Tonight I watched the London Calling 2023 session on targeted sequencing. The first question asked was why select targeted sequencing. One panelist spoke about the ability to try the technology and modify it for their needs. Another speaker explained that creating a custom panel would be easier for the analysis. A third panelist said that a targeted sequencing experiment coupled with adaptive sampling would allow for more useful data. They can combine many samples and save money. One panelist is very interested in having precise control on fragment length and iterate to improve the workflow. A member of the audience asked if they are using custom bioinformatics tools. They are using their own software and working on new tools to balance barcodes. The moderator asked all three panelists what the advantages are of adaptive sampling. In addition to selecting the data they want to analyze, two panelists explained that they can sequence native DNA and obtain methylation information. Another question asked was if adaptive sampling was used with RNA. All three panelists were interested but haven’t used direct RNA with adaptive sampling. The challenges are shorter RNA reads and limits of enrichment. The moderator asked panelists to speculate on how Oxford Nanopore Technologies (ONT) will be used in five years. I thought it was interesting that one panelist thinks that adaptive sampling on the PromethION will be very powerful but also a challenge for the computing and data transfer. One panelist explained that they are using their custom tools on the GridION for adaptive sampling but not yet for PromethION flow cells. Another question was about the “evenness” of DNA regions using adaptive sampling. The last question was on the future applications of adaptive sampling and targeted sequencing. I thought it was telling that one panelist stressed that for clinical applications targeted applications will continue to expand.
