The race to the $1,000 genome heated up today as Life Technologies, based in Carlsbad, Calif., announced that it will debut a new sequencing machine this year that will eventually be capable of decoding entire human genomes in a day for less than $1,000. The machine, called the Ion Proton, will be the successor to the Personal Genome Machine made by the company Ion Torrent, a subsidiary of Life Technologies.

Not to be outdone, Illumina, the present market leader based in San Diego, Calif., said that it will release its own genome-in-a-day contender, the HiSeq 2500, in the second half of this year. Unlike Life Technologies, which is asking customers to buy an entirely new machine, Illumina says that it will be able to upgrade existing customers’ HiSeq 2000 machines for a relatively low price.

So how will this battle of the sequencers shake out?

Ion Torrent is positioning its new machine as a lower-cost alternative to Illumina’s $690,000 HiSeq. Scientists seem willing to believe that the Ion Proton will reach its speed goals, largely because Ion Torrent’s present model, the Personal Genome Machine, is performing well for its customers. That sets Ion Torrent apart from other companies with novel technologies that couldn’t deliver on their first-generation models, such as Pacific Biosciences of Menlo Park, Calif., which switched CEOs last week amidfinancial and legal hiccups, and the Cambridge, Mass.-based Helicos, which continues to struggle with lackluster demand for its machines.

This post at the forum SeqAnswers.com has calculated that the first sequencing chip released with the Ion Proton in mid-2012, the Proton 1, will be capable of sequencing three to six human exomes—the gene-encoding portion of the genome. Life Technologies said that the second sequencing chip released with the machine at the end of this year, the Proton II, will contain enough sensors to sequence an entire genome. Life Technologies is angling the Ion Proton to take on a clinical diagnostic-sequencing market, and plans to ask the U.S. Food and Drug Administration for clearance to use the machine as a medical device this year. So far, Illumina has captured much of the small-but-growing clinical-sequencing market.

But scientists are less convinced that the cost of sequencing a human genome with the Ion Proton will come in under $1,000, or that it would cost less to run than the HiSeq. Researchers note that at present, it would cost tens of thousands of dollars to sequence a human genome using the Personal Genome Machine. Life Technologies told me that the $1,000-human-genome estimate for the Ion Proton includes the cost of the sequencing chip and reagents for the run, but analyst Isaac Ro of Goldman Sachs reports in a research note that the Proton II chip itself will cost $1,000, so it’s unclear how exactly Life Technologies arrived at that $1,000 number.

The Ion Proton machine will cost a relatively inexpensive $149,000, so even though customers will have to pay an additional $95,000 for a server and automated sample-prep device, according to Ro, he notes that "the price point is clearly best-in-class by a wide margin."

But Illumina is offering to upgrade its present customers to the HiSeq 2500 for the fairly low cost of $50,000, so there may be little incentive for them to invest in a new Ion Proton machine, especially because they already know that Illumina’s technology is highly accurate and because the sequencing business has already been hit by the present climate of fiscal austerity. Life Technologies also appears to have annoyed some of its present customers by announcing the debut of a new device barely a year after releasing the Personal Genome Machine: "Was it really a wise move to announce a PGM-killer so early into this [machine's] life?" asks Nick Loman at the blog Pathogens: Genes and Genomes.

Nonetheless, in the Ion Torrent platform, Life Technologies has finally found a way to give Illumina a run for its money in a way that no other company has to date, and the competition can only be a win for customers. With a slew of other sequencing technologies in various stages of development, these announcements kick off what should be another exciting year for new sequencing technologies.

This blog post is reproduced with permission from the magazine Nature. The post was first published on January 10, 2012.