Month: June 2023

Emerging Epigenetic Epidemiology

Eilis Hannon from the University of Exeter in the UK presented at the Nanopore Community Meeting 2021 about “Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays.” Hannon explained that there is increasing interest in epigenome and human population studies. Sodium bisulfite treatment was the most common approach for profiling along […]
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Use of Oxford Nanopore Technologies for Microlab Development

Rajesh Pandey from the CSIR-Institute of Genomics and Integrative Biology in India presented at the Nanopore Community Meeting 2021 on “Genomic surveillance for future pandemic preparedness.” The lab does integrative genomics of host-pathogen interactions focusing on high-throughput and high-priority sequencing while trying to maintain cost efficiency. They have a sample to sequence microlab workflow using […]
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Fragment and Re-ligate for Copy Number Variation Analyses

Thidathip Wongsurawat from Mahidol University in Thailand spoke at the Nanopore Community Meeting 2021 about “Nanopore-based copy number variation approach for adult glioma classification – WHO 2021.” They spoke about glioma, a type of brain tumor that grows in glial cells, and its high mortality. In 2021, WHO incorporated genotype information along with phenotype in […]
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A Quail Genome with Methylated Repeats

Elena Bolshakova from Herzen State Pedagogical University of Russia presented at the Nanopore Community Meeting 2021 on “DNA methylation analysis of a tandem repeat specific to Coturnix japonica using nanopore sequencing.” They mentioned that tandem repeats are poorly understood and yet important for the regulation of gene expression and chromosomal structure. Nanopore sequencing allows methylation […]
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Long-read Sequencing Can Identify RNA Isoforms and NMD Modulators

Evangelos Karousis is a Senior Researcher at the University of Bern, Switzerland and presented at the Nanopore Community Meeting 2021 on “Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells.” They began by describing what nonsense-mediated mRNA decay (NMD) can do how how they can be dangerous. Endogenous mRNAs can be targeted by NMD. In […]
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AmplideX PCR and Nanopore Sequencing for Carrier Screening

Sarah Statt presented at the Nanopore Community Meeting 2021 on “AmplideX PCR and nanopore sequencing deepens analysis and simplifies workflows for carrier screening.” Statt is an R&D Senior Manager at Asurgen, a Bio-Techne Brand. They spoke about the technologies needed for carrier screening. The company created AmplideX that includes long-range PCR and long-read sequencing to […]
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Olive Trees, Bacteria, Fungi, and High-throughput Screens

Manuel Anguita Maeso, a Ph.D. student, presented at the Nanopore Community Meeting 2021 a short session entitled: “Unravelling the whole genome of olive antagonistic xylem-inhabiting bacteria, to fight vascular plant pathogens in olive trees.” Anguita Maeso is from the Institute for Sustainable Agriculture, CSIC, in Cordoba, Spain. They began with an introduction to the two […]
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Genome-wide Protein Interactions with DiMeLo-seq

Annie Maslan from the University of California, Berkley spoke about “Mapping protein-DNA interactions genome-wide with DiMeLo-seq as part of the Nanopore Community Meeting 2021. They explained that existing methods for mapping protein binding use coverage as a proxy for binding.” Maslan noted that short-read methods obscure or complicate the interpretation of joint and independent binding […]
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Multiple Sequencing Approaches for HPV Analyses

Nicole Rossi & Michael Dean presented at Nanopore Community Meeting 2021 on: “Resolution of complex human papillomavirus and human sequences.” Rossi and Dean are from the National Cancer Institute. Rossi spoke about the impact of human papilloma virus (HPV). Cervical cancer causes numerous deaths. The HPV genome has two oncogenes and promotes genome instability. HPV […]
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