Thread by @NanoporeConf

@euanashley's plenary talk: 'The potential of ultra-rapid #nanopore genome sequencing for critical care medicine', will begin in 5 minutes — check out the agenda to find out what else is in store: bit.ly/3M3WlwM #nanoporeconf

@euanashley EA: seeing a $398k car, I recently thought that if luxury cars had dropped in cost as much as sequencing, I could have bought the car for 1c #nanoporeconf

EA: its not enough to have confidence in the genomic data, sometimes we need speed too. #nanoporeconf

EA: introducing Matthew, who was diagnosed with heart failure after admission with suspected COVID. His heart was pushing barely 10% of the blood that was needed. Crashed onto ECMO and prepared for surgical implantation of artifical heart. #nanoporeconf

In cases like this, rapid genetic information could potentially be useful to help understand whether there was a genetic basis for such a heart condition #nanoporeconf

EA: But sequencing is too slow, surely? Not necessarily - Kingsmore et al had already brought whole genome sequencing timelines down significantly. But that wasn't standard - ordering from WGS service providers would still take days #nanoporeconf

EA: when thinking about this problem, we considered that the @nanopore PromethION would be the only tech capable of delivering whole genomes in very short timelines. So, we started working with Gordon and team as well as @Google, @ucscgenomics , @Baylor, @Nvidia #nanoporeconf

EA: we developed a bespoke workflow that compressed each part of the prep, sequencing and analysis workflow. At the time the world record was 19.5 hours #nanoporeconf

EA: needed to parallelize analysis to make it faster; worked on many aspects of the workflow so that we could perform basecalling at the same time as transferring the data to the cloud, analysis, etc. #nanoporeconf

EA: Curation of the data-the "last mile is still manual"; at this stage we could get to identifying variants at 11.25 hours. We were able to repeat the analysis workflow on multiple samples, still improving the process asking questions eg "is barcoding necessary?" #nanoporeconf

EA: we showed that the F1 scores with and without barcodes were identical; with that we had confidence to remove the barcoding step, completing each whole genome sample in under 12 hours. #nanoporeconf

EA: the potential to apply rapid sequencing in the future is huge. A colleague in neonatal ICU told me he would like to sequence two thirds of their cases #nanoporeconf

EA: we summarised this work in publications eg @NatureGenet , and were delighted to be awarded a @GWR Guinness World record #nanoporeconf nature.com/articles/s4158…

EA: the Ferrari would be driving at 14 million metres per second, if we speeded it up as much as we have speeded up whole genome sequencing. Enormous thanks to everyone on the hugely collaborative team #nanoporeconf

You can read more about @euanashley story here at this @StanfordMed blog #nanoporeconf medicine.stanford.edu/news/current-n…

@euanashley @StanfordMed We would be most grateful for an unroll @threadreaderapp