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Medicine Biotech Software

The World's First DNA 'Tricorder' In Your Pocket (phys.org) 54

Posted by BeauHD from the first-of-its-kind dept.
Cold Spring Harbor Laboratory (CSHL) scientists developed the world's first mobile genome sequence analyzer, a new iPhone app called iGenomics. By pairing an iPhone with a handheld DNA sequencer, users can create a mobile genetics laboratory, reminiscent of the "tricorder" featured in Star Trek. Phys.Org reports: The iGenomics app runs entirely on the iOS device, reducing the need for laptops or large equipment in the field, which is useful for pandemic and ecology workers. Aspyn Palatnick programmed iGenomics in CSHL Adjunct Associate Professor Michael Schatz's laboratory, over a period of eight years, starting when he was a 14-year-old high school intern. The iPhone app was developed to complement the tiny DNA sequencing devices being made by Oxford Nanopore.

Users can AirDrop sequencing data to each other, enabling DNA analysis in the most remote locations -- even those without internet access. iGenomics may soon even find its way into the hands of astronauts, Schatz describes: "There's a lot of interest to do DNA sequencing in space. I'm trying to see if there's a way we can get iGenomics up there. There's a lot of people that are interested to do that. It's a real testament about how it would be impossible to do, you know, any sort of analysis on regular computers. It's just impossible to bring them with you." In the journal Gigascience, Palatnick and Schatz report the iGenomics algorithm can quickly map DNA sequences of viral pathogens, such as a flu virus or Zika virus, and identify mutations important for diagnosis and treatment. They also provide an online tutorial for analyzing other viral genomes, such as from a SARS-CoV-2 patient.
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The World's First DNA 'Tricorder' In Your Pocket More

The World's First DNA 'Tricorder' In Your Pocket

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  • Obligatory (Score:5, Funny)

    by John Allsup ( 987 ) <slashdot@chal i s q u e.net> on Monday December 07, 2020 @09:20PM (#60805438) Homepage Journal

    Is that the world's first DNA tricorder in your pocket? Or are you just glad to see me?

    • It's a real DNA tricorder! Now, I just need a good swab from one of your mucous membranes ...

  • Fingers want to know!

  • This Was A Plot Device... (Score:3)

    by IonOtter ( 629215 ) on Monday December 07, 2020 @09:32PM (#60805462) Homepage

    ...in "Transmetropolitan," by Warren Ellis.

    It ended badly.

    "...the G-Reader, a ranged DNA-testing device "so new it hasn't been restricted yet", in the "Lonely City" arc. First Spider uses one to expose a Moral Guardian politician's screwing of mentally disabled sex slaves, but then a gang of bigots use a G-Reader on a carrier of a controversial recessive gene and beat him to death while a police car that also has a G-Reader stands by and does nothing. However in the final arc Spider uses a G-Reader again to bring down the Smiler." - TV Tropes - Transmetropolitan [tvtropes.org]

  • Ok.. (Score:5, Informative)

    by backslashdot ( 95548 ) on Monday December 07, 2020 @09:32PM (#60805464)

    Interesting, commendable .. but must point out that the Oxford Nanopore sequencer they use already runs on any computer with a USB drive. So literally any handheld computer with a USB drive can do this. Arenâ(TM)t there a bunch of those?

    • Re: (Score:3, Informative)

      by Anonymous Coward

      Not only that, but the software and drivers for running it on smartphones are already widely available.

      Here is a video from 2 years ago showing it used on mobile devices: https://vimeo.com/294214884 [vimeo.com]

      Here is an Android toolkit for it: https://github.com/SanojPunchi... [github.com]

    • In short, yes. Basically all phones now have OTG mode.

    • I wouldn't say it's that interesting or commendable. Basically instead of using a big piece of steel instrument of Illumina's, you use a MINion, connect it to your phone, stream the sequencing data to a cloud app to run the analytics, and spit back the answer. Literally this is just cloud connectivity.

      As another poster stated, this is also a far cry from a tricorder. DNA is super easy to get wrong and is hugely prone to contamination. It is well known in the field of genomics that the analytics is a

      • Re: (Score:2)

        by ceoyoyo ( 59147 )

        Nanopore sequencing is a bit different. It can apparently do extremely long reads, the entire sequence for many microorganisms, it does it fast, and it doesn't require amplification via PCR.

        Because it does such long reads, assembling the sequence is pretty easy. I haven't used one of these things, but it sounds like it shouldn't be a problem to do the assembly locally. Most of the heavy lifting involved with other sequencing techniques is taking the bazillions of short fragment reads and assembling them int

        • You're missing the point then. He bought a Nanopore from Oxford Nanopore. Those are cool, but that's not his innovation and MINions have been around for a few years. What they're talking about as a "Tricorder" is not much more than an app on his phone that runs the MINion.

          And be careful what you say when you use "extremely long reads"; that's not a technical term and there are many definitions of "long read". Extremely long reads are human or mammalian; 4 billion base pairs or more. For that need y

          • Re: (Score:2)

            by ceoyoyo ( 59147 )

            I'm not disagreeing that an app, which is what the story is about, is not terribly impressive. Nanopore sequencing *is* impressive, and has particular features that lend it to this kind of technology. I don't want to argue about what makes something "like a tricorder." If you want to get pedantic, a tricorder was originally defined as a '"TRI-function reCORDER", referring to the device's primary functions: sensing, computing, and recording', which makes the argument pretty ridiculous from the start.

            And sorr

            • I wasn't trying to be pedantic; sorry about if it came off that way. I just wouldn't call an app a tricorder. Bones waved a wand and got all sorts of information, but if Star Trek is our future Bones will be taking highly complex samples with extremely precise sample control technology in order to get just 1/10th of the information that the magic of TV and plot could provide. Nanopore technology is great in theory but in practice it's very difficult to get right. You are correct that Nanopores are very

  • "By pairing an iPhone with a handheld DNA sequencer..."

    The article has a lot to say about the app, but very little to say about the sequencer, even how large it is - only that they're made by Oxford Nanopore.

    • According to https://nanoporetech.com/produ... [nanoporetech.com] the sequencer is less than 450 grams, not sure about its dimensions.
      Pretty sure after you put a sample in it you'd want to leave it on a flat surface for a while too - doubt it likes being moved around when sequencing.

      Still I also feel that the sequencer is much more impressive than getting things working on the iPhone.

      That said genomics is a weird mash of old and new technologies, a lot of command line stuff and old Python or R code - it still probably took a

  • I actually own one of the nanopore devices (Score:5, Interesting)

    by nokarmajustviewspls ( 7441308 ) on Monday December 07, 2020 @09:39PM (#60805482)
    I have one of the MinION portable nanopore sequencers. I've been using it with a Mac laptop for sometime and I've used it with the Flongle disposable cartridges that cost about $150 (instead of the $600) reusable ones. It's good that someone has gotten a version of the sequencing software to run on an iPhone, basically it needs to do at least a few things like 1) control the device like keeping the temperature at the proper temp. etc. 2) actually receive and 3) analyze the data. The second one is the hard part, a MinION generates a LOT of data, they recommend a fast laptop with SSD. I guess a fast iPhone with ample flash storage is fast enough (also it'll need a lighting to USB connector). Still the main obstacle isn't really size, I mean a laptop isn't that big. Rather it's the sample prep., for non-human DNA you'll need to grow, isolate, collect, purify and sometimes amplify the DNA (or RNA) before you can put it into the sequencer. This may involve temperature sensitive chemicals, very carefully measured out in micro or nano-liters(!), and centrifuges and PCR cyclers. Are you handy with pipettes? Finally these sequencers, for now, can only realistically do smaller genomes (viruses, bacteria, plasmids, prokaryotes). While they are amazing for what they CAN do, a whole human genome on a portable device is way beyond their capability (due to the error rates you'll need at least 30x coverage). This is critical because if you can't sequence the whole genome, then you will probably not get the part you're looking for (like the breast cancer gene). To do that you'll need to use primers and PCR. Still a potential solution for many of these problems may be at hand, utilizing a unique feature of the MinION devices, they can stop and even reverse the DNA going through individual pores. Software (see below) has been written that, in real time, analyzes what's going through and decides if that strand of DNA is worth sequencing. If not, it reverses it (spits it out) and presumably tries another and another until it finds the one it's looking for. This may allow a nanopore sequencer to target a particular sequence! I'm really hoping that this targeting software works and is released. If so it may, more than the iPhone software, make portable sequencing, fast, cheap and convenient! All you'll need is to take a lot of cells (a spit tube's worth) and using basically soap and salt purify it (I think, I'm not a very good wet lab biologist). Then give the software a target sequence to look for and let the device go. Fun! But before you start sequencing everyone and your dog, think carefully (really) about what you might discover. https://www.sciencedaily.com/r... [sciencedaily.com]
    • Oh also, I took a really quick glance at the article in Gigascience, they're using the MinION to sequence the Ebola genome! DON'T do this at home (unless you've got a BioSafety level 4 facility). By the way, sorry that my parent post is so unreadable, I don't know how to make paragraph spaces.
  • How many times does one need their genome sequenced? Many times, if not done well. So do it right: do it once (before you go into space), at high depth of coverage, long and short reads. Assemble and analyze with the best tools available. Re-analyze later as tools improve. Don’t go for the sideshow version. Yes, it likely has niche uses, but not generally.

  • with a USB pluggin and offer likely chemical matches? It may be useful for testing certain medications and foods for honesty.

  • If that is such a novel app, why suggest it has to be used in space, where there is no life, before we even have used it on most life, down here, where life is?

    • On astronauts and things we take up there to monitor their health and genomic integrity. Duh.

    • Because there is life in space.

      First, there is the life we put into space on the international space station. That life is clearly living in very different conditions than most life. It's important we study how this environment affects DNA both of astronauts and of plant life. Understanding what, if any, areas of a genome are more resistant to these mutations is vital for future strategies.

      Second then building blocks for life are likely scattered in the cosmos. Before bringing back a new life form to ea

    • Re: (Score:2)

      by imidan ( 559239 )
      In addition to the things others have mentioned, there may be value in being able to sample and sequence the microbial life on a spacecraft. For example, tracking the microflora of the ISS. If sampled and sequenced regularly, you could potentially identify when new inoculations occurred, how mutation proceeds, and things like that.

  • Where do you get a portable DNA sequencer? BestBuy? Staples? Office Max?

  • Why locked system? (Score:3)

    by SuperDre ( 982372 ) on Tuesday December 08, 2020 @05:28AM (#60806360) Homepage
    Why are they creating it in a locked system? If it's academic it would have better suited to be developed on Android. Or at least also on Android.

  • "enabling DNA analysis in the most remote locations -- even those without internet access."

    Place with internet and phone can't hardly be categorized as 'remote'.

  • is that anyone who names their kid "Aspyn" is an asshole.
  • So, some day as you walk down the street someone waves a device at you and yells, "Police! This man is defective. Kill him!!!!" Laugh but this is what you will get in the future with Socialist dictators.
  • not for your device
    DNA does not compute
    only for fanbois.

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