkani from Canada’s Michael Smith Genome Sciences Center was the speaker. The goal is to save Canada’s rich biodiversity by sequencing unique species. Loss of biodiversity is an issue: there are over 700 species at […]
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Sequencing a Fungal Banana Pathogen

Luca Degradi from the University of Milan in Italy presented at London Calling 2021 about “Chromosome-level genome assembly of Fusarium musae using MinION.” They described this organism as a “cross-kingdom pathogen” reported by the HUPLANTcontrol program in Europe. The organism can infect bananas and humans! The first infection seems to have been a human. At […]
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