Year: 2024

Shifting to Oxford Nanopore for Clinical 16S rRNA Gene Sequencing

Trish Simner is the Director of Bacteriology and Infectious Disease Sequencing Laboratories. They work at the Johns Hopkins University School of Medicine in Baltimore, Maryland. They presented at London Calling 2024. The session’s title was “Bringing Nanopore Sequencing into the Clinical Microbiology Setting with Targeted Approaches.” Simner spoke about the advantages of long reads and […]
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Ultra-fast Deep-learned CNS Tumor Classification using Nanopore-sequencing

I watched a session from the Oxford Nanopore Technologies Clinical & Biopharma Day tonight. It was held on May 24, 2024 (part of London Calling 2024). Professor Pieter Wesseling is from the Princess Maxima Center for Pediatric Oncology in the Netherlands. He is also from the Amsterdam University Medical Centers. He presented the session titled […]
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Improved Plant Genome Assembly with Ultra-Long Nanopore Sequencing

Bosheng Li from the Institute of Advanced Agricultural Sciences of Peking University in China presented at London Calling 2024. The session’s title was “Plant T2T genome assembly using ultra-long and adaptive nanopore sequencing.” They spoke about the importance of ultra-long reads. These reads produce N50 length >100 kb. These are crucial in the assembly of […]
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Ultra-Rapid, Long-Read Whole-Genome Sequencing with BadgerSeq

Stephen Meyn from the Center for Human Genomics and Precision Medicine at the University of Wisconsin-Madison presented at London Calling 2024. The session title was “BadgerSeq: a deecentralized model for ultra-rapid, long-read, whole-genome sequencing.” Meyn spoke about rare genetic disorders in the NICU and the importance of diagnosis. Meyn emphasized the need for speed and […]
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Long-Read Sequencing and Methylation Pattern Characterization in 1000 Genomes Project

Sophia Gibson from the University of Washington presented at London Calling 2024 on “Haplotype-resolved repeat expansions & methylation patterns in 1000 Genome Project data.” Gibson noted that clinical genetic testing typically requires multiple tests and clinic visits… and is diagnostic in fewer than 50% of cases. This is described as the “diagnostic odyssey.” Long-read sequencing […]
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KeyGene’s Innovative Approach to Banana Pangenome Research

Alexander Wittenberg from KeyGene in the Netherlands spoke at London Calling 2024 about “Unlocking the banana pangenome: harnessing genetic diversity.” They explained that the genetic diversity of bananas is very low because of the passaging of a single clone. Fusarium wilt and black Sigatoka cause disease and elicit the spraying of large amounts of pesticides. […]
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Uncovering Vaccine Resistance: Genome Sequencing of 198 UK Bordetella Pertussis Strains

Sarah Cameron from the University of Bath presented at London Calling 2024 a short session with the title “100 years of Bordetella pertussis evolution in the UK.” They noted that we have had a vaccine for Bordetella for decades and it changed to an acellular version in 2001. The genome of this organism varies through […]
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Genomic Studies of Adeno-Associated Virus Hepatitis: 2022 Pediatric Outbreak and Gene Therapy Effects

Oscar Enrique Torres Montaguth from the University College London in the UK presented a short talk at London Calling. The title was “Genomic studies of adeno-associated virus hepatitis.” They studied the 2022 pediatric hepatitis outbreak using metagenomic sequencing approaches. They identified AAV2 in liver and blood samples of almost all cases, and adenoviruses and herpesviruses […]
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CoRAL Toolkit: Studying Extrachromosomal DNA for Cancer Research

Matthew Jones from Stanford University presented at London Calling 2024 a session titled “CoRAL accurately resolves extrachromosomal DNA structures with long-read sequencing.” This toolkit can be used to study extrachromosomal or ecDNA, a form of oncogene amplification in cancers. ecDNA is not found in normal cells, is associated with shorter patient survival, and is large: […]
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Long-read Sequencing Unveils Parkinson’s Disease Genetic Variants

Guillaume Cogan from the Paris Brain Institute in France and the National Institutes of Health in the US presented at London Calling 2024 on “Long-read sequencing to solve exome negative Parkinson’s disease.” Cogan explained that genetics and environmental susceptibility factors contribute to 90% of Parkinson’s disease in patients. However, 10% of patients have autosomal dominant […]
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