Month: May 2024

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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Duplications, Rearrangements, and Complex Bacterial Genomes

Tonight, I watched the London Calling 2019 session “Ultra-long reads and ultra-long duplications: deciphering the mysteries of the Bordetella pertussis genome.” Natalie Ring from the University of Bath in the UK was the presenter. They spoke about whooping cough and how the introduction of vaccination in the 1950s reduced the number of reported cases. In […]
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Eleven Human Genomes in Nine Days

Tonight, I watched Miten Jain’s London Calling 2019 presentation on “Generating high-quality reference human genomes using PromethION nanopore sequencing.” Jain is from the University of California, Santa Cruz. They have developed a framework to produce reference-quality human genomes in a week. Jain spoke about the need to sequence many human genomes that can serve as […]
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Long-read Human Genome Sequencing Service

Andrea Riposati from Dante Labs in the US presented at London Calling 2019 on “Human long-read whole genome sequencing: applications and results.” Riposati is the co-founder and CEO of Dante Labs. They presented a case of a patient who had suffered 45 years without a diagnosis. Dante Labs provided whole genome sequencing and pharmacogenomics lab. […]
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