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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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Unraveling FSHD with Nanopore Sequencing

Morghan Lucas from the Medical Genetics Center in Germany presented at London Calling 2024 on “Genetic and epigenetic profiling of FSHD by nanopore sequencing.” Facioscapulohumeral muscular dystrophy (FSHD) is a genetic muscle disease affecting the muscles of the face, shoulders, and upper/lower limbs, Lucas explained. It is the third most common muscular dystrophy: 1:20,000. The […]
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Long-Read RNA Sequencing for Retina Transcript Isoform Identification

Rui Chen from Baylor College of Medicine presented at London Calling 2024 a session titled “Single-cell characterization of transcript isoforms with long-read RNA sequencing.” Their lab is interested in the retina since it is “the main target of irreversible blinding diseases.” In mice, there are over one hundred cell subtypes in the retina, noted Chen. […]
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Detecting RNA Modifications with Nanopore Devices and IVT Reference Method

Logan Mulroney from the EMBL-EBI & Center for Genomic Science at the Italian Institute of Technology in Italy presented at London Calling 2024 “A survey of human RNA modifications by direct RNA nanopore sequencing.” Mulroney described RNA modifications as “chemical alterations to canonical nucleotides” and mentioned that they have been implicated in diseases such as […]
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Direct Amplification and Sequencing: Advancing Poliovirus Detection

Alex Shaw from the Imperial College London in the UK spoke at London Calling 2024 about “Early detection of poliovirus outbreaks in the DRC from 2021-2022.” They have been doing poliovirus sequencing training with partners for several years, focusing on direct sequencing methods with Nanopore: Direct molecular Detection and Nanopore Sequencing (DDNS). Shaw explained that […]
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Assembling a T2T Gyr Cattle Genome with Oxford Nanopore Reads

Temitayo A. Olagunju from the University of Idaho presented at London Calling 2024 on “Assembling a T2T cattle genome with Oxford Nanopore reads.”The breed of cattle they focused on is the gyr, with a characteristic hum on the back and important for milk production. They are often intercrossed/interbred with other bos cattle for their features […]
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Epitranscriptomics: Identifying m6A RNA Modifications in Neuroblastoma Cell Lines

Tonight, I watched Jade Foster from the University of Southampton in the UK present at London Calling 2024. The session’s title was “Identifying m6A RNA modifications in neuroblastoma cell lines.” They explained that epitranscriptomics describes the modification of RNA molecules. There are over 150 RNA modifications determined by readers, writers, and erasers! This process is […]
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Alternative Splicing and Neurologic Disorders: Long-read CaptureSeq Findings

Sofia Kudasheva from Earlham Institute in the UK spoke at London Calling 2024 about “Long-read CaptureSeq identifies novel RNA isoforms of psychiatric risk genes.” They noted that alternative splicing is “a key regulator of neuronal differentiation,” occurring in 95% of human genes and involved in disorders. The team wanted to better understand the role of […]
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Population Genomics and Gene Expression in Bullhead Benthic Fish Melanoma

Tonight, I watched the London Calling 2024 session by Julie Dragon from the University of Vermont. The title was “Shining Light on a Dark Mystery: melanoma in Bullhead Benthic Fish in Lake Memphremagog.” Dragon stated the problem: melanoma is found consistently in 30% of one species of fish in one lake! The brown bullhead is […]
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Amyloid Pathology and Synaptic Adaptation: Insights from Long-read Transcriptomics

Umran Yaman from the UK Dementia Research Institute at University College London in the UK presented at London Calling 2024 on “Long-read transcriptomics shows synaptic adaptation to amyloid pathology in Alzheimer’s.” Yaman is a Ph.D. candidate and described how the accumulation of amyloid drives microglial activation. They performed long-read sequencing of cDNA from mice. They […]
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