Technology & genetics in the 21st century

By Razib Khan | December 30, 2010 2:35 am

I assume there will be more stories like this in the next year, Gene Machine:

The machine that could change your life is a compact device, only 24 inches wide, 20 inches deep and 21 inches high. At a glance you might mistake it for a Playskool toy–or, better yet, the Apple II computer, which sparked a revolution. Indeed, this gizmo, developed in a drab office park overlooking a duck pond in Guilford, Conn., could have as dramatic an impact as any technology since the personal computer and help kick off a market that one day could be worth perhaps as much as $100 billion.

Take a closer look. On the right side is an 8-inch touchscreen, on the left a dock that allows data to be downloaded to an iPhone. Below that is a row of four test tubes, marked with a circle, an X, a square and a plus sign. These symbols represent the four basic chemical letters, or bases, the body uses to form DNA–guanine, cytosine, adenine and thymine.

Audaciously named the Personal Genome Machine (PGM), the silicon-based device is the smallest and cheapest DNA decoder ever to hit the market. It can read 10 million letters of genetic code, with a high degree of accuracy, in just two hours. Unlike existing DNA scanners the size of mainframes and servers, it fits on a tabletop and sells for only $50,000, one-tenth the price of machines already out there. For the first time every scientist, local hospital and college will be able to afford one. If the PGM takes off and regulators let him, your family doctor could buy one–and so could you, if, say, you wanted to see how fast that thing growing in your fridge is mutating.

Rothberg faces three formidable hurdles. First, the market for sequencing is dominated by Illumina of San Diego, whose big machines have helped make most of the major discoveries so far–and competing won’t be easy. Next, a novel (and faster) approach could leapfrog the Ion Torrent device. Finally, sequencing could ultimately be a bust if it proves tough to find genes linked to disease, or improved cancer diagnoses and hoped-for improvements in manufacturing drugs.

This seems a case where the technological innovation has raced ahead of the science which could leverage the new possibilities. Then again, it might also be a chicken & egg issue. If firms such as 23andMe get enough customers they might be able to drive the research themselves and therefore create their own demand.

CATEGORIZED UNDER: Genomics
MORE ABOUT: Genomics
  • bob sykes

    $50K is cheap enough to attract charlatans and con artists. Large scale production will make the PGM even cheaper. A whole lot of bogus science/medicine/police is in the offing.

  • bioIgnoramus

    “if it proves tough to find …. improved cancer diagnoses”: the American obsession with cancer is passing strange.

  • Markk

    The fixation on doctors and human genomes is funny. $50K and less means that Botany departments, Ag extension services and such will be able to afford these machines. If every college with a few thousands students buys one, that is a huge market. I remember being at a talk by a naturalist doing research on invasive species, specifically garlic mustard. She was going into how they got soil samples tested in areas where the mustard was rampant and others where it seemed suppressed. And they were finding differences. They were doing rudimentary things and looking for specific bacteria. Just think if they could do wide spectrum analysis of soil and see what kind of correlations pop up.

    I think Google, Amazon or someone new, might see whole new “cloud” markets just to hold the data for this stuff by location and provide analysis for the small user.

  • Markk

    Side Note – for whatever reason I can’t correct my post above – it gives a submit failed error when I try to save the correction. (thousand for thousands … just a typo).

  • Professor Booty

    bioIgnoramus – you’re an idiot. Cancer research is a major biomedical funding priority in most Western countries, and the reason should be obvious to anyone who has known someone in the prime of life (or younger) suddenly get sick and die in terrible pain.

  • Adriana

    I have been to a couple of talks where the Ion Torrent machine was presented. It’s not quite ready for prime time in my opinion because the error rate is still high, but future improvements on polymerase accuracy will help. It does not seem that the target will be full genomes but rather areas of the genome where known mutations or rearrangements occur, for example for cancer genomics, to determine the profile of an individual tumor and decide on treatment. I think the market of this type of machines will be mostly clinical.

    The bottleneck is still the bioinformatics required to align the sequences and call SNPs, mutations, copy number variation and rearrangements. The amount of data that next-gen sequencing technologies generate is amazing.

  • bioIgnoramus

    No, Booty, you are wrong. It is an irrational obsession, and seems to me to be peculiarly American. You surely aren’t suggesting that it’s the only cause of “someone in the prime of life (or younger) suddenly get sick and die in terrible pain”. Maybe you are; maybe you too suffer from this irrationality. And meantime, something could be done about the pain if only people didn’t also have obsessively irrational ideas about opiate painkillers.

    Or, if you want to persuade me that it’s not irrational, tell me why people so often refer to an “epidemic” of cancer, when – apart from those caused by smoking cigarettes – there is no such epidemic once you correct the figures for an ageing population. Tell me why people whip up scare stories about carcinogens, without considering the question of doses. Part of the explanation may lie in “a major biomedical funding priority” of course, but there’s something else behind it besides filthy lucre, I’d guess. It’s some sort of quasi-religious phobia perhaps.

  • AG

    Personal Genome Machine (PGM) will definitely be useful for diagnosis of neoplasm (cancer ect). Neoplasm is disease of altered genes which control cell proliferation. This could be enoumously change the practice of medical pathology. The impact might be even bigger for pathology than IMR for radiology.

    PGM will also be very useful for diagnosis and treatment of infectious disease since genes of microorganism can be dectected directly.

  • BC

    No Bio, you are wrong. I’ve read dozens of your comments over the past few months and you have rarely contributed anything of any value. Your comments are generally loud farts of ignorance. You seem to have the intellectual capacity to contribute value but choose to shout dumb and irrelevant things instead. I don’t know why.

    In this instance for example, the American “obsession” with cancer concerns is actually rather simple, BECAUSE THAT’S HOW PEOPLE DIE. Your choice to spin the subject off by attacking irrelevant strawmen is indicative of just the sort of comments you usually leave.

    Again, I’m confident that you can contribute comments of value instead of the brain farts you usually squeak out on almost every single thread which have nothing to do with the point of the post. Please don’t take Razib’s kindness for granted and be more selective in your comments. The first stage would be stopping and thinking before you write whatever dumb thought just bubbled into your consciousness.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    bio, you truly have tested my patience in the past. i don’t even register your short little quips, but generally focus when you say something more elaborated. no surprise that others would express some exasperation.

  • bioIgnoramus

    “BECAUSE THAT’S HOW PEOPLE DIE”: no, it’s one way that people die. You make my point for me.

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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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