CRISPR

Genomic Surveillance of Multi-Drug Resistant Organisms with Long-Read Sequencing

Today was the first day of our IPERT Summer Workshops! I also started watching London Calling 2024 videos available on the YouTube channel. I began with the session titled “Genomic surveillance of multidrug-resistant organisms based on long-read sequencing.” Fabian Landman works at the Centre for Infectious Disease Control in The Netherlands and the Dutch National […]
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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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Enriching and Guiding Sequencing

Today was Aurelio’s fifth birthday! Tonight, I watched Timothy Gilpatrick’s London Calling 2019 session on “Targeted nanopore sequencing with Cas9 for studies of methylation structural variants and mutations.” Gilpatrick is a Johns Hopkins University. They are interested in specific loci and want to generate high coverage of those areas to examine structural variation. The enrichment […]
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Cas9 Enrichment for ONT Sequencing

Tonight I watched the Oxford Nanopore Technologies Nanopore Learning Knowledge Exchange session on Cas9 PCR-free Enrichment. I think this kit has been discontinued, yet it is important to learn how it works. Anne-Marie Wadsworth presented the method of PCR-free enrichment using Cas9. Wadsworth noted that ONT has developed a method to use Cas9 to target […]
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Sequencing Borg Genomes

Marie Charlotte Schoelmerich from the University of California, Berkley presented at London Calling 2023 about “Confirmation of borg extrachromosomal genomes: analysis of their methylation patterns, metabolism, and tandem repeats.” Schoelmerich is a postdoc in Jill Banfield’s lab and spoke about the key role of microorganisms in methane cycles. Methane emissions are driving climate change, and […]
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CRISPR/Cas9 Targeted Enrichment and Whole Genome Sequencing for Personalized Medicine

Anna Dolnik from the Charite University Medicine Berlin in Germany presented at London Calling 2022 “Combined CRISPR/Cas9 targeted enrichment and whole-genome sequencing allows real-time stratification of acute myeloid leukemia (AML).” AML patient stratification, Dolnik explained, relies on identification of copy number and fusion transcripts. Dolnik mentioned they had presented on ONT-based AML systems before at […]
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