Tonight I watched two short Nanopore Community Meeting 2022 recordings. I started with Sarah Scott from the the Minnesota Public Health Laboratory, USA who presented on the “Exploration of Oxford Nanopore long-read sequencing to contribute to influenza surveillance at the state level.” Scott is an APHL and CDC Fellow. Scott explained that genomic surveillance of SARS-CoV-2 paved the way for more respiratory tracking. Scott shared a graph of influenza during the peak of COVID public health measures. After those measures were cut back, more cases were observed. Scott and team piloted a workflow to sequence influenza samples. The current method for influenza typing is a PCR-based workflow. Their pilot results indicated that 91% of pilot samples were classified with 100% accuracy for influenza strain detection. Future studies aim to reduce the lag time in delivery of summary results and increase throughput. It was interesting to learn that the number of steps was decreased with the whole genome sequencing (WGS) approach! Scott shared that further improvements will decrease hands-on time.
Next, Callum Parr from the RIKEN Center for Integrative Medical Sciences in Japan presented a five-minute talk entitled “A brief history of splicing: direct RNA sequencing of mouse brain samples from the RIKEN Aging Project.” Parr spoke about hallmarks of aging and the environmental factors that affect aging. Diet and the gut microbiota, Parr explained, influence aging. Parr has an interest in the role of RNA and RNA splicing in aging. To focus on RNA splicing and potential targets for therapeutic aging, they worked with the RIKEN Aging Project. They requested brain samples from mice form the project and sequenced 3-5 animals per condition. The transcriptome alignments were fed into a Nanopore pipeline. The direct RNA sequencing protocol allowed for detection of differentially expressed transcripts that may play important roles in aging disregulation. Their categories included typical and germ-free mice. Differential transcript expression of isoforms was identified as well as novel transcripts expressed in the mouse brain with the direct RNA sequencing approach. Parr explained that they will repeat the differential expression analysis with the expanded isoform annotations from TALON. Also, the research team is working on testing several RNA modification detection algorithms. Parr emphasized the work of the many researchers involved with the RIKEN Aging Project. I have been watching and learning about base modification detection and had not thought about RNA modifications.
