sequencing

May 27, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

Cell-free DNA Analyses for Acute Lymphoblastic Leukemia Treatment

Jessica Blackburn from the University of Kentucky spoke at the Nanopore Community Meeting 2021 about “Detection of cell-free DNA in acute lymphoblastic leukemia patients to potentially identify CNS disease and monitor response to therapy.” Blackburn explained that acute lymphoblastic leukemia is the most common pediatric cancer, with ~3,000 children diagnosed each year. They explained that […]

May 26, 2023
By Carlos C. Goller
Information Literacy, Oxford Nanopore Technologies, Reflections, sequencing, Service Learning, Softwares, Student groups, Undergraduate Research

Undergraduate Research with the CREWS Project

Megan Radosevich from Carroll College presented at the Nanopore Community Meeting 2021 on “Analyzing regional and seasonal microbial community variation from a contaminated Montanana river.” Their project is called CREWS: Consortium for Research on Environmental Water Systems that is funded by the Montana NSF EPSCoR Partnership with several colleges and universities in Montana. A central […]

May 25, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

Improving Nanopore Sequencing Chemistries

Miten Jain from the University of California, Santa Cruz presented at the Nanopore Community Meeting 2021 on “Nanopore sequencing updates using Q20+ and R10.4.” While this may not be the latest technology, I think it is useful to learn about the history and how improvement were made. Jain spoke about the early version of ultra-long […]

May 24, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Raw Read Accuracies and Genome Assembly

Alexander Wittenberg from KeyGene in the Netherlands presented at the Nanopore Community Meeting 2021 on “Accuracy improvements in crop genome assembly using the Q20+ chemistry.” They presented on improvements in sequencing and crop assembly using Q20+ chemistry. KeyGene is using genome assembly and the early access ONT program to identify pan-genome and variants. KeyGene has […]

May 23, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Allele-specific Methylation in Fishes

Henri van Kruistum presented at the Nanopore Community Meeting 2021 on “Allele-specific DNA methylation in the live-bearing fish Poeciliopsis gracilis.” Kruistum is a Ph.D. student at Wageningen University in the Netherlands. They are working on the Poecillidae live-bearing fishes. There are sever species and on the genomic level there is interest in learning about the […]

May 22, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

TADs and 3D Chromosome Structure

Jae Young Choi from New York University spoke at the Nanopore Community Meeting 2021 about “Unlocking the plant 3D genome architecture with Pore-C sequencing.” They spoke about how the genome is folded in a 3D conformation in the nucleus. There have also been many techniques to understand the folding. One such technique is Pore-C sequencing: […]

May 21, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Real-time Sequencing of Brain Samples

Franz-Josef Müller & Helene Kretzmer gave a presentation at the Nanopore Community Meeting 2021 about “Real-time cancer classification with nanopore sequencing.” Kretzmer defined real-time sequencing as “short time” sample processing from wet lab to bioinformatics. Muller explained that they have optimized a protocol for identification of brain cancers. They start with a rapid DNA extraction […]

May 20, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

High-throughput Testing in Indonesia

Ariel Pradipta from the Genomik Solidaritas Indonesia Lab (GSI Lab) spoke at the Nanopore Community Meeting 2021 on “The First 100 days of establishing nanopore-based sequencing for national SARS-CoV-2 surveillance.” Pradipta is a senior researcher fellow assisting in the national genomic efforts. They recognized a gap in rapid sequencing. To address this, they worked on […]

May 18, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

Hypermethylation Detection in Disease

Ulf Birkedal from Copenhagen University Hospital in Denmark spoke at the Nanopore Community Meeting in 2021 about “Nanopore sequencing increases resolution of DMPK hypermethylation in myotonic dystrophy type 1 patients.” Myotonic Dystrophy Type 1 (DM1), explained Birkedal, is an autosomal dominant multisystem disorder. Muscle degeneration, weakness, and myotonia are the symptoms, and Birkedal noted that […]

May 17, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Genomic Skimming on the MinION

I continue to watch Nanopore Community Meeting 2021 recordings and will spend some time later this week focusing on the London Calling 2023 Masterclasses. Tonight, I watched Joanna Malukiewicz from the German Primate Center present on “Genomic skimming on the MinION uncovers cryptic hybridization in the buffy-tufted marmoset, one of the world’s most threatened primates.” […]