NCM 2021: Barcode-specific adaptive sampling — from human gene panels to viral amplicons

The ability to selectively sequence individual molecules of DNA from a sequencing library is a unique property of Oxford Nanopore sequencing devices. A key practical application of this technology is processing multiple samples on a single flow cell where each sample is identified by a unique barcode. In this breakout talk, Alex Payne from the University of Nottingham, presented their “barcode-aware” adaptive sampling tool ReadFish, which enables users to select different targets within each barcoded sample or to filter out individual barcodes from a sample. To demonstrate the usefulness of the tool, Alex displayed datasets of three barcoded samples representing well characterised human cell lines, sequenced on a single GridION Flow Cell. For example, barcoded sample 2 was a leukaemia cell line with a known fusion gene, for which the team chose a panel of targeted genes based on the cell line’s characteristics. Alex showed that the target regions were well enriched, and using this data they were able to identify the known fusion event. Moreover, the rejected reads could be used to assess copy number successfully, which showed high concordance with optical mapping data. Furthermore, Alex presented the use of ReadFish adaptive sampling for real-time SARS-CoV-2 sequencing and analysis with MinoTour. This approach allows users to switch off sequencing of individual amplicons for specific barcodes as well as entire barcodes during a sequencing run once sufficient data have been generated.