I watched the London Calling 2024 session about DNA and RNA modification calling tonight. Adrien Leger, Director of Modified Base Research at Oxford Nanopore Technologies, was the presenter. They explained how the research team trains a modified basecaller using synthetic oligos. There is primary and secondary validation with known oligos. Accuracy and several other metrics are then calculated. The team is training a model to detect genomic uracil, deoxy-uracil, found in genomes at a lower level and elevated in some pathogenic conditions. Leger shared that they have improved the accuracy of m6A calling. The pseudo-uridine model is now highly accurate in detecting this abundant modified RNA. The team is working on inosine calling, which has a role in the wobble base in tRNA and a role in transcriptome regulation. Additional models are being considered for development. Also, the new and updated Modkit v0.3 has features that may be of interest. Leger concluded by stating that more updates are coming!
