Last Thursday and Friday Oxford Nanopore Technologies (ONT) hosted it’s first conference ‘London Calling’ where participants of the MinION Access Program (MAP) presented their results and experiences after 11 months of the program. The CTO of ONT also delivered a session where the future directions where outlined. Below a quick recap of two days of London Calling.
There were about 20 talks (agenda) by a broad range of scientist from microbiologists to bioinformaticians. A few observations I found interesting to share:
- John Tyson (University of British Columbia) wrote a script that slightly alters the voltage along the run to keep the yield curve linear, he uses this method standard for each of his runs
- The majority of the presenters just only use the 2D reads
- A nice month-by-month overview of the MAP program can be found in Nick Lomans talk here
- Miles Carroll (Public Health England), Josh Quick (University of Birmingham) and Thomas Hoenen, NIH/NIAID) went to Africa last year to sequence the Ebola virus outbreak and were able to map the outbreak on phylogenetic timescale, they used RT-PCR to generate the input material. Main conclusion here was that field sequencing with the MinION works, the Ebola mutation rate is not higher than other viruses, key drug targets are not mutating.
- People are exploring a lot of options to use it in clinical setting, for example for rapid identification of bacterial infections (Justin O’Grady, University of East Anglia) or for pharmacogenomics (Ron Ammar, University of Toronto); in short which drugs not to prescribe to patients because their liver cannot metabolise them due to a genetic modification, read the paper here.
- A detailed account on how to assemble a bacterial genome with only Nanopore data by Jared Simpson can be found on Slideshare, it’s an interaction version of this pre-print
- Currently MinION + MiSeq data is the way to go short-term future (according to Mick Watson) for genome assembly. Alistair Darby, University of Liverpool argued to just use 1 sequencing technology to perform the whole genome assembly because to much time can/is wasted to integrate all the different sequencing methods with different algorithms.
During the talks some requests were put forward:
- More automation for lib prep / faster lib prep protocol (this will be tackled either with VolTRaxx and/or a bead protocol for low input material and a 10 minute protocol for 1D reads announced by CTO Clive Brown)
- More stable performance between individual flow cells
- Base calling off-line so no need to connect to the cloud
- Tweaking the base caller for base pair modifications (for example methylation)
On Thursday afternoon there was the talk of Clive Brown the CTO of ONT. On Twitter the talk was compared with a “Steve Jobs style” way to reveal the new products.
The talk Clive B just gave at #nanoporeconf has been called the genomics equivalent of Steve Jobs' 2007 iPhone debut pic.twitter.com/jlozGVb7Fa
— Ian Holmes (@ianholmes) May 14, 2015
A few points he presented:
- There will be at the end of the year/next year a new MinION release that has the ASIC electronics not in the flow cell but in the MinION itself, this would drastically cut the price of the flow cells (from 1000$ -> 25$). Another big change here is the chip will contain 3000 channels instead of 512. Furthermore runtime of these device will also be around 2 weeks.
- All the shipments should be room temperature soon
- A “fast mode“ will be available within the next 3 months where a typical run will not generate 2Gbase of data but 40Gbase of data.
- VoltTRAX is developed which can be clicked on a flow cell and will automate the full lib prep process, they imagine users can load a mL of blood sample on the VolTRAX and it will be prepped automatically.
- At the same time ONT will implement a different price structure where you pay per hour of sequencing instead of per flow cell, so you can just run a MinION for 3 hours and pay, say 270$ and don’t pay anything else.
- The PromethION (kind of 48 MinIONs in 1 machine and more channels per chip) will be launched with Sequencing Core facilities as their main costumer in mind, however they will create a MAP for this (PEAP) as well. The PromethION It will include the above improvements as well, making it potentially more productive than a HiSeq.
In conclusion the conference atmosphere was very upbeat with a lot of enthusiasm for the future of nanopore sequencing. Can’t wait to get this MinION started.