The last panelist of the London Calling 2023 liquid biopsy showcase was Andrew Beggs at Birmingham University in the UK. They run a mixed wet/dry oncology lab. The title of this short session was “Nanopore sequencing of ctDNA – better than short read!” They developed a homecrew ctDNA sequencing system. Their input is 5 ng input. They have made it work on Flongles for cost effective sequencing. The example they shared was a low input panel to detect indels and SNVs. Beggs shared three examples of variant frequency detection with 95% of all mutations detected. There was one mutation not detected that they think has something to do with the duplex caller. Their approach uses the LSK114 sequencing kit with R10.4.1 flow cells in duplex mode. I wonder how long the library prep takes including amplification and LSK kit. Beggs mentioned improving the duplex caller workflow and that the “procol generates sufficient data for 10,000x coverage in 8 hours from sample to data.” Beggs emphasized that they can get allele frequency down to 0.1-0.2%. The use of duplex reads and the Flongle flow cells is a great combination that I hope we can take advantage of!
