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Moore's Law Leads to $1000 Genome Device

Life Technologies' cheap genome sequencing chip shows how semiconductor technology is making personal genomes happen

2 min read
Moore's Law Leads to $1000 Genome Device

Carlsbad, Calif.-based Life Technologies plans to introduce today a machine that can map a person’s entire genome for just $1000. One thousand dollars per genome has been a longstanding goal, because it should make the whole genome sequencing useful for medicine and drug discovery.

The machine, the Ion Proton Sequencer, is based on a chip. When the company first reported the sequencing of a person’s genome with it in Nature in July, it was none other than Gordon Moore’s genome they sequenced.

The chip is basically a bunch of wells with transistors at the bottom. The transistors are sensitive to the pH in the well. A bead with a single stranded fragment of DNA is stuck in the well and then each of the chemicals that make up a DNA sequence are washed over the wells in turn. The chemicals bind to their complementary spot on the fragment, dropping the pH in the well, and triggering the transistor. We’ll have more on the workings of the device later, but as you can see it takes direct advantage of everything the chip industry has to offer.

Here at IEEE Spectrum we’ve been betting on a different chip technology to win the $1000 race: nanopore sequencing. Those chips squeeze DNA through a nanoscopic pore in the semiconductor and try to read the distinctive change each letter in the sequence makes in the amount of current flowing through the pore. That technology has yet to sequence anybody’s or anything’s genome, so I think we can safely say that we picked the wrong horse here. However, if somebody does manage to commercialize that technology it could prove to be even faster, if not cheaper than what Life Technologies has done.

If nothing else, Life Technologies’ announcement puts into focus how far semiconductor technology and the computing it enables have taken our quest to figure out the basics of our own biology. The first human genome sequenced, at a cost of US $3 billion, was a triumph of automation and lived or died on the ability of a massive computing effort. (The Neanderthal genome was another computing triumph.) And genome analysis has long been the domain of chips and chip-making technology.

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A photo showing machinery in a lab

Foundries such as the Edinburgh Genome Foundry assemble fragments of synthetic DNA and send them to labs for testing in cells.

Edinburgh Genome Foundry, University of Edinburgh

In the next decade, medical science may finally advance cures for some of the most complex diseases that plague humanity. Many diseases are caused by mutations in the human genome, which can either be inherited from our parents (such as in cystic fibrosis), or acquired during life, such as most types of cancer. For some of these conditions, medical researchers have identified the exact mutations that lead to disease; but in many more, they're still seeking answers. And without understanding the cause of a problem, it's pretty tough to find a cure.

We believe that a key enabling technology in this quest is a computer-aided design (CAD) program for genome editing, which our organization is launching this week at the Genome Project-write (GP-write) conference.

With this CAD program, medical researchers will be able to quickly design hundreds of different genomes with any combination of mutations and send the genetic code to a company that manufactures strings of DNA. Those fragments of synthesized DNA can then be sent to a foundry for assembly, and finally to a lab where the designed genomes can be tested in cells. Based on how the cells grow, researchers can use the CAD program to iterate with a new batch of redesigned genomes, sharing data for collaborative efforts. Enabling fast redesign of thousands of variants can only be achieved through automation; at that scale, researchers just might identify the combinations of mutations that are causing genetic diseases. This is the first critical R&D step toward finding cures.

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