Today's next-generation sequencing systems rely on optical detection to decode nucleotide sequences. But as Jeffrey Perkel reports, a new generation of optics-free sequencing instruments could result in longer reads, faster runs, and lower costs.
Next-generation DNA sequencing certainly had a season for the ages in 2010. Genomes were felled by the technology on a weekly basis, it seemed, including the turkey, the strawberry, Xenopus, and the Neanderthal—and hundreds upon hundreds of humans. Most recently, the technology earned worldwide attention for its breathtaking deciphering of the Haitian cholera epidemic.
The technologies underlying those successes represent just a handful of companies: Illumina, Complete Genomics, Helicos, Roche/454 Life Sciences, Life Technologies, and most recently, Pacific Biosciences, whose first instruments rolled out to beta testers in November. Though each of these companies' sequencers operates on a different principle, they have one thing in common: all rely on optical detection of nucleotide incorporation. Such detection schemes require high-priced components such as lasers, cameras, lenses, and the like, not to mention complicated image-based base-calling algorithms. They also require specialty reagents to run, adding significantly to the cost of ownership.
Yet there's more than one way to sequence a genome, as they say, and not all of them involve optics. In December, Life Technologies officially launched the first commercial sequencing instrument to eschew optical detection. The Personal Genome Machine (PGM), the product of Life Technologies’ recent $375 million acquisition of Ion Torrent, monitors nucleotide incorporation electrochemically. It's what Chad Nusbaum—co-director of the Genome Sequencing and Analysis Program at the Broad Institute of Harvard and MIT—calls a “post-light” sequencing instrument, and it's likely just the first of many. Indeed, waiting in the wings, other companies are pursuing detection strategies based on nanopores and electron microscopy.
Promising longer reads, single-molecule detection, smaller and simpler instruments, and lower costs, these nonoptical methods could fundamentally change the sequencing landscape. According to Harvard geneticist George Church, human genome sequences still cost at least $7000 to produce, but in order to be clinically useful, “probably should get down to below $700. There's probably another factor of 10 at least to be squeaked out.” Plus, he says, there are new niches to explore that current instrumentation cannot handle—cell phone–sized, real-time environmental monitors, for instance. “That seems far-fetched,” says Church, “but where we are right now would have seemed far-fetched a few years ago.” But these new technologies will first have to prove they can make the hop from the drawing board to the marketplace.Sensing the Protons
The first post-light sequencing system has already made that hop. The heart of the Ion PGM is a semiconductor chip studded with over one million wells, each containing one template and a DNA polymerase. As nucleotide triphosphates flow over the chip one at a time, the system registers incorporation events by the concomitant release of a proton.
“Essentially, we've made the smallest pH meter in the world,” says Jay Therrien, vice president of commercial operations for next-gen sequencing at Life Technologies.
According to Maneesh Jain, vice president of marketing and business development at Ion Torrent, the Ion PGM's initial “314” chip will contain 1.4 million sensors and cost $250 (plus another $250 per run for reagents). Out of the gate, that chip will generate at least 100,000 reads per run with an average length of 100 base pairs and a consensus accuracy (on 6× coverage) of 99.99%. That's 10 million bases per run: “significantly greater” than what 5 or 10 classic ABI 3730s could produce, says Therrien, but a mere fraction of what an ABI SOLiD could churn out. A newer “316” chip, slated for release in 2011 with some 7 million sensors, should boost throughput to 100 million bases per run. And the throughput can go up from there, says Jain, as semiconductor fabrication and molecular methods improve. In December, Life Technologies announced three $1 million “Grand Challenges” to get the ball rolling. The goal: enlisting researchers and programmers to improve Ion Torrent's speed, throughput, and accuracy.