Year: 2023

ecDNA Sequencing and Assembly

Tonight, the IPERT summer workshops ended. Sissel Juul & Phill James presented at the Nanopore Community Meeting 2021 about “For want of a nail: investigating somatic and germline variations in cancer.” They are both at Oxford Nanopore Technologies in the Genomics Application Team. In 2021, they spoke about extrachromosomal DNA in cancer. Juul spoke about […]
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Different Cytosine Methylations and DeepSignal-plant

Feng Luo from Clemson University presented at the Nanopore Community Meeting 2021 about “Genome-wide detection of cytosine methylations in plants from nanopore data using deep learning.” They are faculty in computer science at Clemson. They spoke about detecting methylation from nanopore signals. They developed the DeepSignal tool. Nanopore has developed Megalodon, and there is also […]
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Epigenetic Aging Clock for Cattle

Loan to Nguyen from The University of Queensland, Australia presented at the Nanopore Community Meeting 2021 on “An epigenetic aging clock for cattle using portable sequencing technology.” They spoke about the need learn birth date of cattle for breed registrations and genomic selection. However, there is no gene clock for cattle. Thus, they took sixty […]
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Genomic Technologies for STR Analysis

Ira Deveson from The Garvan Institute of Medical Research in Australia presented at the Nanopore Community Meeting 2021 on “Towards comprehensive genetic diagnosis of repeat expansion disorders with targeted nanopore sequencing.” Deveson spoke about the ReadUntil function also known as adaptive sampling to selectively sequence molecules. Short tandem repeats (STRs) are 2-12 bp sequence motifs […]
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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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