2012-03-29

Co.Exist

For The Price Of Two iPads, This Machine Can Sequence An Entire Human Genome

If you want to take advantage of the latest plummeting price of genetic sequencing, it will be because of the Ion Proton. How did scientists find a way to get such a cheap window into our DNA?

The machine that can do that--in just two hours--is the Ion Proton, a genetic sequencer introduced by Life Technologies in January. It’s 1,000 times more powerful than its year-old predecessor, the Ion Personal Genome Machine, and, at $1,000 per genome, a fraction of the price. A combination of Moore’s Law, ingenuity, and demand stand to make the Ion Proton the go-to gene decoder in a market that Life Technologies CEO Greg Lucier estimates will hit $2 billion by 2014. In turn, Life Technologies stands to make possible a future in which medicine is tailored to each individual’s DNA.

“We really are at a tipping point to understanding the molecular basis of cancer,” says Jonathan Rothberg, inventor of the Ion Torrent. It’s a bold but believable claim from the man who, 13 years ago, began mulling over the idea of semiconductor-based genetic testing while gazing at an image of a computer chip on the cover of a magazine. He was looking at that photo right after his newborn son was rushed to the intensive care unit with trouble breathing. “That’s when I first understood what the term ‘personal medicine’ means,” Rothberg recalls. Genetic sequencing was much too slow, he thought: “The human genome effort was done in a Henry Ford style,” and to move it forward, “we had to take an approach analogous to the one that made that Pentium chip possible.”

Rothberg’s first machine was an improvement, but it was still slow, relying on a two-step process of taking pictures of sequences and then analyzing those to build a genome. The idea to switch gears--which would eventually lead to the Ion Torrent--came, like the first epiphany, from Rothberg’s son, who said it would be much cooler for his dad to be able to read minds than genomes. Or, as Rothberg understood it, it would be much cooler if he could read the genes directly, reading their minds instead of talking to them to know what they thought. “We needed to come up with a device that could see chemistry,” he says.

The result is the Ion Torrent, the first semiconductor-based sequencer in the world. Because Rothberg tapped into the existing semiconductor industry, out of which had already come microprocessors, memory chips, and digital-camera chips, he could tap into existing manufacturing equipment and the quick advances driven by Moore’s Law (which predicts exponential improvements in computing). He could also take advantage of the semiconductors themselves—especially the photography chip, which sees light particles. Rothberg used his version to “see” hydrogen ions, which are released every time a letter on a single strand of DNA encounters its match. So, as a strand of DNA is run through the machine, base pairs connect and release hydrogen ions; by keeping track of when those ions are released, the machine sequences the gene.

Life Technologies acquired Rothberg’s Ion Torrent in late 2010 and introduced the sequencer later that year. It took just 13 months for the company to unveil the Ion Proton, an astoundingly more powerful and cheaper instrument. “The reason it got better so fast is because we did a sleight of hand,” Rothberg says. “We time-traveled from the early 1990s to the present.” In other words, instead of waiting for the equipment to make semiconductor chips to be made, Rothberg could just use equipment that was already out there, saving money and time. The result is revolutionary: “We’ve reached that economic tipping point where it’s now affordable enough that it can be used broadly,” Lucier says.

“It’s like all new technology: It needs to be brought online clinically in a very careful and deliberate manner,” says Christopher Corless, chief medical at Knight Diagnostic Laboraties. He hopes to use the machine to screen people who haven’t responded to chemotherapy so they might benefit from experimental personal medicines. Life Technologies encourages that kind of “deliberate manner” with its software, which is designed to guide researchers through specific tasks and mutations. One kit, for instance, lets researchers identify 95% of mutations present in North Americans. “None of this was feasible before because of the costs,” says George Watts, a professor at the University of Arizona’s cancer center who uses a Life Technologies sequencer that screens for 46 common cancer-causing genes.

Still, as Rothberg admits, “This is just the start--it’s not a magic wand, but I do believe in the next few years we’ll see an understanding of many complex disorders.” After all, giving doctors and researchers faster and easier access to DNA gives them a better look into life itself: “Everything in the world starts with DNA,” Lucier says, “so our ability to understand how things work by understanding their computer code will allow us to do amazing things.” So while there’s no easy magic yet, there are the first glimpses into the once unknowable.

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3 Comments

  • campirecord

    The true costs are from that and articles like yours continue to promote a myth about cost of sequencing, no wonder, you just repeating pretty hard marketing crap.

  • Jesse Paquette

    Imagine your genome is a movie that costs $1000 to acquire.  Not bad, but then consider the fact that it takes up 1TB of drive space and costs you $5000 the first time you want to play it (i.e. analyze it).

    The problem with DNA sequencing outpacing Moore's law is that we're gonna fill up all the hard drives in the world really quickly.  And the money to be made will be in analysis software/services - because that's where the challenges remain.

  • AllSeq

    "Ion Proton, an astoundingly more powerful and cheaper instrument". - The Ion Proton, while promising amazing and inexpensive sequencing when it is launched later this year, is actually three times as expensive as the previous instrument from Ion Torrent.