Opiniomics

bioinformatics, genomes, biology etc. "I don't mean to sound angry and cynical, but I am, so that's how it comes across"

Thoughts on Oxford Nanopore’s MinION mobile DNA sequencer

Quite a few others have had their say on Oxford Nanopore‘s MinION sequencer, and so I thought I would write down a few of my own.  At Edinburgh Genomics, we’ve been working with the MinION since the first day of the MAP, and earlier this month we published one of the first bioinformatics tools to help users work with this platform: poRe.  Whilst there have been low points in the process (mostly involving reagents or flowcells that don’t meet ours and ONT’s high standards), we are still incredibly positive about the possibilities this platform offers.

Personally, I am still convinced that the future of DNA sequencing is nanopore based, but I’m getting ahead of myself.  I want to make a few points.

Some perspective (part I)

Illumina are a $7 billion dollar company who currently dominate the sequencing market, and over 90% of DNA sequencing data produced today comes from one of their platforms;  Thermofisher, who own LifeTech, who own Ion Torrent, employ 50,000 people and had revenues of $13.1billion in 2013.  Even Pacific Biosciences, a minnow compared to the previous two, can be considered established, having launched their first sequencer in 2010 and with 100s of publications resulting from ther technology.

Now consider Oxford Nanopore.  A company that employs around 180 people, based in a science park on the outskirts of Oxford.  A company that didn’t have a product up until 2014, when they launched the MinION to lucky collaborators.  A small company with an exciting technology in a competitive market.

Firstly, If you expect ONT to behave like the other three companies I mentioned, then you must be insane.

Secondly, ONT have a disruptive technology that could, potentially, dominate the sequencing market for years to come.  This puts ONT in a position of strength; but it also makes them vulnerable to attack.  They must be very careful about how they operate,  and they need to trust the people that they work with.  I don’t understand what some people don’t get about that.

Some perspective (part II)

If you are currently sat in front of a bunch of MinION data wondering how on earth you’re ever going to make it do what you can do with your Illumina data, then go into your lab, take the MinION, put it back in the box and send it back to ONT.  Seriously.  Wondering how you can fit MinION into your existing workflows is like sitting in front of a space ship and wondering how you’re going to use it to commute to work; it’s like sitting in front of a time machine, and wondering if you could use it to get to the shops before they close.  The potential applications of a mobile DNA sequencer are incredible.

You have in your possession, if you are lucky, the world’s first mobile DNA sequencer.  It’s 4″ long.  The fact it can produce data of any kind from DNA is a miracle.  You are in possession of a miracle.  If your mind isn’t ablaze with amazing applications, then give up on science and go home.  Seriously.

That paper

I have nothing against Alexander Mikheyev or Mandy Tin, I don’t know them nor have I ever met them.  I wish them every success in their future, I genuinely mean that.  Alexander, Mandy, if you are reading this, I mean you no harm.  But that paper is terrible.  It’s just lazy.  You ran the MinION a few times, got poor data, and… that’s it.  That’s not something that should be written up into a paper.  Seriously, what a waste of everyone’s time, yours and mine.  If this is science, then I am depressed for science.  Alexander, Mandy – I am 100% positive that you are better than this.

Some fuss has been made about the authors being kicked out of the MAP.  Let me tell you about the MAP.  The MAP is an amazing thing.  What most sequencing companies do with a new tech, is they take it to the big genome centres (Sanger, Broad, WashU, BGI etc), they get down on their knees and they say “please make it work; please adopt it and say nice things about it”.  This is one of the reasons why most new bioinformatics tech comes out of genome centres – they always get first glance at new sequencing technology, and so they’re in pole position when it comes to writing new algorithms to deal with it.  MAP is different.  I’m not saying they haven’t put MinION into Sanger, Broad etc – but they’ve also given it to lone scientists, to small groups, to medics, to public health, to vets.  ONT have placed around 500 MinIONs in over 20 countries.

The MAP is about collaboration; it is about trust.

At no point have I doubted that ONT would let us publish data.  At no point have I felt controlled, or restricted in what we could do.  ONT simply want to know what MinION data look like in others’ hands, both experts and novices.  In return for the platform, they want to see the data and understand why it looks the way it does.  It’s a collaboration.  It’s about give and take.

The “hit and run” paper of Mikheyev and Tin just doesn’t fit into that framework.  Not in any way.  Technically speaking, “self certification” is a statement to ONT that the platform is delivering data that are “good enough for the applications I want to use it for”.  Mikheyev and Tin self-certified.  Where are the applications then guys?

Don’t you think it was a bit dishonest to self-certfiy and then publish that paper?

Just to be clear – only two groups have left the MAP; one group who left voluntarily as they didn’t have enough time to devote to MinION, and Mikheyev and Tin.  On the flip side, many additional people have been admitted.

Working with the data

Some very talented people in my lab have been working with the data, and I have been remarkably hands off.  However, here are some of my opinions about the data:

  • I don’t get the impression that generating ultra-long reads is going to be a problem.  What goes through the pore is what’s in the sample, and if you have long fragments, you get long reads
  • If you take the reads, align against a reference, you cover the whole genome, and can call the reference with 100% accuracy.
  • You can call SNPs.
  • Larger genome scaffolding is possible, and results are similar to scaffolding with PacBio.
  • (yes I realise these are the boring questions I referred to above; the answer is “yes you can”; now it’s time to go dream of amazing applications)
  • The quality needs to improve, base-calling needs to improve, throughput needs to improve – and I believe all of them will
  • Error correction strategies look very promising and I think you will see papers on this in the next few months

A final word

I have respect for all sequencing companies and I believe all of them have something to offer. Illumina are amazing – talk about a company that delivers!  They are about to enable routine medical genomics, and sequence entire countries.  What they’ve done with their technology is incredible.  Believe me, my pom poms still get used!

As I have said many times, I have huge respect for the way PacBio have turned themselves around.  They were going nowhere just a few years ago, and now they are essential to most new genome sequencing efforts.  Credit where it is due, though I do wonder if they have anything left in the tank.

Now there is ONT – a tantalising technology, their place in history is assured having produced the first mobile DNA sequencer.

Working with companies is a skill, I get that; a skill that many academics clearly lack.  ONT have a great technology, and as a result, they are vulnerable to attack.  As their collaborators, we have to recognise that and work with them, not against them.  For example, it may be coincidence, but take a look at PacBio’s share price on 3rd September, the day Nick Loman gave a talk about the great things he is doing with ONT data.  If those two events are related, then PacBio will be worried.  Does anyone think they will just sit back and let ONT take their long-read crown?

The MinION is incredible.  Nanopore sequencing is here and it’s here to stay, in my opinion.  Don’t get me wrong, there’s a long way to go; lots of improvements need to happen.  And they will.  But the people that will make those improvements, both in the technology and in the bioinformatics algorithms to deal with the data, will be positive, forward-thinking people, people who approach science and data with optimism and an open mind.

Let’s be those people.

17 Comments

  1. > You ran the MinION a few times, got poor data, and… that’s it. That’s not something that should be written up into a paper.

    I think a more effective way to negate Alexander Mikheyev et al.’s criticism is to release some data. What stops the company from releasing one E. coli library for Godssake?

  2. All going well, I don’t think PacBio have a chance at competing given their instrument weighs 1.3 tonnes, costs in the high $100,000’s and has a unique installation process involving knocking a hole in the side of the building and reinforcing the floor.

  3. Where is the data? My biggest issue if they haven’t seen the data yet, and they are loosing everyday pass by…

  4. I’m not convinced nanopore is the future, but even if it is, wouldn’t it be more likely that a big company like Illumina would come out with their own version if it was? (Yes, I know they are currently betting on their TrueSeq long read technology). Think about computers. Xerox invented the GUI, but didn’t get that far with it other than their obscure Star and Alto workstations. Apple picked up on it with their obscure Lisa and somewhat successful Macintosh, but it didn’t really go mainstream until Microsoft did it.

    • Illumina was a small company, before it bought another small company and is now 20Bn market dominator. At the time it was up against ABI (or LIFE). People said, ILMN would never beat LIFE for similar reasons – many people backed SOLiD for that comfort. Roche, another behemoth’s adventures in NGS space have not worked out well. Big isn’t better when it comes to disruptive innovation. Where is Agilent in all this ?

    • Microsoft was a small company also, as was Google. A lot of tech innovation comes from small companies, as big ones starve their research arms and rely on buying other companies rather than developing their own tech.

  5. I’ve not seen and MinION data myself yet, and am curious how it really is. I’ve heard rumors that long reads are routine, that the indel error rates are large (comparable to PacBio and other single-molecule technologies), and that the library prep is as big a problem as it is for all the other sequencing technologies. But I’ve not seen any real data yet. I suspect that the real papers (not the “I-couldn’t-get-it-to-work,-so-I-gave-up-after-one-try papers”) will start coming out around January.

    If the MinION can get into the throughput range of a PacBIO flow cell, it will be a somewhat disruptive technology (mainly knocking out other PacBio). To get to the point of being a really disruptive technology, the Minion will have to reduce the complexity of the library prep, which is probably doable, but is also probably not their main focus right now, as no sequencing technology has a simple, low-cost library prep. (For Illumina, I believe that the library prep costs now dominate the sequencing cots for many applications.)

    I suspect that there is still a fair amount of bioinformatics work needed to get the most out of the MinION platform, from base calling to assembly. Without real data, though, there is not much for bioinformaticians to work on, to find out what the new problems are. A lot are assuming that the errors models will be similar to the error models for PacBio data (random indels), but that depends on whether the basecaller removes or introduces systematic errors. A number of the real data papers may be waiting for in-house bioinformaticians to write code to work with the MinION data, though it would probably be faster to dump a lot of data on the community to get third-party solutions.

  6. We are using the MinION at U of T on our samples. It is incredible! Don’t believe the naysayers – this device has incredible applications and is only getting better with each iteration!

  7. The fact that the MinION is small an handy is nice – but so what? Do I need to sequence on an expedition? Ahhh, forgot the lab for the DNA extraction and library prep and the fridge for the reagents at home. Too bad. Perhaps I better put the sample into RNAlater instead.
    Much more attractive than the size is the relatively low cost.
    The current MinION error rates are far away from expectations.
    What does this very carefully worded sentence mean in the end: “If you take the reads, align against a reference, you cover the whole genome, and can call the reference with 100% accuracy.” If I know the correct answer beforehand I can recover it from the really short pieces of correct data contained in the MinION data – at what coverage?

  8. Of course coverage is an issue but much less so from a cost and practicality perspective with the MinION because there’s no need for PCR and no expensive-fluorescence, lasers or cameras and no chip or wave-guide limiting available space and also the nanopores can keep on sequencing without loss of performance.

    • If I understood the tweets about Nick Loman’s talk, he was claiming about 250Mbases from a MinION before it died. That’s about the same as you get from a PacBIO SMRT cell. Obviously the PacBIO is a huge, expensive piece of equipment, but if I just want long reads, am I better off with a MinION or sending DNA out to be sequenced by a core facility with a PacBIO? The core facilities seem to be charging about $500/SMRT cell plus $500 for library prep for PacBIO. How does that compare with a MinION? If ONT is still aiming for a price point of $1000 per cell, they may be twice the price of PacBIO on a per-experiment basis. If they can survive on less than $400 per cell, then the MinION might knock PacBIO out of its niche as the only currently viable long-read technology.

  9. Two years ago I was attempting to explain DNA sequencing to someone and said in the distant future it will be possible to sequence DNA at home it will become so portable, it will become the same to sequence your own genome as to extract DNA from strawberries for a public engagement event or something.

    MinION came along and I was reluctant to believe the hype because it seems so absurd, but seeing how it can actually aid epidemiologists in West Africa blows my mind. To imagine how this may change again in 5 or 10 years is brilliant.

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