Year: 2024

Direct Sequencing of Cytosine Modification States from Nanopore Long-Read Data

Dominic Halliwell from the University of Bath in the UK presented at London Calling 2024 on “Direct sequencing of cytosine modification states from nanopore long-read data.” They are a doctoral student and were partially funded by Oxford Nanopore Technologies (ONT). Halliwell spoke about 5mC, 5hmC, and later oxidation derivatives, emphasizing that genome methylation can be […]
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Advancing Cancer Detection with RNA Liquid Biopsies

Daniel Kim from the University of California, Santa Cruz, presented at London Calling 2024. The session was on “Advancing RNA liquid biopsy technology via nanopore sequencing.” The Kim lab is working on advancing cancer detection with liquid biopsies. RNA is secreted into the circulation in extracellular vesicles (EVs). Kim noted that EVs can protect RNA. […]
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CariGenetics: Innovating Genomic Sequencing with PromethION in Bermuda

Tonight, I watched the London Calling 2024 product demo. The title of the session was “From sample to insight: exploring human genomics with PromethION end-to-end sequencing solutions.” Rachel Rubinstein, a Technical Product Manager with ONT, was the moderator. They explained that with a single PromethION flow cell, you can obtain 100-200 Gbases of data and […]
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Enhancing Acute Care in New Zealand Through Nanopore Sequencing

Justin O’Sullivan from the Liggins Institute at the University of Auckland in New Zealand presented at London 2024. The session’s title was “Establishing a nanopore sequencing facility for acute care in New Zealand.” They spoke about closing the borders during the pandemic. Being an island, they can control entrance and exit from the country more […]
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Unveiling the Potential of Long-Read Sequencing in Newborn Screening

Tonight, I watched Cate Paschal from the Seattle Children’s Hospital. They spoke about “Exploration of long-read sequencing in the resolution of newborn screening.” This was a London Calling 2024 session. Paschal spoke about newborn screening as a diagnostic test for rare diseases. Paschal explained that Pompe disease is a glycogen storage disorder with a prevalence […]
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HERRO: Haplotype-Aware Error Correction of Ultra-Long Nanopore Reads by Mile Sikic

Mile Sikic from the Genome Institute of Singapore spoke at London Calling 2024. The session’s title was “HERRO: haplotype-aware error correction of ultra-long nanopore reads.” Sikic noted that HERRO can be used for any type of Nanopore reads. They developed Racon seven years ago. Now, there are phased genomes, and the challenge is to maintain […]
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Enhancing Biopharmaceutical Safety Through Sequencing

Thomas R. Kreil from Takeda Austria presented at London Calling 2024. The session title was “Pathogen safety in biopharma: sequencing to come.” Kreil began by noting that they do not want to detect viruses in biopharmaceuticals. For this, they use Adventitious Agent Testing (AAT): they search for cytopathic effects on cells. However, current methods are […]
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Phylogenetics and Phylogeography of HIV: Insights from Big Events Research

Tetyana Vasylyeva from the University of California, Irvine, presented at London Calling 2024. The topic was “Informing infectious disease interventions with genomics during big events.” I was curious about the big events! This session was part of the Clinical & Biopharma Day on Friday, May 24, 2024. Vasylyeva studies phylogenetics, phylodynamics, and phylogeography of HIV! […]
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Long-Read Sequencing for Rare Diseases: Clinical & Biopharma Day Highlights

The London Calling 2024 session I watched tonight was titled “Long-read sequencing for pathogenic and novel variation discovery in rare diseases.” Ahmad Abou Tayoun from the Al Jailila Children’s Specialty Hospital in the United Arab Emirates was the presenter. This session was part of the Clinical & Biopharma Day on Friday, May 24, 2024. They spoke about […]
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