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posted by janrinok on Thursday May 21 2015, @11:26PM   Printer-friendly

[Editor's Comment: This article might sound a bit like a soyvertisement but it has been submitted by one of our community and someone who is well qualified in his field - David Eccles from the Malaghan Institute of Medical Research in New Zealand. It is interesting to read about what is considered currently to be state of the art in field genome sequencing.]

On the 14th and 15th of May, 2015, Oxford Nanopore Technologies held their inaugural nanopore sequencing conference, London Calling. The conference was set up to inform people about the current progress of Oxford Nanopore's first sequencing device, the muesli bar-sized, USB-powered MinION. Over 250 people were in attendance at the conference, representing 35 countries, including two from New Zealand: Nicole Moore from Environmental Science and Research, and David Eccles from the Malaghan Insititute of Medical Research. Over the course of two days, these attendees discovered how the MinION is quietly turning the world of sequencing inside out.

Everything needed for sample preparation and sequencing can fit into a single piece of checked luggage on an airplane. The MinION is robust enough to make it across unsealed roads to remote parts of Africa, where it has been used for sequencing on-location during the Ebola outbreak. The MinION has also been put through its paces for tracking the traffic of organisms. Detection at the species level can be achieved in under 20 minutes of sequencing, and very subtle changes for the same species from different origins can be identified in less than an hour.

Clive Brown, Chief Technical Officer for Oxford Nanopore Technologies, gave a brief summary of what is to come in the near future of nanopore sequencing:

  • A fast mode for sequencing, allowing a human genome to be sequenced with high reliability in a 2-day run.
  • An improved Mk II sequencer, with six time the throughput and six times the run time of the first sequencer.
  • A clip-on sample preparation laboratory (Voltrax), allowing preparation and sequencing directly from blood in 20 minutes.
  • Time-based pricing, reducing the minimum cost of a single-molecule sequencing run to $50.
  • A 48-cell desktop sequencing device (PromethION) that can produce over 6 terabases of sequence per day, making sample preparation time the slowest part of the sequencing process.
 
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  • (Score: 2) by kaszz on Friday May 22 2015, @12:09AM

    by kaszz (4211) on Friday May 22 2015, @12:09AM (#186261) Journal

    Can one sequence specific bits of the genome to reduce cost? is it possible to automatically sniff pieces of dead skin etc from the air and sequence directly? Can this sequencing unit be ordered? What's really inside the box? Any further price drops on the horizon, ie technically possible but not yet explored?

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  • (Score: 5, Informative) by gringer on Friday May 22 2015, @01:27AM

    by gringer (962) on Friday May 22 2015, @01:27AM (#186277)
    1. Yes, targeted sequencing is certainly a good way to reduce the costs. With a combination of targeted sequencing and sample multiplexing via DNA barcoding, you get very accurate (i.e. high coverage) sequences at very low cost.
    2. Automated sampling is not currently possible, but I can imagine that someone will soon work out some clever way to do that. Voltrax is almost there, but still requires a bit of manual pipetting to convert samples into sequences.
    3. The sequencing unit can be ordered by signing up to the access programme [nanoporetech.com]. Despite it's name, the MinION Access Programme is the commercialisation of the sequencing device. Presumably my bit regarding that part was removed from my submission because it was a bit too advertisey.
    4. Details about "what's in the box" can be found on the Oxford Nanopore website [nanoporetech.com]. To try to summarise: 512 very high precision isolated electrical sensors for 2048 sequencing channels, synthetic polymer membrane, protein nanopores, buffer liquids to keep the pores happy, electrical components to deliver a potential across the pore, and a USB cable to transfer sensor readings to a laptop.
    5. As far as I'm aware, ONT is pricing their devices based on the available competition (and demand). They have a lot of room for movement in price if (for example) a competitor magically discovered a way to make sequencing by synthesis more affordable.

    To tone down the buzz a little bit, the conference itself was definitely a big advertising venture on ONT's part. They selected people who were good performers in the MinION community to talk about the research that they'd done, but there are plenty of others in the community who are still struggling with getting the thing to work properly. Having said that, it's unlikely people would be interested in attending a conference where everyone spoke about all the things they weren't able to do.

    --
    Ask me about Sequencing DNA in front of Linus Torvalds [youtube.com]
    • (Score: 2) by opinionated_science on Friday May 22 2015, @01:40AM

      by opinionated_science (4031) on Friday May 22 2015, @01:40AM (#186283)

      I am quite glad something is finally approaching the market, it has been a long time coming...

      Hopefully the cost of 30x human will drop to $250 or less, so National Geographic can organise it. I am not joking! I think they have done a great deal to raise awareness of the utility of DNA sequencing.

    • (Score: 2) by TLA on Friday May 22 2015, @02:05PM

      by TLA (5128) on Friday May 22 2015, @02:05PM (#186454) Journal

      Given the device's name, does it come in a giant Kinder egg wrapped in a pair of dungarees?

      --
      Excuse me, I think I need to reboot my horse. - NCommander