Year: 2024

Methylomics and Fragmentomics: Pioneering Cancer Detection Models

Hanlee Ji from Stanford University presented at London Calling 2024 on “Genomic sequencing for characterizing tumor minimal residual disease versus early cancer.” Ji spoke about apoptosis and circulating tumor DNA. Ji and the team evaluated the recurrence of metastatic colorectal cancer with circulating DNA monitoring. Early detection of breast cancer can benefit from nanopore sequencing […]
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Real-Time Analysis Challenges and RT-Metagenomics Workflow Demo

Tonight, I watched the London Calling 2024 EPI2ME Product Demo. The session title is: “EPI2ME: democratising bioinformatics – from point-and-click analysis to custom integrations.” Sarah Griffiths, ONT Bioinformatics Workflow Developer, gave an overview of the EPI2ME workflows. The workflows use Nexflow and containers. At the time of recording, they had seventeen workflows. Griffiths noted that […]
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Nanopore Sequencing for mRNA Vaccine Quality Assurance

Helen Gunter from the BASE mRNA Facility at the University of Queensland in Australia spoke at London Calling 2024 on “Innovations in mRNA vaccine precision manufacturing.” BASE is the largest mRNA manufacturer in Australia, supplying commercial, government, and academic research labs. The plasmid is amplified, linearized, and used as a template to transcribe the mRNA. […]
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Discovering Deeply Intronic Mutations with Nanopore Sequencing

Tom Walsh from the University of Washington in the USA spoke at London Calling about “Discovery of deeply intronic damaging mutations with nanopore sequencing.” Walsh explained that in the 1990s, genetic testing for predisposition to breast cancer began. In the 200s, additional cancer-risk genes were discovered. Now, there are numerous panels and ten genes for […]
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Nanopore Sequencing Advancements: Optimizing Metagenome Assemblies

It was great to see Lauren Lui from the Lawrence Berkley National Laboratory present at London Calling 2024 on “An unprecedented metagenomic landscape of European and North American coastal samples.” Lui is a research scientist and, while at Miten Jain’s lab at Northeastern University, loaded 34 PromethION flow cells, generating 5 Tbases of data! Lui […]
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Intraoperative Brain Tumor Diagnosis

“Robbing the array to feed the pore: exploring ultra-fast brain tumor diagnosis” is the title of the session Dr. Simon Paine from Nottingham University Hospitals NHS Trust in the UK presented at London Calling 2024. What a creative title! Paine is a clinical consultant and neuropathologist. Paine explained that neuropathologists are trying to predict tumor […]
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Flames and Blaze: Advancing Long-Read scRNA-seq for Brain Development Research

Mike Clark from The University of Melbourne in Australia presented at London Calling 2024 on “Igniting single-cell analysis of full-length RNA isoforms in brain development.” Clark works on RNA isoforms and developing single-cell analysis methods. They noted that almost all human genes express multiple RNA isoforms. Clark emphasized that alternative splicing modifies which exons are […]
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Understanding Drug Resistance in Multiple Myeloma: Insights from Tomas di Domenico

Tonight, I watched Tomas di Domenico from the National Cancer Research Center in Spain present at London Calling 2024 on “An (epi-)genomics analysis of drug resistance in multiple myeloma.” Di Domenico explained how multiple myeloma affects the bone marrow and thickens the blood. Multiple myeloma also causes bone issues. There are several treatments and a […]
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SamnSero Workflow: Real-time Bacterial Genome Analysis

Tonight, I watched the London Calling EPI2ME product demo: “EPI2ME: democratising bioinformatics—from point-and-click analysis to custom integrations.” Natalia Garcia, a Bioinformatics Workflow Developer with Oxford Nanopore Technologies, explained how workflows use Nextflow and Docker containers. Seventeen workflows were available at the time of the recording during London Calling. Workflows can be run via the command […]
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Long-Read Sequencing Innovations in Neurodegenerative Disease Research

Tonight, I watched the London Calling 2024 session on “breaking boundaries in neurodegenerative disease research.” Cora Vacher from Oxford Nanopore Technologies (ONT) introduced the speakers and facilitated the question and answer session. Joanne Trinh from the Institute of Neurogenetics at the University of Lubeck in Germany was the first presenter. Trinh works with a research […]
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