Tonight I watched the London Calling 2022 session by Euan Ashley from Stanford University. The title of this twenty-minute session was “The potential of ultrarapid nanopore genome sequencing for critical care medicine.” Ashley emphasized that the cost of genome sequencing has decreased rapidly over the last decade. With this, the accuracy has also improved. Ashley noted that in some cases speed is critical: how fast results are obtained can be very important in medical cases. Ashley shared that a thirteen year old boy with a dry cough ended up with an artificial heart! The medical staff attending the boy took a biopsy and MRI. Ashley explained that genetic testing turnaround time has decreased from days to hours. Now with a PromethION, Ashley described that sequencing a human genome can happen in minutes with 10x coverage! To provide ultrarapid nanopore genome sequencing, Ashley and others teamed up with Baylor, Oxford Nanopore, NVIDIA… and others. The team developed a workflow with DNA extraction, fragmentation, and library preparation from 2 ml of blood. Sequencing happened in the 48-flow cell PromethION, and bioinformatics tools such as minimap were used. The total time with LSK 109 library prep and native barcoding was around 171 minutes with total time about four hours. The team was able to parallelize and use base calling on GPU. They sequenced this boy’s genome in 8 hours! Since then, they have done ultrafast genome sequencing for seven patients. They tried barcoding and flow cell washing to show that accuracy wasn’t compromised without the barcoding step. Ashley explained that it costs about $10,000 a day for a patient to stay in the critical care unit. Sequencing quickly like this can be a couple of thousand dollars. Ashley ended by comparing the speed of sequencing a genome for a patient and improvements made to the max speed of a Ferrari. Turns out while they haven’t reached the speed of light yet (current estimate by comparison is about 1/20th), the team is getting there! I was curious about how they barcoded and washed flow cells. They also mentioned Ashley’s book which is now on my list.
