Year: 2024

Nonsense-mediated Decay of mRNAs

Evangelos Karousis from the University of Bern in Switzerland presented at London Calling 2019 on “Splice isoform-specific analysis of endogenous NMD targets in human cells.” Karousis explained that RNA degradation is involved in various biological functions, and nonsense-mediated decay (NMD) is not well understood. Nonsense mRNA is dangerous because it can contribute to disease. NMD […]
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The Challenges of Sequencing tRNAs

Tonight, I watched the London Calling 2019 session by Irina Chelysheva from the University of Hamburg in Germany. The session’s title is “Small, modified, and highly structured: the challenge of tRNA sequencing.” Their lab is interested in sequencing tRNA because it is challenging. The major problems for sequencing, Chelysheva noted, include the short length of […]
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Epstein-Barr Virus and Methylation Patterns

Christopher Oakes from The Ohio State University spoke at London Calling 2019 on “Discerning the origin of Epstein-Barr virus in patients using nanopore-derived DNA methylation signatures.” Oakes spoke about how they study tumor viruses and cancer. The Epstein-Barr virus is common, the “prototypical cancer virus,” according to Oakes. Immune cells suppress the virus, but the […]
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Sequencing Sharks

Saili Johri from San Diego State University presented at London Calling 2019 on “Unraveling shark secrets: sequencing genomes and microbiomes for research and conservation.” Johri explained how they are using the MinION to conserve sharks and rays. They emphasized how sharks are apex predators important for oceanic ecosystems and maintaining coral reefs. Sharks make direct […]
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Confirming Large HDR Insertions with Nanopore Sequencing

Mollie Schubert from Integrated DNA Technologies spoke at London Calling 2019 on “Characterizing large HDR insertions by CRISPR/Cas9 using nanopore sequencing.” They use CRISPR in cells to mediate editing. The IDT team then uses Nanopore sequencing. CRISPR-Cas9 genome editing uses RNA guides. Schubert has been delivering CRISPR-Cas9 complexes to cells. Different applications can be used […]
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Determining Breakpoints and Duplications during Genetic Testing

Chris T.L. Chan from the Hong Kong Sanitorium & Hospital in China spoke at London Calling 2019 on “Long-read NGS guided preimplantation genetic testing for chromosomal structural rearrangement.” Chan presented a clinical scenario. They explained that short-read sequencing allowed the analysis of copy number variation from blood samples. Loss of copy can be identified with […]
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Identification of Retrotransposons in Cancer and Germline Samples

Tonight, I watched Kimmo Palin from the University of Helsinki present at London Calling 2019 on “Retrotransposon variation in human genome and tumorigenesis.” They began by discussing retrotransposons and describing them as “copy-paste elements” in the genome that copy themselves with an RNA intermediate. They range in size between 300 bp and 6,000 bp. LINE1 […]
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Complex Karyotype Analysis with Nanopore Sequencing

Anna Dolnik from the Charite University Medical Center in Berlin, Germany, presented at London Calling 2019 on “Genomic profiling in acute myeloid leukemia with complex karyotype.” They presented data on the survival of over 5,100 patients with acute myeloid leukemia (AML). The WHO in 2016 revised the classification of AML. A newly diagnosed AML patient, […]
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