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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Restoring Hearing With Beams of Light

Gene therapy and optoelectronics could radically upgrade hearing for millions of people

13 min read
A computer graphic shows a gray structure that’s curled like a snail’s shell. A big purple line runs through it. Many clusters of smaller red lines are scattered throughout the curled structure.

Human hearing depends on the cochlea, a snail-shaped structure in the inner ear. A new kind of cochlear implant for people with disabling hearing loss would use beams of light to stimulate the cochlear nerve.

Lakshay Khurana and Daniel Keppeler
Blue

There’s a popular misconception that cochlear implants restore natural hearing. In fact, these marvels of engineering give people a new kind of “electric hearing” that they must learn how to use.

Natural hearing results from vibrations hitting tiny structures called hair cells within the cochlea in the inner ear. A cochlear implant bypasses the damaged or dysfunctional parts of the ear and uses electrodes to directly stimulate the cochlear nerve, which sends signals to the brain. When my hearing-impaired patients have their cochlear implants turned on for the first time, they often report that voices sound flat and robotic and that background noises blur together and drown out voices. Although users can have many sessions with technicians to “tune” and adjust their implants’ settings to make sounds more pleasant and helpful, there’s a limit to what can be achieved with today’s technology.


8 channels


64 channels

Since optogenetic therapies are just beginning to be tested in clinical trials, there’s still some uncertainty about how best to make the technique work in humans. We’re still thinking about how to get the viral vector to deliver the necessary genes to the correct neurons in the cochlea. The viral vector we’ve used in experiments thus far, an adeno-associated virus, is a harmless virus that has already been approved for use in several gene therapies, and we’re using some genetic tricks and local administration to target cochlear neurons specifically. We’ve already begun gathering data about the stability of the optogenetically altered cells and whether they’ll need repeated injections of the channelrhodopsin genes to stay responsive to light.

Our roadmap to clinical trials is very ambitious. We’re working now to finalize and freeze the design of the device, and we have ongoing preclinical studies in animals to check for phototoxicity and prove the efficacy of the basic idea. We aim to begin our first-in-human study in 2026, in which we’ll find the safest dose for the gene therapy. We hope to launch a large phase 3 clinical trial in 2028 to collect data that we’ll use in submitting the device for regulatory approval, which we could win in the early 2030s.

We foresee a future in which beams of light can bring rich soundscapes to people with profound hearing loss or deafness. We hope that the optical cochlear implant will enable them to pick out voices in a busy meeting, appreciate the subtleties of their favorite songs, and take in the full spectrum of sound—from trilling birdsongs to booming bass notes. We think this technology has the potential to illuminate their auditory worlds.

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