Proton promises us $1,000 genome mapping by year end

At CES, scientific-equipment giant Life Technologies unveiled a DNA sequencer designed to decode an entire human genome in a day for $1,000 by the end of 2012.

The Ion Proton Sequencer, priced at $149,000, isn't your typical hot commodity on the show floor. But the benchtop sequencer costs far less than its bulkier, slower predecessors (typically in the $500,000 to $750,000 range), and the $1,000 price tag--once costs fall to that level--could put personal gene sequencing directly into the hands of the masses.

"This is such an amazing moment in history," said Jonathan Rothberg, founder and CEO of Ion Torrent (a subsidiary of Life Technologies and developer of the sequencer), by phone on the eve of CES. Rothberg--an unquestionably brilliant guy who is nonetheless prone to flights of overstatement--continued:

We really will understand the basis of cancer. Of autism. We'll understand hypertension and diabetes. You can have this mental image of this fruit tree, with this beautiful ripe fruit hanging from seven feet, and now we have a stepladder.

The Ion Proton, roughly the size of a laser printer, is already in use at the Yale School of Medicine, Baylor College of Medicine, and the Broad Institute. While typical sequencers today deliver multiple-genome data after a few weeks, which are then batch-transferred for secondary analysis, Chad Nusbaum of the Broad Institute's Genome Sequencing and Analysis Program said the Proton device could process single genomes in a few hours, improving production efficiencies on a large scale.

Rothberg, a frenetic character featured on the cover of Forbes a year ago when Life Technologies launched his Personal Genome Machine, soon became the proud father of the fastest-selling DNA sequencer on the market. But for him, the title "father" has more than one meaning.

"Next-gen sequencing was born when my son was born about 12 years ago, and he wasn't breathing, and at that moment, I didn't care about the academics of the human genome project," Rothberg said. (His son had trouble breathing shortly after birth, and there was no rapid test to rule out inherited conditions. The boy is now fine.) "I cared about my son and his genome, and I wanted to know at that moment why he was having difficulty breathing. So this sequencer we have now is the culmination of these past 12 years."

Last year, Rothberg's Personal Genome Machine was not only the first to introduce semiconductor technology to the world of DNA sequencing, it was also famously used to identify the E. coli bacteria in the summer's outbreak in Europe--opening up a new discipline dubbed "prospective genomics epidemiology."

The Proton sequencer as it exists today is ideal for sequencing exomes, or just part of a whole genome that can help identify mutations that are associated with abnormalities and diseases via the device's Proton I chip. The Ion Proton II chip, which developers estimate will be available in a year, will enable whole human genome sequencing.

If all goes well, the next big step will be to quickly and accurately interpret the resulting data for diagnostics and treatment. To this end, Ion Torrent is working with Carnegie Mellon University to develop open-source "doctor-in-a-box" software to help speed up the interpretation of the vast amount of genetic data.

Rothberg's sequencers may be at the front of a sizable pack--firms such as Complete Genomics, Intelligent Bio-Systems, and Helicos are all working to improve the speed, cost, and accuracy of gene sequencing--but when it comes to whole gene sequencing, his main competition is Illumina, whose top-of-the-line sequencer goes for $750,000.

Illumina, which develops sequencers based not on semiconductor technology but optical sensors, boasts control of the lion's share of DNA sequencing today. Just hours after Life Technologies unveiled its Proton sequencer, Illumina announced its own machine that it claims can sequence a whole genome in just over a day. But if the Proton cost really does come down to $1,000 per genome by year's end, it could leave Illumina, whose current per-genome price tag is $4,000, in the proverbial (if not sequenceable) dust.